Combined detection instrument for culture specimen containers and instrument for identification and/or characterization of a microbial agent in a sample

CROSS-REFERENCE TO RELATED APPLICATIONS

0001This application claims priority under 35 U.S.C. § 119(e) to (1) <patcit id="pcit0001" dnum="US61216339A" dnum-type="L"><text>US provisional application serial no. 61/216,339</text></patcit>, entitled "System for Combining a Non-invasive Rapid Detection Blood Culture System with an Invasive Microbial Separation and Characterization System", filed May 15, 2009; (2) <patcit id="pcit0002" dnum="US61277862A" dnum-type="L"><text>US provisional application serial no. 61/277,862</text></patcit>, entitled "Automated Loading Mechanism for Microbial Detection Apparatus", filed September 30, 2009; and (3) <patcit id="pcit0003" dnum="US61337597A" dnum-type="L"><text>US provisional application serial no. 61/337,597</text></patcit>, entitled "Automated Microbial Detection Apparatus", filed February 8, 2010, the content of which are incorporated by reference herein.

0002This application is also related to the following US patent applications, the content of which is incorporated by reference herein: <ul id="ul0001" list-style="none" compact="compact"><li><patcit id="pcit0004" dnum="US12589929B"><text>US Serial No. 12/589,929</text></patcit>, entitled "Methods for the isolation and identification of microorganisms", filed October 30, 2009.</li><li><patcit id="pcit0005" dnum="US12589969B"><text>US Serial No. 12/589,969</text></patcit>, entitled "Separation device for use in the separation, identification and/or characterization of microorganisms", filed October 30, 2009.</li><li><patcit id="pcit0006" dnum="US12589952B"><text>US Serial No. 12/589,952</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using spectroscopy", filed October 30, 2009.</li><li><patcit id="pcit0007" dnum="US12589936B"><text>US Serial No. 12/589,936</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using mass spectrometry", filed October 30, 2009.</li><li><patcit id="pcit0008" dnum="US12589985B"><text>U.S Serial No. 12/589,985</text></patcit>, entitled "Method for separation and characterization of microorganisms using identifier agents", filed October 30, 2009.</li><li><patcit id="pcit0009" dnum="US12589968B"><text>US Serial No. 12/589,968</text></patcit>, entitled "Method for detection, identification and/or characterization of microorganisms in a sealed container", filed October 30, 2009.</li><li><patcit id="pcit0010" dnum="US12589976B"><text>US Serial No. 12/589,976</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using Raman spectroscopy", filed October 30, 2009.</li></ul>

0003This application is also related to the following applications filed on the same date as this application, the content of which is incorporated by reference herein: <ul id="ul0002" list-style="none" compact="compact"><li>Docket no. 01121, serial no.__________ "Automated microbial detection apparatus."</li><li>Docket no. 09-271-A, serial no.__________, "Methods for rapid identification and/or characterization of a microbial agent in a sample."</li><li>Docket no. 09-271-B, serial no.__________, "System for rapid identification and/or characterization of a microbial agent in a sample."</li></ul>

STATEMENT OF FEDERALLY SPONSORED RESEARCH

0004Not applicable.

BACKGROUND

0005This invention solves a long-felt need in the art for an automated instrument and method for rapidly characterizing and/or identifying a microbial agent in a sample, such as blood or other biological sample, stored in a specimen container. As an example, the instrument of this disclosure provides information as to Gram type (positive or negative), morphology, species or other relevant clinical information of the microbial agent rapidly and automatically.

0006Instruments currently exist on the market in the U.S. that detect the growth and therefore the presence of a microorganism in a blood sample. One such instrument is the BacT/ALERT 3D instrument of the present assignee bioMérieux, Inc. The instrument receives a blood culture bottle containing a blood sample, e.g., from a human patient. The instrument incubates the bottle. Periodically during incubation an optical detection unit in the incubator analyzes a colorimetric sensor incorporated into the bottle to detect whether microbial growth has occurred within the bottle. The optical detection unit, specimen containers and sensors are described in the patent literature, see <patcit id="pcit0011" dnum="US4945060A"><text>U.S. patents 4,945,060</text></patcit>; <patcit id="pcit0012" dnum="US5094955A"><text>5,094,955</text></patcit>; <patcit id="pcit0013" dnum="US5162229A"><text>5,162,229</text></patcit>; <patcit id="pcit0014" dnum="US5164796A"><text>5,164,796</text></patcit>; <patcit id="pcit0015" dnum="US5217876A"><text>5,217,876</text></patcit>; <patcit id="pcit0016" dnum="US5795773A"><text>5,795,773</text></patcit>; and <patcit id="pcit0017" dnum="US5856175A"><text>5,856,175</text></patcit>, the entire content of each of which is incorporated by reference herein. Other prior art of interest relating generally to the detection of microorganisms in a biological sample includes the following patents: <patcit id="pcit0018" dnum="US5770394A"><text>U.S. 5,770,394</text></patcit>, <patcit id="pcit0019" dnum="US5518923A"><text>U.S. 5,518,923</text></patcit>; <patcit id="pcit0020" dnum="US5498543A"><text>U.S. 5,498,543</text></patcit>, <patcit id="pcit0021" dnum="US5432061A"><text>U.S. 5,432,061</text></patcit>, <patcit id="pcit0022" dnum="US5371016A"><text>U.S. 5,371,016</text></patcit>, <patcit id="pcit0023" dnum="US5397709A"><text>U.S. 5,397,709</text></patcit>, <patcit id="pcit0024" dnum="US5344417A"><text>U.S. 5,344,417</text></patcit>, <patcit id="pcit0025" dnum="US5374264A"><text>U.S. 5,374,264</text></patcit>, <patcit id="pcit0026" dnum="US6709857B"><text>U.S. 6,709,857</text></patcit>; and <patcit id="pcit0027" dnum="US7211430B"><text>U.S. 7,211,430</text></patcit>.

0007In detection instruments such as the BacT/ALERT 3D and similar instruments, once the blood culture bottle has been tested positive for microorganism presence, it is difficult to obtain a high level of characterization of the microbial agent, or identification of the species of the microbial agent, due to the interference of blood components and artifacts of the disposable system (e.g., bottle) containing the sample. Therefore, current methods use a bottle or other suitable disposable container and a related instrument for natural growth and detection of a microorganism in the sample, as described above. Once the instrument indicates that the bottle is positive for presence of a microbial agent, according to current methods the "positive" bottle is manually retrieved from the instrument and a portion of the sample is manually removed from the bottle and cultured on an agar plate. There are instruments in the art that automate the streaking of a sample medium on a culture plate and incubating the plate. One such instrument is described in <patcit id="pcit0028" dnum="US6617146B"><text>U.S. Patent 6,617,146</text></patcit>. After streaking, the plate is manually placed in an incubator and periodically inspected for growth of a subculture of the microorganism. After the subculture has grown sufficiently, a sample of the culture is taken from the plate and placed in a test tube. The test tube is then introduced into yet another instrument for identification testing via a disposable test sample card having a multitude of individual wells. The disposable test cards are known in the patent literature, see e.g., <patcit id="pcit0029" dnum="US4118280A"><text>U.S. Patents 4,118,280</text></patcit>, <patcit id="pcit0030" dnum="US3963355A"><text>3,963,355</text></patcit>,<patcit id="pcit0031" dnum="US401865A"><text> 4,018,65</text></patcit>; <patcit id="pcit0032" dnum="US4116775A"><text>4,116,775</text></patcit> and <patcit id="pcit0033" dnum="US4038151A"><text>4,038,151</text></patcit>, <patcit id="pcit0034" dnum="US5609828A"><text>5,609,828</text></patcit>, <patcit id="pcit0035" dnum="US5746980A"><text>5,746,980</text></patcit>, <patcit id="pcit0036" dnum="US5766553A"><text>5,766,553</text></patcit>, <patcit id="pcit0037" dnum="US5843380A"><text>5,843,380</text></patcit>, <patcit id="pcit0038" dnum="US5869005A"><text>5,869,005</text></patcit>, <patcit id="pcit0039" dnum="US5916812A"><text>5,916,812</text></patcit>, <patcit id="pcit0040" dnum="US5932177A"><text>5,932,177</text></patcit>, <patcit id="pcit0041" dnum="US5951952A"><text>5,951,952</text></patcit>, and <patcit id="pcit0042" dnum="US6045758A"><text>6,045,758</text></patcit>, the entire content of which is incorporated by reference herein.

0008The test sample card is then processed in an analytical instrument known in the art as the VITEK 2 instrument of the assignee. The VITEK 2 instrument incubates and periodically reads the wells of the test sample card with a reader unit. Growth of the sample in one or more of the wells of the cards results in identification of the microbial agent. The VITEK 2 instrument is described in the patent literature, see e.g., <patcit id="pcit0043" dnum="US5762873A"><text>U.S. Patents 5,762,873</text></patcit> and <patcit id="pcit0044" dnum="US6086824A"><text>6,086,824</text></patcit>, the content of which is incorporated by reference herein.

0009This entire process from the time of introducing the sample into the blood collection bottle to culture, detection of microorganism presence, and then identification of the microorganism by the VITEK 2 instrument typically takes 2-5 days. The identification steps alone, occurring after positive bottle detection, typically occupy 1-3 of these days.

0010Substantial, and potentially life saving, clinical benefits for a patient are possible if the time it takes for detection and identification of a microbial agent in a blood sample and reporting the results to a clinician could be reduced from the current 2-5 days to less than one day. A system that meets this need has heretofore eluded the art. However, such rapid identification and/or characterization of a microbial agent in a biological sample such as a blood sample is made possible by this invention.

0011The document <patcit id="pcit0045" dnum="US4250266A"><text>US 4,250,266</text></patcit> discloses an automated system for detection of a microbial agent in a probe with selection of positive probes. The document <patcit id="pcit0046" dnum="US5578269A"><text>US 5,578,269</text></patcit> discloses an automatic blood analysis system with integral centrifuge. The document <patcit id="pcit0047" dnum="US4212948A"><text>US 4,212,948</text></patcit> describes an apparatus for detecting microbial pathogens with the steps of lysis, concentration and separation of the agents of interest. The document <patcit id="pcit0048" dnum="FR2888328A1"><text>FR2888328 A1</text></patcit> describes an automatic analyzer of blood probes with robotic arm. The detection of pathogens by fluorescence measurement is described in <patcit id="pcit0049" dnum="WO2008105893A2"><text>WO 2008/105893 A2</text></patcit>. The detection and identification of microorganisms by Raman spectroscopy is disclosed in <patcit id="pcit0050" dnum="US6844199B1"><text>US 6,844,199 B1</text></patcit>.

0012The system for rapidly identifying and/or characterizing a microbial agent set forth herein can be advantageously combined with an automated detection instrument for detecting the presence of an agent in the specimen container, as described in embodiments disclosed herein. In this combination, the inventive system and methods combine a detection instrument operative to detect a container containing a blood or other sample as being positive for microbial agent presence, and rapid and automated identification of the agent. In one embodiment, the detection instrument may be coupled to or integrated with an automated identification and/or characterization instrument as described herein performing additional steps necessary for identification and/or characterization of a microbial agent at the time of detection. The resulting combined system presents a unique automated solution for rapid identification and/or characterization at the time of detection, providing a complete system solution. The total time from first loading a biological sample into a detection container (e.g., bottle) to identification and/or characterization is typically less than 24 hours in most cases. Moreover, instead of it taking one to three additional days to obtain the identification and/or characterization of the microbial agent after a bottle is tested positive, as in the prior art, such results can potentially be obtained in less than one hour with the present inventive system and methods. The instrument of this disclosure also provides the ability to provide a rapid and automated identification and/or characterization result at any time of the day or night.

0013The systems and methods of this disclosure have other incidental benefits and features, including the potential to: (a) reduce exposure of lab personnel to sharps and biohazard materials; (b) reduce laboratory labor and user errors; (c) improve sample tracking, traceability and information management; (d) interface to laboratory automation systems; (e) improve workflow and ergonomics; (f) improve patient care by delivering clinically relevant actionable information; and (g) provide faster results thereby potentially decreasing costs by focusing earlier on appropriate antimicrobial therapy and reducing hospital stay.

0014Many further advantages and benefits over the prior art will be explained below in the following detailed description.

SUMMARY

0015In general, an automated system is disclosed for rapid detection of a microbial agent in a sample and identifying and/or characterizing the microbial agent. In one form, the system includes a detection instrument receiving a specimen container containing a sample. The detection instrument includes a heated enclosure for incubating the specimen container and a detection unit interrogating the specimen container to detect whether the specimen container is positive for the presence of a microbial agent in the sample. The system includes a supply of disposable separation devices. The system further includes and an automated identification/characterization instrument. This instrument receives a specimen container detected positive by the detection instrument. The identification/characterization instrument includes (a) a sample removal apparatus coupled to a robotic transfer mechanism operative to remove a portion of the sample from the specimen container and add the portion to a separation device obtained from the supply of separation devices; (b) a separation and concentration station operative on the separation device after receiving the portion of the sample so as to separate the microbial agent from other products in the sample and concentrate the microbial agent within the separation device; and (c) an identification and/or characterization module interrogating the concentrated microbial agent to identify and/or characterize the microbial agent, wherein the robotic transfer mechanism moves the separation device from the separation and concentration station to the identification and/or characterization module.

0016In another aspect, the invention can be viewed as a method for rapid identification and/or characterization of a microbial agent present in a sample, the sample loaded into a specimen container, comprising performing the following steps in an automated manner: <ol id="ol0001" compact="compact" ol-style=""><li>(a) incubating the specimen container;</li><li>(b) periodically interrogating the specimen container to determine whether it is positive for presence of a microbial agent within the specimen container;</li><li>(c) when the specimen container is determined positive, withdrawing a portion of the sample from the specimen container with a sample removal apparatus coupled to a robotic transfer mechanism;</li><li>(d) introducing the portion of the biological sample into a disposable separation device;</li><li>(e) lysing components in the portion of the biological sample, either before or after performing step (d);</li><li>(f) transferring the separation device to a separation and concentration station using the robotic transfer mechanism,</li><li>(g) separating and concentrating the microbial agent within the separation device;</li><li>(h) transferring the separation device to an identification and/or characterization module using the robotic transfer mechanism, and</li><li>(i) analyzing the concentrated microbial agent to identify and/or characterize the microbial agent,</li></ol> wherein steps (a)-(i) are performed automatically within an integrated detection and identification/characterization instrument.

0017Steps (a)-(g) can be performed automatically within an integrated detection and identification/characterization instrument as described herein.

0018The analyzing step (i) can comprise the step of performing a spectroscopic analysis of the concentrated microbial agent. In another embodiment the spectroscopic analysis comprise one of (i) intrinsic fluorescence spectroscopy or (ii) Raman spectroscopy.

0019The method may further include step (g)(1) withdrawing the concentrated microbial agent from the separation device and wherein step (i) is performed on the concentrated microbial agent after withdrawal from the separation device.

0020The analyzing step (i) may include at least one of (i) performing a spectroscopic analysis on the concentrated microbial agent, (ii) performing mass spectrometry on the concentrated microbial agent, (iii) performing molecular testing of the concentrated microbial agent and (iv) introducing the concentrated microbial agent into a microbial characterization test device and subjecting the test device to analysis.

0021In yet another aspect, the invention can be viewed as an automated method for rapid characterization and/or identification of a microbial agent has been disclosed, comprising the steps of: (a) providing a detection subsystem having an entrance location for receiving specimen containers containing samples to be tested, and detection apparatus for detecting when a specimen container has become positive for presence of a microbial agent in a sample within the specimen container; (b) when a specimen container has become positive, automatically moving the specimen container to an identification and/or characterization subsystem remote from the detection subsystem; (c) within the characterization and/or identification subsystem, automatically performing the steps of: (1) withdrawing a portion of the sample from the specimen container; (2) dispensing the withdrawn portion of the sample into a disposable separation device; (3) concentrating the microbial agent within the withdrawn portion of the sample within the separation device; and (4) analyzing the concentrated microbial agent to characterize and/or identify the microbial agent.

0022In still another aspect, an automated method for rapid characterization and/or identification of a microbial agent has been disclosed, comprising the steps of: (a) receiving a specimen container containing a sample to be tested in a detection instrument; (b) detecting when the specimen container has become positive for presence of a microbial agent in the sample; (c) when such detection has occurred, automatically removing a portion of the sample from the specimen container and placing the portion of the sample into a disposable separation device; (d) separating and concentrating the microbial agent in a disposable separation device, and (e) analyzing the concentrated microbial agent to identify and/or characterize the microbial agent.

0023In still another aspect, a sample testing system has been disclosed, comprising, in combination: a detection subsystem having an entrance location for receiving specimen containers containing samples to be tested, and detection apparatus for detecting when a specimen container has become positive for presence of a microbial agent in the sample; an identification and/or characterization subsystem receiving a positive specimen container and having modules for automatically characterizing and/or identifying the microbial agent in the positive specimen container; and apparatus for automatically transferring a positive detection container from the detection subsystem to the identification and/or characterization subsystem.

0024The apparatus for automatically transferring can take the form of a conveyor system as described in several scenarios below. The automatically transferring can also take the form of a robotic arm assembly. Also described is a the conveyor system including a first conveyor and a second conveyor, and wherein the system comprises two detection subsystems daisy chained and coupled to each other by the first conveyor, and wherein the one of the detection subsystems is coupled to the identification and/or characterization subsystem by the second conveyor, and wherein a positive specimen detected in either the two detection subsystems is moved to the identification and/or characterization subsystem by means of the second conveyor.

0025In some embodiments described herein, the identification module in the automated identification and/or characterization instrument interrogates the concentrated microbial agent while it is contained within the separation device, and to that end the separation device may be made from suitable materials and optically transparent to facilitate an optical interrogation. For example, the identification module may include the features of <patcit id="pcit0051" dnum="US12589929B"><text>US Serial No. 12/589,929</text></patcit>, entitled "Methods for the isolation and identification of microorganisms", filed October 30, 2009; <patcit id="pcit0052" dnum="US12589969B"><text>US Serial No. 12/589,969</text></patcit>; entitled "Separation device for use in the separation, identification and/or characterization of microorganisms", filed October 30, 2009; <patcit id="pcit0053" dnum="US12589952B"><text>US Serial No. 12/589,952</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using spectroscopy", filed October 30, 2009; <patcit id="pcit0054" dnum="US12589936B"><text>US Serial No. 12/589,936</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using mass spectrometry", filed October 30, 2009; <patcit id="pcit0055" dnum="US12589985B"><text>U.S Serial No. 12/589,985</text></patcit>, entitled "Method for separation and characterization of microorganisms using identifier agents", filed October 30, 2009; <patcit id="pcit0056" dnum="US12589968B"><text>US Serial No. 12/589,968</text></patcit>, entitled "Method for detection, identification and/or characterization of microorganisms in a sealed container", filed October 30, 2009 and <patcit id="pcit0057" dnum="US12589976B"><text>US Serial No. 12/589,976</text></patcit>, entitled "Method for separation, identification and/or characterization of microorganisms using raman spectroscopy", filed October 30, 2009, the entire contents of which are incorporated by reference herein. A variety of optical technologies are envisioned for use in the identification instrument, including for example, spectroscopic measurements such as fluorescence spectroscopy measuring intrinsic fluorescence from the concentrated microbial agent, diffuse reflectance spectroscopy, Raman spectroscopy, or other optical technique capable of characterizing and/or identifying a microorganism based on its chemical or physical make-up. In other embodiments, the identification instrument may include a further instrument that removes all or a portion of the concentrated microbial agent from the separation device and analyzes the concentrated microbial agent directly, e.g., via a mass spectrometer, or via another disposable testing device (e.g., test strip or test card).

0026In applications where a lysis of the sample is desirable as an incident to separation and concentration of the microbial agent in the separation device, a particular selective lytic buffer ("lytic agent") may not be optimal for all organisms expected to be encountered in the sample. In this case where a positive sample does not yield an identification or characterization result due to a non-optimal lysis process, the system can be configured to automatically re-process the sample using an alternative lytic buffer formula. Information on the growth rates measured in an associated detection instrument could be used to select the most optimal lysis buffer formula for re-processing. Upon re-processing, it is expected that a true positive will yield a result. Otherwise, the sample is considered to be a false positive determination from the detection subsystem. Accordingly, in one configuration of the instrument several containers of different lysis buffers are included in the instrument and a selected lysis buffer is obtained, e.g., loaded into a sampling device used to withdraw a sample from the specimen container.

0027False positives occur with detection technology known in the art (e.g., in the BacT/ALERT instrument) at a very low rate. However, until the culture sample has been tested under incubation conditions for five days, a final negative determination of the sample cannot be made. Therefore, in one possible embodiment, the identification/characterization instrument may continue to test a false "positive" culture sample by automatically returning the specimen container to the incubation/agitation/detection mode of testing. In accordance with this embodiment continued testing occurs within a incubation rack housed in the identification/characterization instrument. An alternative embodiment is to return the specimen container to an associated detection instrument. Automation to re-initiate the incubation of the specimen container is thus additional optional aspect of the present disclosure. Operator intervention to re-initiate incubation could be employed, but would require vigilance on the part of the institution that operates the identification instrument.

0028These and many more aspects and features of the disclosure will be discussed below in conjunction with the appended drawing figures.

BRIEF DESCRIPTION OF THE DRAWINGS

0029The following detailed description makes reference to the appended drawing figures. It is intended that the embodiments and figures disclosed herein are to be considered illustrative and offered by way of example rather than restrictive. <ul id="ul0003" list-style="none" compact="compact"><li><figref idref="f0001">Figure 1</figref> is a perspective view of an automated system for rapid non-invasive detection of a microbial agent in a test sample. As shown, the system includes an automated loading mechanism.</li><li><figref idref="f0002">Figure 2</figref> is a perspective view of the detection system of <figref idref="f0001">Figure 1</figref>, showing a close-up view of the automated loading mechanism.</li><li><figref idref="f0002">Figure 3</figref> is a perspective view of the detection system of <figref idref="f0001">Figure 1</figref>, which shows an automated loading mechanism and a lower drawer that opens to reveal a waste container for containers that tested negative for presence of a microbial agent.</li><li><figref idref="f0002">Figure 4</figref> is a side view of one of the specimen containers processed in the detection system of <figref idref="f0001 f0002">Figure 1-3</figref>. While the detection container can take a variety of forms, in one embodiment it is configured as a blood culture bottle.</li><li><figref idref="f0003">Figure 5A</figref> is a side elevation view of one configuration of the detection system of <figref idref="f0001">Figure 1</figref>., with the upper and lower doors open showing the interior chambers and racks for holding multiple containers of the type shown in <figref idref="f0002">Figure 4</figref>.</li><li><figref idref="f0003">Figure 5B</figref> is a perspective view of the detection system shown in <figref idref="f0003">Figure 5A</figref>, with the upper and lower doors open showing the interior chambers and racks for holding multiple containers of the type shown in <figref idref="f0002">Figure 4</figref>.</li><li><figref idref="f0004">Figure 6</figref> is a perspective view of the transfer mechanism shown in <figref idref="f0003">Figures 5A and 5B</figref>, showing the horizontal and vertical support rails. Also shown are first and second rotational mechanisms, which are operable to rotate the transfer mechanism about one or more axes.</li><li><figref idref="f0005">Figure 7A</figref> is a perspective view of the robotic head and vertical support rail shown in <figref idref="f0003">Figures 5A and 5B</figref>. As shown in <figref idref="f0005">Figure 7A</figref>, the robotic head is position in a vertical orientation, such that a specimen container held within the robotic head is also in a vertical orientation.</li><li><figref idref="f0006">Figure 7B</figref> is another perspective view of the robotic head and vertical support rail shown in <figref idref="f0003">Figures 5A and 5B</figref>. As shown in <figref idref="f0006">Figure 7B</figref>, the robotic head is positioned in a horizontal orientation, such that the container held within the robotic head is also in a horizontal orientation.</li><li><figref idref="f0007">Figures 8A-C</figref> shows a time-elapsed loading of a specimen container into the holding chamber of the robotic head shown in <figref idref="f0003">Figures 5A and 5B</figref>. As shown in <figref idref="f0007">Figure 8A</figref>, the gripping mechanism grips the top or cap of the container. <figref idref="f0007">Figure 8B</figref> shows the container in an intermediate position in the loading process. <figref idref="f0007">Figure 8B</figref>, shows the container after being loaded into the robotic head.</li><li><figref idref="f0008">Figures 9A and 9B</figref> are perspective and side views, respectively, of an alternative configuration of the detection system of <figref idref="f0001 f0002">Figures 1-3</figref> and <figref idref="f0003">5A-5B</figref>, with the upper and lower doors open showing an alternative configuration of the container holding structures. In the embodiment of <figref idref="f0008">Figures 9A and 9B</figref>, the racks are arranged in a drum or cylinder-type configuration.</li><li><figref idref="f0009">Figure 10</figref> is a perspective view of another configuration of the automated loading mechanism, showing a first conveyor belt operable in a horizontal plane and a second conveyor belt operable in a vertical plane.</li><li><figref idref="f0009">Figure 11</figref> is a perspective view of yet another configuration of the automated loading mechanism, showing a first conveyor belt operable in a horizontal plane and a second conveyor belt having a plurality of paddles and operable in a vertical plane.</li><li><figref idref="f0010">Figure 12</figref> is a perspective view of a casing and cover provided with an automated loading mechanism.</li><li><figref idref="f0011">Figure 13</figref> is a perspective view of one embodiment of an automated loading mechanism shown isolated from the detection system. In accordance with this embodiment, the automated loading mechanism comprises a loading station or area, a transport mechanism and an entrance location, for the fully automated loading of a specimen container. A portion of one side of the loading area has been removed to show additional details of the automated loading mechanism of this embodiment.</li><li><figref idref="f0011">Figure 14</figref> is another perspective view of the automated loading mechanism shown in <figref idref="f0011">Figure 14</figref>. The container loading area is shown as a see through feature to reveal other features of the automated loading mechanism, as described herein.</li><li><figref idref="f0012">Figure 15</figref> is a close up perspective view of the drum-like loading mechanism, vertical chute, locating device and system transfer device in <figref idref="f0011">Figure 14</figref>. The drum-like loading mechanism, vertical chute, locating device and system transfer device are shown isolated from the detection system.</li><li><figref idref="f0013">Figure 16</figref> is a cross-sectional view of the automated loading mechanism shown in <figref idref="f0011 f0012">Figures 14-15</figref>. More specifically, <figref idref="f0013">Figure 16</figref> is a cross-sectional view of the drum-like loading mechanism and vertical chute showing a specimen container falling through the chute. As shown in <figref idref="f0013">Figure 16</figref>, the top or cap of the specimen container is held in place briefly by the tapered ledge as the bottom of the container falls through the chute, thereby up-righting the specimen container.</li><li><figref idref="f0014">Figure 17</figref> is a perspective view of the automated detection apparatus comprising the automated loading mechanism shown in <figref idref="f0011">Figure 14</figref>. The container loading area of the automated loading mechanism is shown in a user accessible location on the front of an automated system for rapid non-invasive detection of a microbial agent. The automated detection system and the container loading area are shown with side panels removed and/or as see through features to reveal other features, as described herein.</li><li><figref idref="f0014">Figure 18</figref> is a perspective view of the automated detection apparatus comprising an alternative loading mechanism. The container loading area of the automated loading mechanism is shown in a user accessible location on the front of an automated system for rapid non-invasive detection of a microbial agent. The automated detection system and the container loading area are shown with side panels removed and/or as see through features to reveal other features, as described herein.</li><li><figref idref="f0015">Figure 19</figref> is a side view of the lower portion of the automated system for rapid non-invasive detection of a microbial agent shown in <figref idref="f0014">Figure 17</figref>. The automated detection system is shown with side panel removed to reveal other features of the system, as described herein.</li><li><figref idref="f0016">Figure 20</figref> is a perspective view of the holding structure and automated transfer mechanism shown in <figref idref="f0014 f0015">Figures 17-19</figref>. As shown, in this embodiment, the automated transfer mechanism comprises a lower horizontal support, a vertical support, a pivot plate and a robotic head for transferring a specimen container within a detection apparatus. For clarity, the holding structure and automated transfer mechanism are shown isolated from the detection apparatus.</li><li><figref idref="f0017">Figures 21A-B</figref> are perspective views of the pivot plate and robotic head of the automated transfer mechanism shown in <figref idref="f0016">Figure 20</figref>. The robotic head is shown with a cross-sectional view of the gripping mechanism and specimen container to reveal the features of the gripping mechanism. As shown in <figref idref="f0017">Figure 21A</figref>, the robotic head is located at a first end of the pivot plated and in a horizontal orientation, such that the specimen container is also orientated in a horizontal orientation. In <figref idref="f0017">Figure 21B</figref>, the robotic head is shown located at a second end of the pivot plate and in a vertical orientation, such that the specimen container is also orientated in a vertical orientation.</li><li><figref idref="f0018">Figure 22</figref> is a perspective view of an alternative configuration of the automated detection apparatus showing a user interface, a status screen, a locator device cover and two positive container ports.</li><li><figref idref="f0018">Figure 23</figref> is a perspective view showing another design configuration of the detection apparatus. As shown in <figref idref="f0018">Figure 23</figref>, the detection system comprises a first detection apparatus and a second detection instrument.</li><li><figref idref="f0019">Figure 24</figref> is a perspective view of yet another embodiment of the automated detection system. As shown, the automated detection system comprises a first detection apparatus having an automated loading mechanism and a second or down-stream detection apparatus linked or "daisy-chained" to the first detection apparatus, as described herein.</li><li><figref idref="f0020 f0021">Figures 25A-C</figref> show a time-elapsed pusher arm mechanism for pushing a specimen container from a first detection apparatus to a second or down-stream detection apparatus.</li><li><figref idref="f0022">Figure 26</figref> shows a perspective view of the holding structure and agitation assembly shown isolated from the detection system.</li><li><figref idref="f0023">Figure 27A</figref> is a perspective view of a rack holding structure and retention feature for holding a specimen container securely within the rack holding structure.</li><li><figref idref="f0023">Figure 27B</figref> shows a cross-sectional view of the rack holding structure and retention feature shown in <figref idref="f0023">Figure 27A</figref>.</li><li><figref idref="f0024">Figure 27C</figref> is a top cross-sectional view of the rack holding structure and retention feature of <figref idref="f0023">Figure 27A</figref>, showing a schematic representation of a canted coil spring.</li><li><figref idref="f0025">Figure 28A-B</figref> show first and second perspective views of a carrier for carrying a plurality of specimen containers to the detection apparatus. As shown, the carrier comprises a plurality of holding wells for holding a plurality of specimen containers. <figref idref="f0025">Figure 28A</figref> also shows two opposed gripping features or handles and a release mechanism for releasing the plurality of specimen containers at the loading station, as described herein.</li><li><figref idref="f0026">Figure 29</figref> shows a perspective view of another possible configuration for the detection system. As shown in <figref idref="f0026">Figure 29</figref>, the detection system includes a release mechanism for releasing one or more specimen containers from the carrier shown in <figref idref="f0025">Figures 28A-B</figref>.</li><li><figref idref="f0027">Figure 30</figref> is a flow chart showing the steps performed in the operation of the detection system.</li><li><figref idref="f0028">Figure 31</figref> is a block diagram of an automated instrument for rapid identification and/or characterization of a microbial agent present in a sample.</li><li><figref idref="f0029">Figure 32</figref> is a perspective view of one possible configuration of the instrument shown in <figref idref="f0028">Figure 31</figref>. The instrument includes a rack for holding specimen containers, a cassette of disposables (including sampling devices and separation devices), a robotic transfer mechanism, sample removal apparatus, a separation and concentration device in the form of a centrifuge, and a identification and/or characterization module (read station) operating to interrogate a separation device containing a concentrated microbial agent for identification and/or characterization of the microbial agent. In one possible embodiment, the instrument of <figref idref="f0029">Figure 32</figref> could be integrated with an automated detection instrument (See <figref idref="f0043">Figure 58</figref>, <figref idref="f0058">77-78</figref> below), in which case the rack for the specimen containers is the same structure holding the specimen containers during the detection operations. Alternatively, the identification and/or characterization instrument is located remotely from but coupled to an automated detection instrument as shown in <figref idref="f0058">Figure 77</figref> and described in our prior provisional application and in conjunction with <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>.</li><li><figref idref="f0029">Figure 33</figref> is top plan view of the identification and/or characterization instrument of <figref idref="f0029">Figure 32</figref>, showing the rack of positive specimen containers in one position for incubation.</li><li><figref idref="f0029">Figure 34</figref> is a top plan view of the instrument of <figref idref="f0029">Figure 32</figref>, showing the rack for the positive specimen containers moved to a position for withdrawal of the sample from the bottle for identification and/or characterization testing.</li><li><figref idref="f0030">Figure 35</figref> is another perspective view of the embodiment of <figref idref="f0029">Figures 32-34</figref>.</li><li><figref idref="f0031">Figure 36</figref> is a perspective view of a separation device which is used in conjunction with the identification/characterization instrument of <figref idref="f0028">Figure 31</figref>. The separation device receives a portion of the sample from a positive specimen container. The microbial agent is concentrated at the bottom of a capillary tube located in the separation device in the manner described herein. The concentrated microbial agent is then interrogated by a identification and/or characterization reading module to characterize and/or identify the microbial agent.</li><li><figref idref="f0031">Figure 37</figref> is a perspective view of the separation device of <figref idref="f0031">Figure 36</figref>.</li><li><figref idref="f0031">Figure 38</figref> is a cross-sectional view of the separation device of <figref idref="f0031">Figures 36 and 37</figref>.</li><li><figref idref="f0031">Figure 39</figref> is a cross-sectional view of an end-cap which is fitted to the lower end of the separation device of <figref idref="f0031">Figures 36-38</figref>.</li><li><figref idref="f0031">Figure 40</figref> is a cross-sectional view of the separation device of <figref idref="f0031">Figure 36</figref>, showing the concentrated microbial agent in the capillary tube of the separation device after centrifugation.</li><li><figref idref="f0031">Figure 41</figref> is a schematic illustration of the concentrated microbial agent in the separation device of <figref idref="f0031">Figure 36</figref> being interrogated by the identification/characterization or reading module.</li><li><figref idref="f0031">Figure 42</figref> is a perspective view of an alternative embodiment of the separation device of <figref idref="f0031">Figure 36</figref>.</li><li><figref idref="f0031">Figure 43</figref> is a cross-section of the separation device of <figref idref="f0031">Figure 42</figref>.</li><li><figref idref="f0032">Figure 44</figref> is an illustration of one embodiment of a disposable sampling device which is used within the identification and/or characterization instrument.</li><li><figref idref="f0032">Figure 45</figref> is a detailed perspective view showing the operation of the sample removal apparatus in the identification and/or characterization instrument to pick up one of the sampling devices of <figref idref="f0032">Figure 44</figref> from a cassette of disposable devices. The cassette includes a multitude of the separation devices of <figref idref="f0033">Figure 46</figref> or <figref idref="f0031">42</figref> and a multitude of the sampling devices of <figref idref="f0032">Figure 44</figref>.</li><li><figref idref="f0033">Figure 46</figref> is a detailed perspective view showing the operation of the sample removal apparatus to sterilize the stopper at the top of the detection container and vent the detection container.</li><li><figref idref="f0033">Figure 47</figref> is a more detailed illustration of the sample removing apparatus in the position shown in <figref idref="f0033">Figure 46</figref>.</li><li><figref idref="f0034">Figure 48</figref> is a detailed perspective view showing the operation of the sample removal apparatus to withdraw a portion of the sample within the detection container into one of the disposable sampling devices of <figref idref="f0032">Figure 44</figref>.</li><li><figref idref="f0034">Figure 49</figref> is a more detailed illustration of the sample removal apparatus in the position of <figref idref="f0034">Figure 48</figref>.</li><li><figref idref="f0035">Figures 50A-50C</figref> are three perspective views of the sample removal apparatus showing the operations of dispensing the sample into one of the separation devices and transfer the sampling device to the waste container.</li><li><figref idref="f0036">Figure 51</figref> is sequence of perspective views of the sample removal apparatus showing the operations of transferring the separation device to the separation and concentration station and optical interrogation of the separation device in the identification and/or characterization module.</li><li><figref idref="f0036">Figure 52</figref> is a more detailed illustration of the separation and concentration station and the identification and/or characterization module.</li><li><figref idref="f0037">Figure 53</figref> is a sequence of three perspective views of the identification and/or characterization instrument showing the operations of picking up the separation device, transferring the separation device to the waste container and placing the separation device in the waste container.</li><li><figref idref="f0037">Figure 54</figref> is a more detailed illustration of the operation of placing the separation device into the waste container.</li><li><figref idref="f0038">Figure 55</figref> is a block diagram of an alternative configuration of the identification and/or characterization instrument in which the concentrated microbial agent is removed from the separation device and analyzed after removal. The analysis could be performed by any one of a number of different types of systems or units, including a molecular diagnostic test unit, a mass spectrometry unit, or a microbial identification test device and associated processing instrument.</li><li><figref idref="f0039 f0040 f0041">Figures 56A-56C</figref> are a flow chart showing the steps performed in the operation of both automatically detecting the presence of a microbial agent in a specimen container (<figref idref="f0039">Figure 56A</figref>) and automatically identifying and/or characterizing the microbial agent (<figref idref="f0040">Figure 56B</figref> and <figref idref="f0041">56C</figref>).</li><li><figref idref="f0042">Figure 57</figref> is a perspective view of a second embodiment of an instrument for rapid and automated identification and/or characterization of a microbial agent in a sample.</li><li><figref idref="f0043">Figure 58</figref> is a perspective view of the instrument of <figref idref="f0042">Figure 57</figref>, showing one possible configuration of the racks for holding the specimen containers. In the embodiment of <figref idref="f0043">Figure 58</figref>, the racks include features for incubation of the specimen containers, agitation of the specimen containers, and automated detection of microbial growth within the specimen containers. Thus, <figref idref="f0043">Figure 58</figref> shows one embodiment in which the automated detection and identification instruments can be combined into a single instrument.</li><li><figref idref="f0044">Figure 59</figref> is another perspective view of the embodiments of <figref idref="f0042">Figures 57</figref> and <figref idref="f0043">58</figref>. A multiple axis robot is used access the specimen containers and perform the sampling operation using disposable sampling devices.</li><li><figref idref="f0044">Figure 60</figref> is a perspective view of cassettes holding disposable sampling devices and disposable separation devices, which can be used in the instruments of either <figref idref="f0029 f0030">Figures 32-35</figref> or <figref idref="f0042 f0044">57-59</figref>.</li><li><figref idref="f0045">Figure 61</figref> is a perspective view of a multiple axis robot used in the embodiment of <figref idref="f0044">Figure 59</figref>.</li><li><figref idref="f0045">Figure 62</figref> is a perspective view of an alternative embodiment of a disposable sampling device, presenting a variation on the general design shown in <figref idref="f0032">Figure 44</figref>.</li><li><figref idref="f0045">Figure 63</figref> is a cross sectional view of the sampling device of <figref idref="f0045">Figure 62</figref>.</li><li><figref idref="f0046">Figure 64</figref> is a detailed perspective view of the distal end of the arm of the robot of <figref idref="f0045">Figure 61</figref> shown gripping the sampling device of <figref idref="f0045">Figure 62</figref>.</li><li><figref idref="f0047">Figure 65</figref> is another detailed perspective view of the distal end of the arm of the robot of <figref idref="f0045">Figure 61</figref> shown gripping the sampling device of <figref idref="f0045">Figure 62</figref>.</li><li><figref idref="f0047">Figure 66</figref> is a perspective view of the pump assembly on the robot of <figref idref="f0045">Figure 61</figref> which operates to provide vacuum and positive pressure to the sampling device in order to (a) withdraw a small portion of the sample from one of the specimen containers and (b) dispense the sample (optionally after lysing the sample) into one of the disposable separation devices of <figref idref="f0031">Figures 36</figref> and <figref idref="f0044">60</figref>.</li><li><figref idref="f0048">Figure 67</figref> is a perspective view of the robot of <figref idref="f0045">Figure 61</figref> performing a sampling operation on one of the specimen containers using the sampling device of <figref idref="f0045">Figure 62</figref>.</li><li><figref idref="f0049">Figure 68</figref> is a more detailed view of the sampling operation shown in <figref idref="f0048">Figure 67</figref>.</li><li><figref idref="f0050">Figure 69</figref> is a perspective view of the sampling device of <figref idref="f0045">Figure 62</figref> being placed into a vortexer shown in <figref idref="f0039 f0040 f0041">Figures 56</figref> and <figref idref="f0042">57</figref> in order to facilitate lysing of cellular components in the sample withdrawn from one of the specimen containers.</li><li><figref idref="f0050">Figure 69A</figref> is a perspective view of the vortexer having an optional coil heater around the holder of the sampling device in order to heat the holder and maintain the sample within the sampling device at 37 degrees C.</li><li><figref idref="f0051">Figure 70</figref> is a perspective view of the sampling device of <figref idref="f0045">Figure 62</figref> being held by the robot hand during the vortexing operation.</li><li><figref idref="f0052">Figures 71A and 71B</figref> are side and cross-sectional views of the vortexer and sampling device.</li><li><figref idref="f0053">Figures 72A and 72B</figref> are cross-sectional and perspective views of a holder for the sampling device incorporated into the vortexer.</li><li><figref idref="f0054">Figures 73A, 73B</figref> and <figref idref="f0055">73C</figref> are cross-sectional, side and perspective views, respectively, of the sampling device and the separation device prior to introduction of the sample from the sampling device into the separation device. <figref idref="f0055">Figure 73D</figref> is another perspective view of the sampling and separation device, with the rubber needle sheath of the sampling device shown partially removed in order to show the needle of the sampling device.</li><li><figref idref="f0056">Figure 74</figref> is a perspective view of the sampling device in position to inject a portion of the sample into the separation device.</li><li><figref idref="f0056">Figure 75</figref> is a side view of the injection operation shown in <figref idref="f0056">Figure 74</figref>.</li><li><figref idref="f0057">Figure 76</figref> is a cross-section view of the sampling and separation devices showing the injection operation.</li><li><figref idref="f0057">Figure 76A</figref> is a detailed view of the cup and cup holder of <figref idref="f0042">Figure 57</figref>, showing the cup receiving one of the separation devices; <figref idref="f0057">Figure 76B</figref> shows a separation device being inserted into the cup of <figref idref="f0057">Figure 76A; Figure 76C</figref> is a cross-section of the cup holder, cup and separation device of <figref idref="f0057">Figure 76A</figref>.</li><li><figref idref="f0058">Figure 77</figref> is a schematic representation of a detection instrument for detection of a microbial agent in a biological sample coupled to an automated identification and/or characterization instrument via a conveyor.</li><li><figref idref="f0058">Figure 78</figref> is a schematic representation of a combined automated detection and identification instrument which receives specimen containers in an automated fashion e.g., via a conveyor.</li><li><figref idref="f0058">Figure 79</figref> is a schematic representation of a combined automated detection and identification instrument which receives specimen containers manually from a user, e.g., via opening a door in a front panel of the instrument. The embodiment of <figref idref="f0058">Figure 79</figref> could be implemented, for example, using the arrangement shown in <figref idref="f0042">Figure 57</figref>.</li><li><figref idref="f0059">Figure 80</figref> is schematic block diagram showing a computer system controlling the operation of the instrument of <figref idref="f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057 f0058 f0059 f0060 f0061 f0062 f0063 f0064 f0065 f0066 f0067">Figures 57-86</figref>.</li><li><figref idref="f0060 f0062">Figures 81A-C</figref> are a flow chart showing a sequence of processing instructions which perform identification and/or characterization of the concentrated microbial agent using intrinsic fluorescence measurements.</li><li><figref idref="f0063 f0042">Figures 82-57</figref> are plots of intrinsic fluorescence (IF) measurements, and transforms thereof which illustrate the benefit of the pre-processing instructions of <figref idref="f0036">Figure 51A</figref> in terms of minimizing strain-to-strain variations within an organism group.</li><li><figref idref="f0069">Figures 88</figref> and <figref idref="f0070">89</figref> are plots of first derivative of logarithm transformed IF measurements showing the discrimination potential between a subset of species for excitation wavelengths of 315 and 415 nm.</li><li><figref idref="f0071">Figure 90</figref> is a perspective view of a second embodiment of a separation device which can be used in conjunction with the identification/characterization instrument of <figref idref="f0001">Figure 1</figref>. The separation device of this embodiment has a separate lytic chamber and a separate separation chamber which are connected by a fluid flow-channel.</li><li><figref idref="f0071">Figure 91</figref> is a perspective view of the separation device embodiment of <figref idref="f0071">Figure 90</figref>, showing a top plate and base plate separated from the separation device.</li><li><figref idref="f0072">Figure 92</figref> is a top view of the body portion of the separation device embodiment shown in <figref idref="f0071">Figure 90</figref>.</li><li><figref idref="f0072">Figure 93</figref> is a cross-sectional view along line A-A of the separation device embodiment shown in <figref idref="f0072">Figure 92</figref>.</li><li><figref idref="f0072">Figure 94</figref> is a cross-sectional view along line B-B of the separation device embodiment shown in <figref idref="f0072">Figure 92</figref>.</li><li><figref idref="f0073">Figure 95</figref> is a perspective view of a combined sampling and separation device which can be used in conjunction with the identification/characterization instrument of <figref idref="f0028">Figure 31</figref>.</li><li><figref idref="f0074">Figure 96</figref> is a front view of the combined sampling and separation device shown in <figref idref="f0047">Figure 65</figref> with a pinch valve shown in the open position.</li><li><figref idref="f0074">Figure 97</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0074">Figure 96</figref> with the pinch valve shown in the open position.</li><li><figref idref="f0074">Figure 98</figref> is a front view of the combined sampling and separation device shown in <figref idref="f0073">Figure 95</figref> with a pinch valve shown in the closed position.</li><li><figref idref="f0074">Figure 99</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0074">Figure 97</figref> with the pinch valve shown in the closed position.</li><li><figref idref="f0075">Figure 100</figref> is a perspective view of a second embodiment of a combined sampling and separation device.</li><li><figref idref="f0075">Figure 101</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0075">Figure 100</figref>.</li><li><figref idref="f0076">Figure 102</figref> is a cross-sectional view of the valve shown in <figref idref="f0075">Figure 101</figref>.</li><li><figref idref="f0076">Figure 103</figref> is a side view of a third embodiment of a combined sampling and separation device which can be used in conjunction with the identification/characterization instrument of <figref idref="f0028">Figure 31</figref>.</li><li><figref idref="f0076">Figure 104</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0076">Figure 103</figref>.</li><li><figref idref="f0077">Figure 105</figref> is an exploded view of the combined sampling and separation device shown in <figref idref="f0076">Figure 103</figref>.</li><li><figref idref="f0077">Figure 106</figref> is a perspective view of a third embodiment of a combined sampling and separation device which can be used in conjunction with the identification/characterization instrument of <figref idref="f0028">Figure 31</figref>.</li><li><figref idref="f0078">Figure 107A</figref> is a side view of the combined sampling and separation device shown in <figref idref="f0077">Figure 106</figref>.</li><li><figref idref="f0078">Figure 107B</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0078">Figure 107A</figref>.</li><li><figref idref="f0078">Figure 108A</figref> is a side view of the combined sampling and separation device shown in <figref idref="f0077">Figure 106</figref>.</li><li><figref idref="f0078">Figure 108B</figref> is a cross-sectional view of the combined sampling and separation device shown in <figref idref="f0078">Figure 108A</figref>.</li></ul>

DETAILED DESCRIPTION

0030As noted in the summary section, this document describes an automated system for and instrument and methodology for detection of microbial agent presence within a specimen container and an instrument and methodology for automated identification and/or characterization of the microbial agent. The instrument and methodology for detection of microbial agent presence will be set forth in Part 1 (<figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>). The instrument and methodology for identification and/or characterization of the microbial agent will be described in Part 2 (<figref idref="f0028 f0078">Figures 31-108</figref>). Feature for integrating the two instrument into either separate instruments one in one combined instrument will be described at various points in this document. These features may include automated loading and unloading features, conveyor features, and robotic handling features that operate on specimen containers, including but not limited to specimen containers in the form of bottles or the like.

0031Although there is discussion of various 'embodiments' of the invention in the present description, it should be noted that the invention is defined by the claims appended herein. For the avoidance of doubt, the present invention relates to an automated system and to a method as follows: An automated system for rapid detection of a microbial agent in a sample and identifying and/or characterizing the microbial agent, comprising, in combination: <ul id="ul0004" list-style="none" compact="compact"><li>a detection instrument receiving a specimen container containing a sample, the detection instrument including a heated enclosure for incubating the specimen container and a detection unit interrogating the specimen container to detect whether the specimen container is positive for the presence of a microbial agent in the sample;</li><li>a supply of disposable separation devices; and</li><li>an identification/characterization instrument receiving a specimen container detected positive by the detection instrument, the characterization/identification instrument comprising: <ol id="ol0002" compact="compact" ol-style=""><li>(a) a sample removal apparatus coupled to a robotic transfer mechanism and operative to remove a portion of the sample from the specimen container and add the portion to a separation device obtained from the supply of separation devices;</li><li>(b) a separation and concentration station operative on the separation device after receiving the portion of the sample so as to separate the microbial agent from other products in the sample and concentrate the microbial agent within the separation device; and</li><li>(c) an identification and/or characterization, module interrogating the concentrated microbial agent to identify and/or characterize the microbial, agent, wherein the robotic transfer mechanism moves the separation device from the separation and concentration station to the identification and/or characterization module.</li></ol></li></ul>

0032A method for rapid identification and/or characterization of a microbial agent present in a sample, the sample loaded into a specimen container, comprising performing the following steps in an automated manner: <ol id="ol0003" compact="compact" ol-style=""><li>(a) incubating the specimen container;</li><li>(b) periodically interrogating the specimen container to determine whether it is positive for presence of a microbial agent within the specimen container;</li><li>(c) when the specimen container is determined positive, withdrawing a portion of the sample from the specimen container with a sample removal apparatus coupled to a robotic transfer mechanism;</li><li>(d) introducing the portion of the biological sample into a disposable separation device;</li><li>(e) lysing components in the portion of the biological sample, either before or after performing step (d);</li><li>(f) transferring the separation device to a separation and concentration station using the robotic transfer mechanism,</li><li>(g) separating and concentrating the microbial agent within the separation device;</li><li>(h) transferring the separation device to an identification and/or characterization module using the robotic transfer mechanism, and</li><li>(i) analyzing the concentrated microbial agent to identify and/or characterize the microbial agent,</li></ol> wherein steps (a)-(i) are performed automatically within an integrated detection and identification/characterization instrument.

Part 1 Automated Instrument for Detection of Specimen Container for Microbial Agent Growth (Figures 1-30)

0033An automated system or instrument for non-invasive detection of the presence of a microbial agent (e.g., a microorganism) in a test sample contained within a sample container, e.g., a culture bottle, is described herein. One embodiment of the automated system or instrument is described herein in conjunction with <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007">FIGS. 1-8C</figref>. Other possible embodiments and design alternatives are shown in conjunction with <figref idref="f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">FIGS. 9A-30</figref>, and described herein. The automated system can include one or more of the following features: (1) a housing, enclosing an interior chamber; (2) an automated loading mechanism for loading one or more containers into the interior chamber of the system; (3) an automated container management mechanism or locator device for moving or locating a container among various work-flow stations within the system; (4) an automated transfer mechanism, for transfer of a container within the system; (5) one or more container holding structures for holding a plurality of specimen containers, optionally provided with an agitation assembly; (6) a detection unit for detection of microbial growth; and/or (7) mechanism for automated unloading of a specimen container from the system. In order to better appreciate how the illustrated embodiment of the detection system operates, this specification may describe the automated detection apparatus in the context of a particular detection instrument (a blood culture instrument) and specimen container (a blood culture bottle). However, persons skilled in the art will readily appreciate that the detection apparatus can be practiced in other embodiments, that variations from the specific embodiments disclosed herein can be arrived at to suit particular implementations, and that therefore the present description of a preferred embodiment and best mode for practicing the invention is provided by way of illustration and not limitation.

System Overview

0034An automated detection system 100 (for example, as illustrated in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>) is described herein that provides a new architecture and method for automated detection of a microbial agent (e.g., a microorganism) that may be present in a test sample or specimen sample. In general, any known test sample (e.g., a biological sample) can be used. For example, the test sample can be a clinical or non-clinical sample suspected of containing one or more microbial agents. Clinical samples, such as a bodily fluid, include, but are not limited to, blood, serum, plasma, blood fractions, joint fluid, urine, semen, saliva, feces, cerebrospinal fluid, gastric contents, vaginal secretions, tissue homogenates, bone marrow aspirates, bone homogenates, sputum, aspirates, swabs and swab rinsates, other body fluids, and the like. Non-clinical samples that may be tested include, but not limited to, foodstuffs, beverages, pharmaceuticals, cosmetics, water (<i>e.g.</i>, drinking water, non-potable water, and waste water), seawater ballasts, air, soil, sewage, plant material (<i>e.g.</i>, seeds, leaves, stems, roots, flowers, fruit), blood products (<i>e.g.</i>, platelets, serum, plasma, white blood cell fractions, <i>etc.</i>), donor organ or tissue samples, biowarfare samples, and the like. In one embodiment, the biological sample tested is a blood sample.

0035Referring now to the <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>, several configurations are possible for the detection system 100. As shown, for example, in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>, the automated detection system 100 comprises a housing 102 and one or more automated mechanisms for loading (see, e.g., 200, <figref idref="f0001">FIG. 1</figref>), moving or locating (not shown), transferring (see, e.g., 650, <figref idref="f0003">FIGS. 5A-5B</figref>), agitating (not shown) and/or unloading of specimen containers 500 within or from the detection system 100. The housing 102 comprises front and back panels 104A and 104B, opposing side panels (e.g., left-side and right-side panels) 106A and 106B, a top or roof panel 108A and a bottom or floor panel 108B, which form an enclosure, enclosing an interior chamber 620 (see, e.g., <figref idref="f0003">FIGS. 5A-5B</figref>) of the detection system 100. In one embodiment, the interior chamber 620 of the detection system 100 is a climate-controlled chamber (e.g., a temperature-controlled incubation chamber wherein the temperature is maintained at approximately 37° C.) to promote or enhance microbial growth. As shown in <figref idref="f0001 f0002">FIGS. 1-3</figref>, the housing also may include a first port or container entrance location 110, a second port or misread/error location 120, a third port or positive container exit location 130, a lower access panel 140 (<figref idref="f0001">FIG. 1</figref>) or drawer 142 (<figref idref="f0002">FIG. 3</figref>), and/or a user interface display 150. As known in the art, the lower access panel 140 or drawer 142 may include a handle 144. Also as shown in <figref idref="f0001">FIG. 1</figref>, the housing 102 may also comprise upper and lower sections 160 and 170, optionally each comprising an operable door (i.e., upper and lower doors) 162 and 172 (see, e.g., <figref idref="f0003">FIG. 5B</figref>). The upper door 162 and lower door 172 are operable to allow access to the interior chamber 620 of the detection system 100. However, as one of skill in the art would appreciate other design configurations are possible. For example, in another possible embodiment, the entire front panel may comprise a single operable door (not shown).

0036In one design possibility, as shown for example in <figref idref="f0001 f0002">FIGS. 1-3</figref>, the lower section 170 may have a larger profile or footprint than the upper section 160. In accordance with this embodiment the housing of the larger lower section 170 forms a shelf 180 on a top surface of the lower section 170 and adjacent to or in front of the upper section 160. This shelf 180 may provide a user workstation and/or workflow access points to the detection system 100. Furthermore, the shelf 180 may comprise an automated loading means or mechanism 200. The shelf 180 may further provide access locations for the first port or container entrance location 110, the second port or misread/error location 120, and the third port or positive container exit location 130.

0037In one embodiment, as shown for example in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>, the detection system 100 may comprise an automated loading mechanism 200, for the automated loading of a specimen container 500 into the detection system 100. The automated loading mechanism 200 may comprise a container loading station or area 202, a transport mechanism 204 and a first port or container entrance location 110. In operation, a user or technician can place one or more specimen containers 500 (see, e.g., <figref idref="f0002">FIG. 4</figref>) at the container loading station or area 202. A transport mechanism 204, for example, a conveyor belt 206, will transport the specimen container to the first port or container entrance location 110, and subsequently through the entrance location 110 and into the detection system 100, thereby loading the container into the system. The automated loading mechanism 200 is described in greater detail herein.

0038As one of skill in the art would appreciate, other designs may be employed for the automated loading mechanism and are described elsewhere herein. For example, alternative automated loading mechanisms are shown in <figref idref="f0009 f0010 f0011 f0012 f0013">FIGS. 10-16</figref>. In one embodiment, as shown in <figref idref="f0011 f0012 f0013">FIGS. 13-16</figref>, and as described in greater detail herein, the detection system 100 may employ a container loading area or reservoir 302 and a drum-like loading device 308 for the automated loading of a specimen container into the detection system 100.

0039In another embodiment, as shown for example in <figref idref="f0011 f0012">FIGS. 14-15</figref> and <figref idref="f0014">18</figref>, the automated detection system 100 may contain one or more work-flow stations 404 for obtaining one or more measurements, readings, scans and/or images of a specimen container, thereby providing information, such as, container type, container lot number, container expiration date, patient information, sample type, test type, fill level, weight measurement, etc. Furthermore, the one or more work-flow stations 404 may comprise one or more container management stations, such as, a container pick-up station or a container transfer station. For example, the automated detection system may contain one or more of the following work-flow stations: (1) a bar code reading station; (2) a container scanning stations; (3) a container imaging station; (4) a container weighing station; (5) container pick-up station; and/or (6) a container transfer station. In accordance with this embodiment, the detection system 100 may further have a container management means or container locator device 400, as shown, for example, in <figref idref="f0011 f0012">FIGS. 13-15</figref>, <figref idref="f0014">18</figref> and <figref idref="f0019">24</figref>. In operation, the container management device or locator device 400, operates to move or otherwise locate a specimen container 500 to one or more work-flow stations 404. In one design configuration, one or more of the work-flow stations are included within the housing 102 of the detection system 100. In one embodiment, as best shown in <figref idref="f0011 f0012">FIGS. 14-15</figref>, the drum or drum-like loading device 308 and vertically orientated chute 332 of automated loading mechanism 300 can operated to deposit or place a specimen container into a locator well 402, as described elsewhere herein. In another embodiment, as best shown, in <figref idref="f0014">FIGS. 18</figref> and <figref idref="f0019">24</figref>, the transport mechanism 204, or conveyor belt 206, of automated loading mechanism 200 can operate to deposit or place a specimen container into a locator well 402, as described elsewhere herein. As known in the art, the detection system 100 may further comprise one or more guide rails (not shown) to guide the specimen container into the locator well 402. In accordance with both of these embodiments, the container management device or locating device 400 can then rotate to move or locate the specimen container among various work-flow stations 404 within the system, such as for example, a bar code reading station, a container scanning stations, a container imaging station, a container weighing station, container pick-up station, and/or a container transfer station. The container management device or locator device 400 is described in greater detail herein.

0040As shown, for example, in <figref idref="f0003 f0004 f0005 f0006 f0007">FIGS. 5A-8C</figref> the detection system 100 may also comprise an automated transfer means or mechanism 650 for transferring the specimen containers 500 within the housing 102 of the detection system 100. For example, the transfer mechanism 650 may transfer the specimen container 500 from an entrance location or port 110 (see, e.g., <figref idref="f0001 f0002">FIGS. 1-3</figref>), into the interior chamber 620 of the detection system 100, and place the container 500 into one of the receiving structures or wells 602 contained in one of a plurality of holding structures or racks 600. In another embodiment, the transfer mechanism 650 may also be used to rearrange, transfer or otherwise manage specimen containers 500 within the system. For example, in one embodiment, the transfer mechanism 650 can be used to transfer a specimen container 500, detected as positive for microbial growth (referred to herein as a "positive" container), from the holding structure or rack 600 to a positive container location, such as a positive container exit location or port 130 (see, e.g., <figref idref="f0001">FIG. 1</figref>) where a user or technician can easily remove the positive container 500 from the detection system 100. In another embodiment, the transfer mechanism 650 can be used to transfer a container 500 determined as negative for microbial growth after a designated time has passed (referred to herein as a "negative" container), from the holding structure or rack 600 to a negative container location within the system (e.g., a negative container waste bin 146 (see, e.g., <figref idref="f0001">FIG. 1</figref>)) where a user or technician can easily access the waste bin 146 for removal and disposal of the container 500. As one of skill in the art would appreciate, other designs may be employed for the automated transfer mechanism and are described elsewhere herein. For example, another design configuration is described herein in conjunction with <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21B</figref>.

0041The detection system 100 will also include a means for detecting growth (e.g., a detection unit) in the specimen containers 500 (see, e.g., <figref idref="f0023 f0024">Figure 27</figref>). In general, any known means in the art for detecting microbial growth in a container can be used. For example, as is well known in the art, each holding station or rack 600 may contain a linear scanning optical system that has the capability of non-invasive monitoring of microorganism growth in each specimen container 500. In one embodiment, the optical system can interrogate a sensor (e.g., a Liquid Emulsion Sensor (LES) sensor) 514 (see, e.g., <figref idref="f0002">FIG. 4</figref>) in the containers 500, thereby detecting for microorganism growth within the container.

0042The detection system 100 may also include an automated unloading mechanism for the unloading of "positive" and/or "negative" specimen containers 500. This automated unloading mechanism can operate to ensure that once a "positive" or "negative" reading has been made for each specimen container 500, the container 500 is removed from the container receiving structures or wells 602 (see, e.g., <figref idref="f0003">FIGS. 5A and 5B</figref>), making room for another container to be loaded into the detection system 100, thereby increasing system through-put.

Specimen Container

0043The specimen container 500, shown for example in <figref idref="f0002">FIGS. 4</figref> and <figref idref="f0023">27B</figref>, and other figures, is shown in the form of a standard culture bottle (e.g., a blood culture bottle). However, the description of a culture bottle (e.g., a blood culture bottle) is offered by way of example and not limitation. As shown in <figref idref="f0002">FIG. 4</figref>, the specimen container 500 comprises a top portion 502, a body 504, and a base 506. The container 500 may include a bar code label 508 for automated reading of the container 500 within either the detection system or off-line equipment. As shown in <figref idref="f0002">FIGS. 4</figref> and <figref idref="f0023">27B</figref>, the top portion 502 of the container 500 typically comprises a narrow portion or neck 510 through which an opening 516 extends to provide communication with the interior chamber 518 of the container. As shown in <figref idref="f0023">FIG. 27B</figref>, the container also includes a closure device 512 (e.g., a stopper), optionally having a pierceable septum and may also have a sensor 514 (e.g., an LES sensor) formed or placed in the bottom of the container 500 for purposes of colorimetric detection of the presence of microbial growth in the container 500. The configuration of the container 500 is not particular important and the inventive system and methods can be adapted to a variety of containers designed for culturing a test sample (e.g., a biological test sample). Containers 500 of the type shown in <figref idref="f0002">FIGS. 4</figref> and <figref idref="f0023">27B</figref> are well known in the art and described in the patent literature cited in the Background section of this document.

0044In one embodiment, the specimen containers 500 are inoculated with a test sample (e.g., a clinical or non-clinical biological sample) and are loaded/unloaded into/out of the detection system 100. The container 500 may further comprise a growth or culture medium (not shown) for promoting and/or enhancing microbial or microorganism growth. The use of a growth or culture media (or medium) for the cultivation of microorganisms is well known. A suitable growth or culture medium provides the proper nutritional and environmental conditions for growth of microorganisms and should contain all the nutrients required by the microorganism which is to be cultivated in the specimen container 500. After a sufficient time interval to allow natural amplification of microorganisms (this time interval varies from species to species), the container 500 is tested within the detection system 100 for the presence of microbial or microorganism growth. The testing may occur continuously or on a periodic basis so that the container can be determined as positive for microorganism growth as soon as possible.

0045In one embodiment, once a container 500 is detected as positive in the detection system 100, the system will notify the operator through an indicator 190 (e.g., a visual prompt), and/or via a notification at the user interface display 150, or by other means.

Automated Loading Means or Mechanism

0046The detection system 100 may include a means or mechanism for automated loading of a specimen container 500 into the detection system 100. In one embodiment, as shown for example in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>, the automated loading mechanism 200 may comprise a container loading station or area 202, a transport mechanism 204 and an entrance location or port 110. However, as would be appreciated by one of skill in the art, the automated loading mechanism can take on many different configurations. For example, another design configuration of an automated loading mechanism 300 is described herein in conjunction with <figref idref="f0011 f0013">FIGS. 13-16</figref>. The various design configurations described herein are by way of illustration and not limitation. The automated loading mechanisms shown herein (e.g., <figref idref="f0001 f0002">FIGS. 1-3</figref>, <figref idref="f0003">5A-5B</figref> and <figref idref="f0011 f0013">13-16</figref>) are shown schematically and the parts are <u>not to scale.</u>

0047A user or technician can transport one or more specimen containers 500 to the detection system 100 by any known means and place the containers 500 at a container loading station or area 202. For example, in one embodiment, a user or technician can use a carrier designed to transport a plurality of specimen containers to the loading station or area 202 of the detection system 100.

0048One possible carrier design is shown in <figref idref="f0025">FIGS. 28A and 28B</figref>. As shown in <figref idref="f0025">FIGS. 28A and 28B</figref>, the carrier 350 comprises a body 351 having top and bottom surfaces 352A and 352B, respectively, front and back surfaces 354A and 354B, respectively, opposing side surfaces 356A and 356B (e.g., a right side surface and left side surface), respectively, and a pair of opposing user handles 358A and 358B, attached to said opposing side surfaces 356A, 356B. The body further comprises a plurality of through holes 360, each configured to hold a single specimen container 500 therein. The body 351 may also comprise a slide plate 362 operable within a slide joint 364 to slide back-and-forth (see, e.g., arrow 366 in <figref idref="f0025">FIG. 28A</figref>) between a "closed" position, to retain the specimen containers 500 loaded within the carrier 350, and an "open" position, to release the specimen containers 500 from the carrier 350, and deposit them onto or into an automated loading mechanism. The slide joint 364 may further comprise a spring, or like means, for locking the slide plate 362 in the "closed" position during transport by a user to a detection system.

0049As shown in <figref idref="f0025 f0026">FIGS. 28A-29</figref>, the carrier 350 may further comprise a pair of alignment arms 368A and 368B and a release tab 370 operable with a release mechanism 372 for releasing the specimen containers 500 at an automated loading mechanism 200 of a detection system 100. The release mechanism 372 comprises a pair of slots 374 that correspond to the pair of alignment arms 368A and 368B, to ensure the carrier 350 is properly aligned at the loading station or area 202 for depositing the specimen containers 300, and a release bar 376. In operation, a technician transports a carrier 350, containing one or more specimen containers 500, to the automated loading mechanism 200 and presses the carrier 350 against the release bar 376, with the alignment arms 368A and 368B aligned with the corresponding slots 374 of the release mechanism 372. By pressing the carrier 350 against the release bar 376, the release tab 370 is pushed in or depressed, thereby moving the slide plate 362 to the "open" position and allowing the specimen containers 500 to fall out of the through holes 360 and onto the loading station or area 202. The technician can then lift the carrier 350 upward until the carrier body 351 and plurality of through holes 360 clear the specimen containers 500, thereby depositing the containers at the automated loading mechanism 200 for automated loading into the detection system 100. As one of skill in the art would appreciate other design configurations are possible.

0050As shown in <figref idref="f0001 f0002">FIGS. 1-3</figref>, the loading station or area 202 is typically an easily accessible location or area of the automated loading mechanism 200 where a user or technician can place one or more specimen containers 500 for loading into the detection system 100. Once at the loading station 202, the containers 500 will be transported, using a transport mechanism 204, from the loading station or area 202 to an entrance location or port 110, and subsequently through the entrance location or port 110 and into the detection system 100. Accordingly, a user or technician can simply place one or more specimen containers 500 at the loading station or area 202 and walk away, while the containers 500 are automatically loaded into the detection system 100. Once the specimen containers 500 have been transported into the system, they can be moved to one or more work-flow stations using a container management device or locator device, and/or transferred to a holding structure or rack, as described elsewhere herein.

0051In one embodiment, as shown in <figref idref="f0001 f0002">FIGS. 1-3</figref>, <figref idref="f0003">5A and 5B</figref>, the transport mechanism 204 is a conveyor belt 206 operable to transport (e.g., convey) the containers 500 to an entrance location or port 110 and subsequently through the entrance location or port 110 and into the detection system 100. However, other means or mechanisms for transporting the specimen containers 500 from the loading station or area 202 to the entrance location or port 110 are envisioned, and may include, but are not limited to, feed screws, timing belts having grooves or molded plates, and the like. In other embodiments, the process of automated loading of a specimen container 500 into the detection system 100 may further comprise transferring the container to a holding structure or rack using a transfer mechanism 650 or moving the container to one or more work-flow stations using a container locator device (see, e.g., <figref idref="f0019">FIG. 24</figref>, 400A), as described below.

0052As shown in <figref idref="f0001 f0002">FIGS. 1-3</figref>, <figref idref="f0003">5A and 5B</figref>, the loading station or area 202 and transport mechanism 204 comprise a conveyor belt 206. In accordance with this embodiment, the user or technician can place one or more specimen containers 500 at a specific location or area (i.e., the loading station or area 202) of the conveyor belt 206 for automated loading of the containers 500 into the detection system 100. The conveyor belt 206 may run continuously, or may be activated by the physical presence of the container 500 at the loading station or area 202. For example, a system controller can be used to operate the conveyor belt 206 (i.e., turn it on or off) based on a signal (e.g., a light sensor) indicating the presence, or absence, of one or more specimen containers at the loading station 202. Similarly, one or more sensors can be used at the entrance location or port 110 to indicate if a container is improperly loaded and/or has fallen over and may cause jamming. The conveyor belt 206 operates to move or transport the containers 500 from the loading station or area 202 (e.g., the left portion of the conveyor belt 206, as shown in <figref idref="f0001">FIG. 1</figref>) to the entrance location or port 110, thereby accumulating one or more containers 500 at the entrance location or port 110 to be loaded into the detection system 100. Typically, as shown in <figref idref="f0001 f0002">FIGS. 1-3</figref> and 5A-5B, the loading station or area 202, transport mechanism 204 or conveyor belt 206, and entrance location or port 110 are located outside, or on the housing 102 of the detection system 100. In one embodiment, the automated loading mechanism 200 is located on a shelf 180 located on top of the lower section 170 and adjacent to the upper section 160 of the system 100. Also, as shown, the transport mechanism or conveyor belt 206 typically operates in a horizontal plane, so as to maintain the specimen containers 500 in a vertical or up-right orientation (i.e., such that the top portion 506 of the container 500 is up) for loading into the detection system 100 (see, e.g., <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>). As shown in <figref idref="f0001 f0002">FIGS. 1-3</figref>, the transport mechanism or conveyor belt 206 moves, for example, from left-to-right, or from the loading station or area 202 towards the entrance location or port 110, to transport one or more free standing containers 500 (see, e.g., <figref idref="f0002">FIG. 2</figref>, arrow 208).

0053In one embodiment, as shown, for example in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0009">10-11</figref>, the automated loading mechanism 200 will further comprise one or more guide rails 210 located juxtaposed to one or both sides of the transport mechanism or conveyor belt 206. The one or more guide rails 210 function to guide or direct the specimen containers 500 to the entrance location or port 110 during operation of the transport mechanism or conveyor belt 206. In one embodiment, the guide rails operate to funnel or guide the specimen containers into a single file line at the back of the automated loading mechanism 200, where they await their turn to be loaded, one container at a time, into the detection system 100. In another design aspect, as shown for example in <figref idref="f0018">FIG. 22</figref>, the detection system 100 may further comprise a locator device cover 460 that covers a locator device (described elsewhere herein) and encloses an interior locator device chamber (not shown) therein. The locator device cover 460 may comprise one or more container guide rails 462 for guiding a specimen container 500, as it is transported from the automated loading mechanism 200 to the entrance location or port 110, and subsequently into the interior chamber, thereby automatically loading the specimen contain into the system. In accordance with this embodiment, the interior locator device chamber (not shown) is considered to be a part of the interior chamber, which is described elsewhere herein.

0054In still another embodiment, the automated loading mechanism 200 may further comprise a means or device for reading or otherwise identifying the specimen containers 500 as the containers enter the detection system 100. For example, the containers 500 may include a bar code label 508 which can be read for container identification and tracking within the system. In accordance with this embodiment, the detection system 100 will include one or more bar code readers (see, e.g., 410 in <figref idref="f0011 f0012">FIGS. 14-15</figref>) at one or more locations within the system. For example, the detection system 100 may include a bar code reader at the entrance location or port 110 to read, identify and log the individual containers 500 into the detection system controller as they enter the system. In another embodiment, the entrance location or port 110 may also include a means or device (e.g., a container rotator or rotating turntable, as described elsewhere herein) for rotating the container within the entrance location or port 110 to enable reading of the bar code label 508. In another possible embodiment, the transfer mechanism (see, e.g., <figref idref="f0003">FIG. 5B</figref>, 650) may rotate the container 500 to enable reading of the bar code label 508. Once the bar code has been read, the transfer mechanism will typically transfer the container 500 from the entrance location or port 110 to one of a plurality of receiving structures or wells 602 in one of a plurality of holding structures or racks 600.

0055In yet another embodiment, if the bar code 508 cannot be properly read, (e.g., the label is misread or a reading error occurs) the detection system controller (not shown) can direct the container 500 to a misread/error location or port 120 for user access to the unreadable or misread container 500. The user can re-load the container using the automated loading mechanism 200 and/or at the user's discretion, may optionally manually load the container 500 and hand enter container 500 information into the system controller (e.g., using the user interface 150). In another embodiment, the detection system 100 may contain a high priority (or STAT) loading location (not shown) for the loading of high priority containers and/or for manual loading of containers where the label has been misread or a reading error has occurred.

0056Another design configuration of the automated loading mechanism is shown in <figref idref="f0009">FIG. 10</figref>. As shown in <figref idref="f0009">FIG. 10</figref>, the automated loading mechanism 200 comprises a loading station or area 202, a first conveyor belt 206, and an entrance location or port 110. The conveyor belt 206 operates to transport the specimen containers 500 from the left edge of the system 100 (i.e., the location of the loading station 202) to the entrance location or port 110. In this example, the movement is from left-to-right and is represented by arrow 220 in <figref idref="f0009">FIG. 10</figref>. The automated loading mechanism 200 may further comprise a guide rail 210 and a second conveyor belt 212, which operates around a set of gears or wheels 214, 216. In accordance with this embodiment, the second conveyor belt 212 is orientated and operable in a vertical plane above the first horizontal conveyor belt 206, and can operate in a clockwise or counter-clockwise manner (i.e., to move the belt from left-to-right or from right-to-left). The clockwise or counter-clockwise operation of the second vertically orientated conveyor belt 212 can provide the specimen container 500 with a counter-clockwise or clockwise rotation, respectively, about a vertical axis of the container. Applicants have found that providing a specimen container 500 with clockwise or counter-clockwise rotation can prevent and/or reduce jamming or clogging of the automated loading mechanism 200 as a plurality of specimen containers 500 accumulate at the entrance location or port 110. Once the containers 500 have arrived at the entrance location or port 110 they can be moved into the detection system 100.

0057In still another embodiment, the automated loading mechanism 200 may also contain a backer board (not shown) located in a horizontal plane underneath the first conveyor belt 206. As one of skill in the art would appreciate, the conveyor belt 206 may have some give, flexibility, or may otherwise be considered "springy". This springy nature of the conveyor belt 206 may lead to instability of the specimen container 500 as the container is transported across the conveyor belt 206 from the loading station or area 202 to the first port or entrance location 110 and may result in specimen containers 500 tipping or falling over. Applicants have found that by including a rigid or semi-rigid backer board underneath the conveyor belt 206, this problem can be reduce and/or eliminate altogether, thereby, reducing and/or preventing jamming or clogging of the loading mechanism 200 (e.g., with containers 500 that have fallen over). In general, any known backer board material may be used. For example, the backer board can be a rigid or semi-rigid board made of plastic, wood, or metal.

0058Yet another configuration of the automated loading mechanism is shown in <figref idref="f0009">FIG. 11</figref>. As shown in <figref idref="f0009">FIG. 11</figref>, the automated loading mechanism 200 may comprise a loading station or area 202, a conveyor belt 206, and an entrance location or port 110. Also as shown, the conveyor belt 206 can operate to transport the specimen containers 500 from the front edge of the system 100 (i.e., the loading station 202) to the entrance location or port 110. In this example, the movement of the loading mechanism 200 is from front-to-back (i.e., from the front edge of the instrument to the loading port 110) and is represented by arrow 240 in <figref idref="f0009">FIG. 11</figref>. As shown, the automated loading mechanism 200 may further comprise one or more guide rails 210 to guide the one or more specimen containers 500 to the entrance location or port 110, as they are transported by the conveyor belt 206.

0059Optionally, as shown in <figref idref="f0009">FIG. 11</figref>, the automated loading mechanism 200, in accordance with this embodiment, may include a second transport mechanism 230. In one embodiment, the second transport mechanism 230 may comprise a second conveyor belt 232 located in, and operable in, a vertical plan above the first conveyor belt 206. As shown, the second transport mechanism 230 may further comprise a plurality of paddles or plates 236 attached to the second conveyor belt 232. In accordance with this embodiment, the first conveyor belt 206 operates to move or transport one or more specimen containers 500 from the loading station or area 202 to the second transport mechanism 230, where the containers 500 are individually moved or transported into a well or space 234 between the paddles or plates 236. The second conveyor belt 232 operates around a set of gears or drive wheels (not shown), and runs or moves, for example, from left-to-right across the back edge of the automated loading mechanism 200, thereby transporting the containers 500 from left-to-right along the back of the loading mechanism 200 and to the entrance location or port 110 (see, e.g., arrow 250). Once the containers 500 have arrived at the entrance location or port 110 they can be moved into the detection system 100.

0060In yet another embodiment, the automated loading mechanism 200 can be enclosed or encased in a protective housing or casing 260, as shown for example in <figref idref="f0010">FIG. 12</figref>. In accordance with this embodiment, the automated loading mechanism 200, or one or more components thereof (i.e., one or more of the loading area, transport means (e.g., conveyor belt 206) and/or entrance location or port (not shown)), can be housed or encased in a protective housing or casing 260. The protective housing or casing 260 will have an opening 262 providing access to, and for loading specimen container 500 into/onto the automated loading mechanism 200 housed therein. Optionally, the protective housing or casing 260 can further include a cover means 264 that can be closed or shut to protect the automated loading mechanism 200, and/or containers 500, contained therein. The cover can be a closable lid 266, as shown, or other structure or means for closing the housing or casing 260. For example, in another embodiment, the cover 264 can be a lightweight curtain (not shown) that can be pulled shut over the opening 262. The protective housing or casing 260 may also provide a priority container loading port 270 for the loading or high priority containers (i.e., STAT container) and/or misread containers. In one embodiment, a container 500 can be manually loaded into the priority port 270.

0061Another embodiment of an automated loading mechanism is shown in <figref idref="f0011 f0012">FIGS. 13-15</figref>. Like the previously described automated loading mechanism, the automated loading mechanism 300 shown in <figref idref="f0011 f0012">FIGS. 13-15</figref>, comprises a container loading station or area 302, a transport mechanism 304 and a container entrance location 306, for the fully automated loading of one or more specimen containers 500 into the detection system 100.

0062The container loading area 302 is in an easily accessible location on the detection system 100 to allow a user to easily place one or more specimen containers 500 therein, as shown for example in <figref idref="f0014">FIG. 17</figref>. In accordance with this embodiment, the specimen containers 500 are loaded in a horizontal orientation, such that they are lying on their side, as shown for example in <figref idref="f0011">FIG. 13</figref>. Once at the container loading area 302, the specimen containers 500 can be transported by a transport mechanism 304 from the container loading area 302 to an entrance location 306, from where the containers 500 will enter the detection system 100, as described in more detail herein. Surprisingly, regardless of the specimen container 500 orientation in the loading area 302 (i.e., regardless of whether the top portion 506 of the container 500 is facing the detection system 100 or facing away from the detection system 100 (as shown, e.g., in <figref idref="f0011">FIG. 14</figref>)), the automated loading mechanism 300 of this embodiment is capable of loading the specimen containers 500 into the detection system 100.

0063In one embodiment, the container loading station or area 302 comprises a loading reservoir 303 that is capable of holding one or more specimen containers 500, as shown for example in <figref idref="f0011">FIG. 13</figref>. The loading reservoir 303 can be designed to hold from 1 to 100 specimen containers, from 1 to 80 specimen containers, or from 1 to 50 specimen containers. In other design concepts, the loading reservoir may hold 100 or more specimen containers 500. The automated loading mechanism 300 of this embodiment may further comprise a lid or cover (not shown), which the user or technician can optionally close to cover the loading reservoir 303 and loading area 302. Various designs are possible and contemplated for the lid or cover.

0064As show in <figref idref="f0011">FIGS. 13-14</figref>, the loading reservoir 303 contains a transport mechanism 304, for example, a sloped ramp that slopes downwards towards an entrance location 306 so as to transport the specimen containers 500 from the loading area 302 to the entrance location 306. In accordance with this embodiment, the sloped ramp will allow the specimen containers to roll or slide down the ramp to the entrance location 306. Although, a sloped ramp is exemplified in the figures other designs are possible and contemplated for the transport means or mechanism 304 for transporting the specimen containers to the entrance location 306. For example, in one alternative design concept the transport mechanism 304 may comprise a conveyor belt (not shown). In accordance with this design concept the conveyor belt can be designed to hold one or more specimen containers and may optionally be designed such that the conveyor belt slopes downward towards the entrance location 306.

0065Once at the entrance location 306, a drum or drum-like loading device 308 will be used for loading the specimen containers 500 into the detection system 100. As shown, the drum-like loading device 308 has one or more horizontally orientated slots 310 for holding one or more specimen containers therein. Each individual slot 310 is capable of holding a single specimen container 500. In one embodiment, the drum-like loading device 308 has a plurality of slots, for example, from 1 to 10 slots, from 1 to 8 slots, from 1 to 6 slots, from 1 to 5 slots, from 1 to 4 slots, or from 1 to 3 slots for holding specimen containers 500 therein. In another embodiment, the drum-like loading device 308 can be designed to have a single slot capable of holding a single specimen container 500 therein.

0066The drum-like loading device 308 is capable of rotating (either in a clock-wise direction, or counter-clock wise direction) about a horizontal axis, and is capable of picking-up and loading individual specimen container 500 into the detection system 100. In operation, the rotation of the drum or drum-like loading device 308 picks up a horizontally orientated specimen container 500 in one of a plurality of horizontally orientated slots 310, and moves the container 500, by rotation of the drum or drum-like loading device to a tumbler device 330 (see, e.g., <figref idref="f0013">FIG. 16</figref>). Any known means in the art can be used for rotation of the drum or drum-like loading device 308. For example, the system may employ the use of a motor (not shown) and drive belt 316 for rotation of the drum-like loading device 308.

0067In another embodiment, as shown in <figref idref="f0011">FIG. 13</figref>, the automated loading mechanism 300 of this embodiment may further comprise a single container loading port 312. In operation, a user or technician can place a single specimen container into the single container loading port 312 for quick, or immediate loading, for example of a STAT specimen container, Once placed in the single container loading port 312, the container will drop or fall via gravity onto a second transport mechanism 314, for example, a sloped ramp that slopes downward toward the drum-like loading device 308 for quick or immediate automated loading of the specimen container into the detection system 100.

0068As shown in <figref idref="f0011 f0012 f0013">FIGS. 13-16</figref>, the drum or drum-like loading device 308 rotates in a vertical plane (i.e., around or about a horizontal axis) to move the specimen container 500 from the entrance location 306 to a tumbler device 330. The tumbler device comprises an open slot at the top of a vertically orientated chute 332. Once moved to the tumbler device 330, the specimen containers are up-righted (i.e., the specimen containers are re-positioned from a horizontal container orientation to an up-right vertical container orientation) by a cam mechanism and vertically orientated chute 332. In operation, the cam mechanism (not shown) is capable of sensing the top and/or bottom of the specimen container, and pushing the specimen container 500 in a horizontal direction from the base of the specimen container, thereby allowing the base to drop or fall through the opening of a vertically orientated chute 332. Accordingly, the tumbler device 330 operates to allow the container 500 to drop (via gravity) bottom first through the vertical chute 332 and into a first locator well of a container locator device 400 (described elsewhere herein), thereby re-orientating the container 500 in a vertical, up-right orientation.

0069As shown for example in <figref idref="f0013">FIG. 16</figref>, the tumbler device 330 has two tapered ledges 334, one on each side of the drum, each being narrow at a front edge and thicker at a back edge. The ledges 334 are aligned so that the cap portion 502 of the container 500 will be caught or held by the ledge (i.e., the cap will move over the top side of the ledge such that the cap will rest on the top of ledge 334) as the drum rotates. The ledge 334 only holds the cap portion 502 of the container 500 in place briefly, as the bottom of the container falls through the vertical chute 332. Furthermore, the bottom or base 506 of the container will not be caught or held by the ledge. Instead, the tapered ledge 334 will act to push or slide the bottom or base 506 of the container 500 in a horizontal direction, from the bottom 506 of the container 500 towards the top or cap portion 502 of the container (see <figref idref="f0002">FIG. 4</figref>), as the drum or drum-like loading device 308 rotates. This action helps to ensure that the cap end 502 of the container is held by the top edge of the ledge 334, thereby allowing the bottom 506 of the container 500 to fall freely through the vertical chute 332 and into the container locator device 400. By having a ledge 334 on each side of the drum or drum-like loading device 308, container 500 orientation in the rotating drum in not essential. The container 500 will be up-right by the tumbler device 330 regardless of whether the cap end 502 of the container is on the right or left side (see, e.g., <figref idref="f0013">FIG. 16</figref>) of the drum-like loading device 308, as the corresponding ledges 334 will function to hold the cap or top 502 of the container as the bottom 506 falls through the vertical chute 332. In another embodiment, the vertical cute 332 may further comprise a narrower section 333 that helps direct the falling container 500 into the container locating device 400. In operation, as the drum or drum-like loading device 308 rotates over the open slot at the top of the vertically orientated chute 332, the cap or top portion 502 of the container 500 is held at the outer edge of the drum by one or more ledges 334 (see, e.g., <figref idref="f0013">FIG. 16</figref>). The ledges 334 hold the cap or top portion 502 of the container 500 in place while allowing the bottom 506 of the container to swing or fall freely out of the drum or drum-like loading device 308 and into the vertically orientated chute 332, thereby up-righting or vertically orientating the container 500 as it drops or falls via gravity through the vertically orientated chute 332 bottom first, as previously described.

Container Management Means or Locator Device

0070As shown, for example in <figref idref="f0011 f0012">FIGS. 13-15</figref><figref idref="f0014">18</figref>, and <figref idref="f0020 f0021">25A-25C</figref> the detection system 100 may further comprise a container management device or locator device 400. The container management device or locator device 400 can be used to manage, move or otherwise locate a container 500, once inside the housing 102 of the detection system 100, among various work-flow stations 404. In one embodiment, the container management device or locator device 400 can be used in combination with the automated loading mechanism 300 shown in <figref idref="f0011 f0012">FIGS. 13-15</figref>, as shown. In another embodiment, the container management device or locator device 400 can be used in combination with the automated loading mechanism 200 shown, for example, in <figref idref="f0014">FIG. 18</figref>. The container management device or locator device 400 in <figref idref="f0011 f0012">FIGS. 13-15</figref> and <figref idref="f0014">18</figref> is shown schematically and the parts not to scale.

0071The container management device or locator device 400 comprises a rotatable wheel-like device or rotatable disk that contains one or more locator wells 402, for example 1 to 10 locator wells, 1 to 8 locator wells, 1 to 5 locator wells, 1 to 4 locator wells, or 1 to 3 locator wells 402. In one embodiment, the locator device comprises opposable parallel plates or discs (see, e.g., <figref idref="f0020 f0021">FIGS. 25A-25C</figref>). Each individual locator well 402 is capable of holding a single specimen container 500. In operation, the locator device 400 rotates (either clock-wise or counter clock-wise) in a horizontal plane (and around or about a vertical axis) to move an individual container 500 to or among various work-flow stations 404 (i.e., from station-to-station). In one embodiment, the work-flow station 404 is operable to obtain one or more measurements or readings of the specimen container, thereby providing information about the container, such as, container lot number, container expiration date, patient information, sample type, fill level, etc. In another embodiment, the one or more work-flow stations 404 may comprise one or more container management stations, such as, a container pick-up station or a container transfer station. For example, the locator device 400 is capable of moving an individual specimen container 500 to one or more work-flow stations 404, such as: (1) a bar code reading station; (2) a container scanning stations; (3) a container imaging station; (4) a container weighing station; (4) container pick-up station; and/or (5) a container transfer station. In another embodiment, one or more of these measurements and/or readings can occur at the same station. For example, container weight, scanning, imaging and/or pick-up may occur at a single station location. In yet another embodiment, the detection system may contain a separate pick-up station. A container can be picked-up by a transfer mechanism (as described herein) at the pick-up location, and transferred to other locations (e.g., to a holding structure and/or agitation assembly) within the detection system 100. In still another embodiment, the detection system 100 may contain a transfer station for the transfer of a specimen container 500 to another instrument, e.g., a second automated detection instrument. In accordance with this embodiment, the transfer station may communicate with a system transfer device 440. For example, as shown, the system transfer device 440 may be a conveyor belt that allows the specimen container to be transferred to another location within the detection system 100, or in another embodiment, to another instrument (e.g., a second detection system (e.g., as shown in <figref idref="f0019">FIG. 24</figref>)). As shown in <figref idref="f0011 f0012">FIG. 14-15</figref>, the locator device 400 comprises: (1) an entrance station 412; (2) a bar code reading and/or scanning station 414; (3) a container weighing station 416; (4) a container pick-up station 418; and (5) a system transfer station 420 for transfer of the container to another instrument. The locator device may further comprise a rotatable turntable device 406, for rotating a container to facilitate bar code reading and/or container scanning, and/or a scale or weighing device 408, for weighing a container.

0072As previously described, in operation, the container management device or locator device 400, operates to move or otherwise locate a given specimen container 500 to a given work-flow station 404. In one embodiment, these work-flow stations 404 are included within the housing 102 of the detection system 100. For example, as shown in <figref idref="f0011 f0012">FIGS. 13-15</figref> and <figref idref="f0014">18</figref>, an automated loading mechanism can deposit or place a specimen container 500 into a locator well 402, as described elsewhere herein. The container management means or locating device 400 can then rotate to move or locate the specimen container among various work-flow stations within the system, such as for example, a bar code reading station, a container scanning stations, a container imaging station, a container weighing station, container pick-up station, and/or a container transfer station.

Transfer Means or Mechanism

0073As shown, for example in <figref idref="f0003 f0004 f0005 f0006 f0007 f0008">FIGS. 5-9B</figref> and <figref idref="f0014 f0017">17-21</figref>, the automated detection system 100 may further comprise an automated transfer means or mechanism operable for the transfer of a specimen container 500, and/or for container management, within the system. As already described, the entrance location or port 110 receives containers from, for example, a conveyor system 206 shown best in <figref idref="f0001 f0002">FIGS. 1-3</figref>. As the containers accumulate in the entrance location or port 110, the containers are moved within the detection system 100 whereby a transfer mechanism (e.g., a robotic transfer arm with a container gripping means) can pick-up, or otherwise receive, an individual specimen container 500 and transfer and place that container into a holding structure or rack 600 within the detection system 100, as described in more detail herein. As known in the art, the transfer mechanism may use a vision system (e.g., camera), pre-programmed dimensional coordinates and/or precision motion controlling to transfer a specimen container to, and load the specimen container into, the holding structure or rack 600.

0074As shown in <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0011 f0012">13-15</figref>, specimen containers 500 are loaded into, and/or transported within, the detection system 100 using an automated loading mechanism 200 (<figref idref="f0001 f0002">FIGS. 1-3</figref>) or 300 (<figref idref="f0011 f0012">FIGS. 13-15</figref>). As shown, the containers 500 are typically loaded into the detection system 100 in a vertical orientation (i.e., such that the top or cap portion 502 of the container 500 is up-right). In accordance with one embodiment, the containers 500 are placed or held in a plurality of holding structures or racks 600, and optionally agitated to enhance microorganism growth therein. As shown for example in <figref idref="f0003">FIGS. 5A and 5B</figref>, the receiving structures or wells 602 of the holding structures or racks 600 can be orientated in a horizontal axis. Accordingly, in accordance with this embodiment, an automated transfer mechanism (see, e.g., <figref idref="f0003">FIG. 5B</figref>, 650) must re-orientate the container 500, from a vertical orientation to a horizontal orientation, during the transfer of the container 500 from the automated loading mechanism 200, 300 to the receiving structures or wells 602.

0075In operation, the automated transfer mechanism (e.g., <figref idref="f0003">FIG. 5B</figref>, 650 or <figref idref="f0016">FIG. 20</figref>, 700) can operate to transfer or otherwise move, or relocate, a specimen container 500 within the interior chamber 620 of the detection system 100. For example, in one embodiment, the transfer mechanism can transfer a specimen container 500 from an entrance location or port 110 to one of a plurality of holding structures or racks 600. In another embodiment, the transfer mechanism can pick-up a specimen container 500 from a well 402 of the container locator device 400 and transfer the container to a holding structure or well 602 of the holding structure or rack 600. The transfer mechanism can operate to place the container 500 in one of a plurality of container receiving structures or wells 602 that are located in one of a plurality of holding structures or racks 600. In another embodiment, the transfer mechanism can operate to remove or unload "positive" and "negative" containers from the holding structures or racks 600. This automated unloading mechanism can operate to ensure that once a "positive" or "negative" reading has been made for each specimen container 500, the container 500 is removed from the container receiving structures or well 602, making room for another container to be loaded into the detection system 100, thereby increasing system through-put.

0076In one embodiment, the transfer mechanism can be a robotic transfer arm. In general, any type of robotic transfer arm known in the art can be used. For example, the robotic transfer arm can be a multi-axis robotic arm (for example, a 2-, 3-, 4-, 5-, or 6-axis robotic arm). The robotic transfer arm can operate to pick-up and transfer a specimen container 500 (e.g., a blood culture bottle) from an entrance location or port 110 to one of a plurality of container receiving structures or wells 602 located in one of a plurality of holding structures or racks 600 (optionally having an agitation assembly). Furthermore, to facilitate the necessary movements of the transfer mechanism or robotic transfer arm, the interior chamber 620 of the detection system 100, may includes one or more supports for the robotic transfer arm. For example, one or more vertical supports and/or one or more horizontal supports may be provided. The transfer mechanism or robotic transfer arm will slide up and down and across the supports as necessary to access any of the receiving structures or wells 602 of the holding structures or racks 600. As previously described, the robotic transfer arm can operate to change the orientation of a specimen container from a vertical orientation (i.e., up-right orientation such that the top 502 of the container 500 is up) to a horizontal orientation (i.e., such that the container 500 is laying on it's side), for example, to facilitate in container transfer from a loading station or location, and placement within a holding structure and/or agitation assembly.

0077In one embodiment, the robotic transfer arm is a 2-, or 3-axis robotic arm and will be capable of transferring the container 500 in one or more horizontal axes (for example, the x- and/or z-axes) and optionally a vertical axis (y-axis) to a specific location, such as the container receiving structures or wells 602 described herein. In accordance with this embodiment, a 2-axis robotic arm will allow movement in 2-axes (for example, the x-, and z-axes), whereas a 3-axis robotic arm will allow movement in 3-axes (for example, the x-, y-, and z-axes).

0078In another embodiment, the 2-, or 3-axis, robotic arm may further employ one or more rotational movements, capable of transferring or moving the specimen container 500 rotationally about one or more axes. This rotational movement may allow the robotic transfer arm to transfer a specimen container 500 from a vertical loading orientation to a horizontal orientation. For example, the robotic transfer arm may employ a rotational movement to move the specimen container rotationally about or around a horizontal axis. This type of robotic transfer arm would be defined as a 3-, or 4- axis robotic arm. For example, a robotic arm that allows movement in one horizontal axis (the x-axis), one vertical axis (e.g., the y-axis) and one rotational axis would be considered a 3-axis robotic arm. Whereas, a robotic arm that allows movement in two horizontal axes (e.g., the x-, and z-, axes), a vertical axis (the y-axis) and one rotational axis would be considered a 4-axis robotic arm. Similarly, a robotic arm that allows movement in a single horizontal axis (e.g., the x-axis), a vertical axis (the y-axis) and two rotational axes would also be considered a 4-axis robotic arm. In yet another embodiment, the robotic transfer arm 700 can be a 4-, 5-, or 6-axis robotic arm, thereby allowing movement in the x-, y-, and z-axes, as well as rotational movement about, or around, one-axis (i.e., a 5-axis robot), two axes (i.e., a 5-axis robotic arm), or all three horizontal (x-, and z-axes) and vertical axes (y-axes) (i.e., a 6-axis robotic arm).

0079In yet another embodiment, the robotic transfer arm may include one or more devices for obtaining measurements, scans and/or readings of a specimen container 500. For example, the robotic transfer arm may include one or more video cameras, sensors, scanners, and/or bar code readers. In accordance with this embodiment, the video camera, sensor, scanner and/or bar code reader may aid in container location, reading of container labels (e.g., bar codes), container scanning, remote field servicing of the system, and/or detecting for any possible container leaks within the system. In yet another design possibility, the robotic transfer arm may include a UV light source to aid in automated decontamination, if necessary.

0080One design possibility of the transfer mechanism is shown in <figref idref="f0004 f0005 f0006 f0007">FIGS. 6-8C</figref>. As shown in <figref idref="f0004">FIG. 6</figref>, the transfer mechanism comprises a robotic transfer arm 650, which comprises an upper horizontal support rail 652A, a lower horizontal support rail 652B, a single vertical support rail 654 and a robotic head 656 that will includes a gripping mechanism (not shown) for picking-up, gripping or otherwise holding a specimen container 500. The transfer mechanism shown in <figref idref="f0004 f0005 f0006 f0007">FIGS. 6-8C</figref> is shown schematically and the parts not to scale, for example, the horizontal supports 652A, 652B, vertical support and robotic head 656 shown are not to scale. As one of skill in the art would readily appreciate, the horizontal supports 652A, 652B, and vertical support can be increased or decreased in length as needed. As shown, the robotic head 656 is supported by the vertical support rail 654, which in turn is supported by, coupled to, and/or attached to the horizontal support rails 652A and 652B. Also as shown in <figref idref="f0004">FIG. 6</figref>, the transfer mechanism may comprise one or more mounting supports 696 that can be used to mount the transfer mechanism in the detection system.

0081In operation, the vertical support rail 654 can be moved along the horizontal support rails 652A and 652B, thereby moving the vertical support rail 654 and the robotic head 656 along a horizontal axis (e.g., the x-axis). In general, any known means in the art can be used to move the vertical support rail 654 along the horizontal support rails 652A and 652B. As shown in <figref idref="f0004">FIG. 6</figref>, the upper and lower support rails 652A and 652B, can comprise upper and lower threaded shafts (not shown) operable to drive upper and lower horizontal slide blocks 659A and 659B, respectively. Also, as shown in <figref idref="f0004">FIG. 6</figref>, the upper and lower shafts 652A and 652B can include hollow, elongate reinforcing sleeves 653A, 653B that extends the length of the upper and lower support rails 652A, 652B, and thereby surrounds the upper and lower threaded screws (see, e.g., <patcit id="pcit0058" dnum="US6467362B"><text>U.S. Patent No. 6,467,362</text></patcit>). The sleeves 653A, 653B will each further comprise a slot (see, e.g., 653C) in the sleeve 653A, 653B that extends the length of the upper and lower support rails 652A, 652B. Threaded tongues (not shown) are provided that extend through the slot (see, e.g., 653C) and have threads engageable with the threaded shafts (not shown) which are encased in the reinforcing sleeves 653A, 653B. As the threaded shafts (not shown) of the upper and lower support rails 652A, 652B are turned by a first motor 657, the threaded tongues (not shown) moves horizontal slide blocks 659A, 659B along the longitudinal length of the upper and lower support rails 652A, 652B, thereby moving the robotic head 656 along a horizontal axis (e.g., the x-axis) (again, see, e.g., <patcit id="pcit0059" dnum="US6467362B"><text>U.S. Patent No. 6,467,362</text></patcit>). A first motor 657 can operate to turn the upper and lower threaded shafts (not shown) and thereby drive upper and lower horizontal slide blocks 659A and 659B (each having internal threads that engage the threaded shafts, respectively) in a horizontal direction along the upper and lower threaded shafts. In one design possibility, the first motor 657 can be used to turn both the upper and lower threaded shafts by including a drive belt 660 and set of pulleys 662 to turn one of the threaded shafts (e.g., the lower threaded shaft) in parallel with the first threaded shaft, as the first threaded shaft is turned by the motor 657.

0082As shown in <figref idref="f0004">FIG. 6</figref>, the vertical support rail 654 may further comprise vertical threaded drive shaft (not shown) operable to drive a vertical slide block 655 and thereby move the robotic head 656 along a vertical axis (e.g., the y-axis). In operation, a second motor 658 can operate to turn a vertical threaded shaft (not shown) and thereby drive vertical slide block 655 in a vertical direction along the vertical threaded shaft. In another embodiment, as shown in <figref idref="f0004 f0005 f0006">FIGS. 6-7B</figref>, and as described hereinabove, the vertical threaded shaft may further comprise a hollow, elongate reinforcing sleeve 654A that extends the length of the vertical support rail 654, and thereby surrounds the vertical threaded shaft (not shown). The sleeve 654A will further comprise a slot 654B that extends the length of the vertical support rail 654. A threaded tongue (not shown) is provided that extends through the slot (not shown) and has threads engageable with the threaded shaft (not shown). As the threaded shaft (not shown) is turned by motor 658, the threaded tongue (not shown) moves a vertical slide block 655, thereby moving the robotic head 656 along a vertical axis (e.g., the y-axis) (again, see, e.g., <patcit id="pcit0060" dnum="US6467362B"><text>U.S. Patent No. 6,467,362</text></patcit>). The vertical slide block 655 may be directly attached to the robotic head 656, or as shown in <figref idref="f0004">FIG. 6</figref>, may be attached to a first rotational mechanism 664. The vertical slide block 655 has internal threads (not shown) that engage the threaded vertical shaft and operated to drive the vertical slide block, and thus the robotic head 656, in a vertical direction, along the threaded vertical shaft.

0083The transfer mechanism 650 may further comprise one or more rotational mechanisms operable to provide rotational movement about or around one or more axes. For example, as shown in <figref idref="f0004">FIG. 6</figref>, the robotic head may comprise a first rotational mechanism 664 for providing rotational movement about or around the y-axis and a second rotational mechanism 665 for providing rotational movement about or around the x-axis. The first rotational mechanism 664 comprises a first rotational plate 667 that can be attached to the robotic head 656. The first rotational mechanism 664 further comprises a first rotational motor 668, and a first pinion gear 670 and a first opposable ring gear 672, which operate to rotate the first rotational plate 667, and thus the robotic head 656, about a vertical axis (e.g., about the y-axis). In one embodiment, as is well known in the art, the first pinion gear 670 and first ring gear 672 may be provided with gripping teeth (not shown) or other gripping feature (not shown). The first rotational plate 667 may be directly attached to the robotic head 656, or as shown in <figref idref="f0004">FIG. 6</figref>, may be attached to a second rotational mechanism 665. Also as shown in <figref idref="f0004">FIG. 6</figref>, the first rotational plate 667 may comprise a bent plate to facilitate attachment to the second rotational mechanism 665. The second rotational mechanism 665, like the first rotational mechanism 664, comprises a second rotational plate 674. As shown in <figref idref="f0004">FIG. 6</figref>, the second rotational plate 674 is attached to the robotic head 656. The second rotational mechanism 665 further comprises a second rotational motor 678, a second pinion gear 680 and a second opposable ring gear 682, which operate to rotate the second rotational plate 674, and thus the robotic head 656, about a horizontal axis (e.g., the x-axis). In one embodiment, as is well known in the art, the second pinion gear 680 and second ring gear 682 may be provided with gripping teeth (not shown) or other gripping feature (not shown).

0084The robotic head 656, best shown in <figref idref="f0006">FIG. 7B</figref>, comprises a housing 684 enclosing a holding chamber 685 for holding a single specimen container 500 therein. The robotic head further comprises a gripping mechanism 686 and a drive mechanism 688 to move the gripping mechanism 686, and thereby a single specimen container 500, into and out of the housing 684 and holding chamber 685. The gripper mechanism 686, as shown in 7B, may comprise a spring clip 687 operable to snap over the lip of a specimen container 500. After transferring the specimen container 500 to a holding structure 600, as described elsewhere herein, the robotic head 656, and thus the gripping mechanism 686, can be raised or lowered relative to the holding structure 600 to release the specimen container 500. The drive mechanism 688 further comprises a motor 690, a guide rail 692, a threaded gripper shaft 694 and a gripper drive block 696, as shown in <figref idref="f0006">FIG. 7B</figref>. In operation, the motor 690 turns the threaded gripping shaft 694, thereby moving the gripping drive block 696, and thus the gripping mechanism 686 along the guide rail 692.

0085Another design possibility of the transfer mechanism is shown in <figref idref="f0008">FIGS. 9A-9B</figref>. As shown in <figref idref="f0008">FIGS. 9A-9B</figref> an automated transfer mechanism 820 is incorporated into the detection system 100 shown in <figref idref="f0008">FIGS. 9A-9B</figref> in order to grasp or pick-up a container 500 from the entrance location or port 110, and move or transfer a container 500 to a give receiving structure or well 802, of an upper or lower drum holding structure 800 (described elsewhere herein). The automated transfer mechanism 820 in this embodiment is also operable to move a negative container 500 to a waste location and subsequently dropping or otherwise depositing the container 500 into a waste bin 146, or operable to move a positive container to a positive container location (see, e.g., 130 in <figref idref="f0001">FIG. 1</figref>). To provide such movement, the transfer mechanism 820 includes a robotic head 824 which may include a gripping mechanism 826 for picking-up and holding a container 500, and a rotatable support rod 828 that extends across the interior chamber 850 of the system 100. As shown, the robotic head 824 is supported by, coupled to, and/or attached to the rotatable support rod 828. In general, the gripping mechanism can be any known gripping mechanism in the art. In one embodiment, the gripping mechanism may be the gripping mechanism and drive mechanism described hereinabove in conjunction with <figref idref="f0004 f0005 f0006 f0007">FIGS. 6-8C</figref>. The robotic head 824 is moveable to any position along the rotatable support rod 828. In operation, the support rod 828 can be rotated about its longitudinal axis, so as to orient the robotic head 824 towards either the upper or lower cylinder or drum holding structures 800A, 800B.

0086In one embodiment, the robotic head 820 is operable to pick-up a container 500 from the entrance location or port 110 and load the container 500 head-first (i.e., top portion 502 first) into the receiving structures or wells 802 of the drum holding structures 800A, 800B. This orientation exposes the bottom or base 506 of the container 500 to a detection unit 810 which can read the sensor 514 located at the bottom of the container 500 to detect microbial or microorganism growth within the container.

0087Yet another design possibility for the transfer mechanism is shown in <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21B</figref>. As shown in <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21B</figref>, the robotic transfer arm 700 will include one or more horizontal support structures 702, one or more vertical support structures 704, and a robotic head 710 that will include one or more features or devices (e.g., a gripping mechanism) to pick-up, grip and/or hold a specimen container 500. The robotic head 710 can be supported by, coupled to, and/or attached to one of the horizontal supports and/or vertical supports. For example, in one embodiment, as shown in <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21B</figref>, the robotic transfer arm 700 comprises a lower horizontal support structure 702B and a single vertical support structure 704. Although, not shown, as one of skill in the art would appreciate an upper horizontal support structure (not shown), or other similar means can be used to further support or guide the vertical support structure. In general, any known means in the art can be used to move the robotic head 710 up and down the vertical support rail 704 (as represented by arrow 726 (see <figref idref="f0014">FIG. 18</figref>)), and move the vertical support rail 704 back-and-forth along the horizontal support structure(s) 702B (as represented by arrow 736 (see <figref idref="f0016">FIG. 20</figref>)). For example, as shown in <figref idref="f0016">FIG. 20</figref>, the robotic transfer arm 700 may further comprises a vertical drive motor 720 and vertical drive belt 722 that will operate to transfer or move the robotic head 710 up and down (arrow 726) the vertical support rail 704 to transfer or move a container 500 along (i.e., up and down) a vertical axis (i.e., the y-axis). The vertical support structure 704 may further comprise a vertical guide rail 728 and a robotic head support block 708, as shown in <figref idref="f0016">FIG. 20</figref>. Accordingly, the vertical support structure 704, vertical guide rail 728, vertical drive motor 720 and vertical drive belt 722 allow the robotic transfer arm 700 to move or transfer the robotic head support block 708, and thus, the robotic head 710 and a specimen container 500 along the y-axis. Likewise, also as shown in <figref idref="f0016">FIG. 20</figref>, the robotic transfer arm 700 may further comprise a first horizontal drive motor 730, first horizontal drive belt 732 and horizontal guide rail 738 that will operate to move the vertical support structure 704 back-and-forth (i.e., from left-to-right and/or from right-to-left) along the horizontal guide rail 738, and thus, along a first horizontal axis (i.e., the x-axis) within the housing 102 of the detection system 100 (see arrow 736)). Accordingly, the horizontal support structure(s) 702B, first horizontal drive motor 730, first horizontal drive belt 732 and horizontal guide rail 738 allow the robotic transfer arm 700 to move or transfer a specimen container 500 along the x-axis. Applicants have found that by including a vertical support that is movable along a horizontal axis allows for an increased capacity within the detection system, as the robotic transfer arm is movable over an increased area within the instrument. Furthermore, Applicants believe a robotic transfer arm having a movable vertical support may provide a more reliable robot transfer arm.

0088As shown best in <figref idref="f0014 f0015 f0016 f0017">FIG. 17-21B</figref>, the automated transfer mechanism or robotic transfer arm 700 may further comprise a linear or horizontal slide 706 and pivot plate 750. As shown, for example in <figref idref="f0014 f0015 f0016">FIGS. 17- 20</figref>, the linear or horizontal slide 706 supports the robotic head 710 and gripper mechanism 712. The linear or horizontal slide 706 and robotic head 710 may be supported by, coupled to, and/or attached to, a robotic head support block 708 and vertical guide rail 728 (previously described). In accordance with this embodiment, the linear or horizontal slide 706 can be moved up and down (see <figref idref="f0014">FIG. 18</figref>, arrow 726) along a vertical axis (i.e., the y-axis), via the a robotic head support block 708 and vertical guide rail 728, to move or transfer the robotic head 710 and/or specimen container 500 up and down within the housing 102 of the detection system 100 (i.e., along the vertical axis (y-axis)). As shown in <figref idref="f0017">FIGS. 21A-21B</figref>, the linear or horizontal slide 706 may further comprises a pivot plate 750 comprising a pivot plate guide rail 752, a pivot slot 754 and pivot slot cam follower 756 operable to allow the robotic head 710 to slide or moved along the linear or horizontal slide 706, from front-to-back or from back-to-front (see <figref idref="f0014">FIG. 18</figref>, arrow 746), to transfer or move a container 500 along a second horizontal axis (i.e., the z-axis). In accordance with this embodiment, a second horizontal drive motor or horizontal slide motor 760 and a slide belt (not shown) can be used to move the robotic head 710 along the z-axis. Accordingly, the linear or horizontal slide 706, the horizontal slide motor and slide belt, allows the robotic head 710 to move or transfer a specimen container 500 along the z-axis. As known in the art, one or more sensors (see, e.g., 764 in <figref idref="f0017">FIG. 21A</figref>) can be used to indicate the position of the robotic head 710 on the linear or horizontal slide 706.

0089As shown in <figref idref="f0017">FIGS. 21A-21B</figref>, as the robotic head 710 is moved along the linear or horizontal slide 706, pivot plate 750, and pivot plate guide rail 752the pivot slot 754 and pivot slot cam follower 756 rotate the pivot carriage 758 about or around a horizontal axis (i.e., the z-axis), and thus, rotates the robotic head 710 from a horizontal orientation (as shown in <figref idref="f0017">FIG. 21A</figref>) to a vertical orientation (as shown in <figref idref="f0017">FIG. 21B</figref>), or vice versa. As described elsewhere herein, the transfer of a container 500 from a vertical entry orientation to a horizontal orientation may be necessary for depositing or placing the container in a horizontally orientated receiving structure or well 602 of the holding structure or rack 600. Accordingly, the pivot plate 750, pivot slot 754 and pivot carriage 758 allow the robotic head 710 to re-orientate a specimen container 500 from a vertical orientation, as loaded (see, e.g., <figref idref="f0014">FIG. 18</figref>) to a horizontal orientation (as seen, e.g., in <figref idref="f0017">FIG. 21A</figref>), thereby allowing a specimen container 500 to be transferred from an automated loading mechanism (see, e.g., 200 in <figref idref="f0014">FIG. 18</figref>) to a well in a holding structure (e.g., 602 and 600 in <figref idref="f0014">FIG. 18</figref>). As shown in <figref idref="f0016">FIG. 20</figref> the automated transfer mechanism may also comprise one or more cable management chains 782, for cable management within the detection system 100, and a circuit board 784 for controlling the robotic transfer mechanism. In yet another embodiment, the robotic transfer arm 700 may further comprise a break mechanism 786 that can operate to break the vertical drive belt 722, thereby preventing if from falling to the bottom of the instrument (e.g., due to a power outage).

0090The robotic transfer arm 700 may further comprise a gripping mechanism 712 to pick-up, grip or otherwise hold a specimen container 500. As shown, for example in <figref idref="f0017">FIGS. 21A and 21B</figref>, the gripping mechanism may comprise two or more gripping fingers 714. Furthermore, the gripping mechanism 712 may further comprise a linear actuator 716 and a linear actuator motor 718 which can operate to move the linear actuator to open and close the gripper fingers 714. In operation, as is well known in the art, the actuator motor 718 can be used to move the linear actuator 716 of the gripper mechanism 712 thereby moving the gripper fingers 714. For example, the linear actuator can be moved in a first direction (e.g., toward the motor) to close the fingers and grip the container 500. Conversely, the linear actuator can be moved in a second direction (e.g., away from the motor) to open the gripper fingers and release the container 500. Applicants have unexpectedly found that the use of one or more gripping fingers 714 allows the gripping mechanism 712 to accommodate (i.e., pick-up and/or hold) a large variety of different specimen containers 500. Moreover, Applicants have found that by using gripper fingers 714 that extend from about one-quarter (1/4) to about one-half (1/2) the length of the specimen container 500, the gripper fingers will accommodate (i.e., pick-up and/or hold) a number of well known containers (e.g., long neck blood culture bottles) in the art.

0091As described further herein, the automated transfer mechanism or robotic transfer arm 700 can be placed under the control of a system controller (not shown) and programmed for specimen container 500 management (e.g., pick-up, transfer, placement and/or container removal) within the detection system 100.

0092In yet another embodiment, as discussed further hereinbelow, the transfer mechanism 700 can be used for automated unloading of "positive" and "negative" specimen containers 500.

Holding Means or Structure with Optional Agitation Means

0093The holding means or structure of the detection system 100 can take a variety of physical configurations for handling a plurality of individual specimen containers 500 so that a large number of containers (e.g., 200 or 400 containers, depending on the specific holding structures used) can be processed simultaneously. The holding means or structure can be used for storage, agitation and/or incubation of the specimen containers 500. One possible configuration is shown in <figref idref="f0003">FIGS. 5A-5B</figref>, and another possible configuration is shown in <figref idref="f0008">FIGS. 9A and 9B</figref>. These configurations are provided by way of illustration and not limitation. As one of skill in the art will appreciate, other designs are possible and contemplated.

0094As shown in <figref idref="f0003">FIGS. 5A-5B</figref> and <figref idref="f0014 f0015 f0016">FIGS. 17-20</figref>, one possible configuration uses a plurality of vertically stacked container holding structures or racks 600 each having a multitude of specimen container receiving structures or wells 602 each for holding individual specimen containers 500. In accordance with this embodiment, two or more vertically stacked holding structures or racks 600 can be used. For example, from about 2 to about 40, from about 2 to about 30, from about 2 to about 20, or from about 2 to about 15 vertically stacked holding structures or racks can be used. Referring to <figref idref="f0003">FIGS. 5A- 5B</figref> and <figref idref="f0014 f0016">17-20</figref>, in this configuration the detection system 100 includes a climate controlled interior chamber 620, comprising an upper interior chamber 622 and a lower interior chamber 624, and a plurality of vertically disposed holding structures or racks 600 (e.g., as shown in <figref idref="f0003">FIGS. 5A-5B</figref>, <figref idref="f0012">15</figref> vertically stacked holding structures or racks 600) each having a plurality of individual container receiving structures or wells 602 therein. Each individual holding structure or rack 600 can comprise two or more container receiving structures of wells 602. For example, each holding structure or rack 600 can comprise from about 2 to about 40, from about 2 to about 30, or from about 2 to about 20 receiving structures of wells 602 therein. In one embodiment, as shown in <figref idref="f0003">FIGS. 5A-5B</figref>, the receiving structures or wells 602 can comprise 2 rows of vertically aligned receiving structures or wells 602. In an alternative embodiment, the receiving structures or wells 602 can be staggered, thus reducing the vertical height of each individual holding structure or rack 600 (see, e.g., <figref idref="f0016">FIG. 20</figref>), and thereby allowing for an increased number of total holding structures or racks 600 in a given vertical distance within the incubation chamber 620. As shown, for example in <figref idref="f0003">FIGS. 5A-5B</figref>, the detection system comprises 15 holding structures or racks 600 each comprising two rows of 10 individual container receiving structures or wells 602, thereby giving the system exemplified in <figref idref="f0003">FIGS. 5A-5B</figref> a total container capacity of 300. In another possible design configuration, the detection apparatus may comprise 16 vertically stacked racks, each containing 25 receiving structures or wells, thereby giving a total container capacity of 400.

0095Furthermore, each of the individual container receiving structures or wells 602 has a specific X and Y coordinate position or address, where X is the horizontal location and Y is the vertical location of each container receiving structure or well 602. The individual wells 602 are accessed by a transfer mechanism, such as a robotic transfer arm, for example, as described hereinabove in conjunction with <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21</figref>). As shown in <figref idref="f0014 f0015 f0016 f0017">FIGS. 17-21</figref>, the automated transfer mechanism 700 can operate to move the robotic head 710, and thus, the specimen container 500, to a specific of the X, Y positions in the rack 600 and deposit the container 500 therein. In operation, the automated transfer mechanism 700 can operate to pick-up a specimen container 500 at the entrance station 110 or the pick-up station 418 of the container locator device 400, move a container 500 determined positive for microbial growth therein to a positive container or exit location 130, and/or to move a container 500 determined negative for microbial growth to a negative container location or waste bin 146.

0096In one embodiment, the entire holding structure or rack 600 can be agitated by an agitation assembly (not shown) to promote or enhance microorganism growth. The agitation assembly can be any known means or mechanism for providing agitation (e.g., a back-and-forth rocking motion) to the holding structures or racks 600. In another embodiment, the holding structures or racks 600 can be rocked in a back-and-forth motion for agitation of the fluid contained within the containers. For example, the holding structures or racks 600 can be rocked back-and-forth from a substantially vertical position to a substantially horizontal position, and repeated to provide agitation of the fluid contained within the container. In yet another embodiment, the holding structures or racks 600 can be rocked back-and-forth from a substantially horizontal position to a vertical position 10 degrees, 15 degrees, 30 degrees, 45 degrees or 60 degrees from horizontal, and repeated to provide fluid agitation within the containers. In one embodiment, a racking motion from a substantially horizontal position to a vertical position from about 10 degrees to about 15 degrees from horizontal may be preferred. In still another embodiment, the holding structure or racks 600 can be rocked back-and-forth in a linear or horizontal motion to provide agitation of the fluid contained within the containers. In this embodiment, the holding structures or racks 600 and receiving structures or wells 602 can be orientated in a vertical, or alternatively in a horizontal position. Applicants have found that a linear or horizontal agitation motion, with the holding structures 600, and thus the receiving structures or wells 602 and specimen containers 500, in a horizontal orientation can provide substantial agitation with a relatively minimum energy input. Accordingly, in some embodiments, a horizontal holding structure or rack 600 orientation and a linear or horizontal agitation motion, may be preferred. Other means of agitating the holding structures or racks 600, and thus, the fluid within specimen containers 500 are contemplated and would be well understood by one skilled in the art. These back-and-forth, liner and/or horizontal rocking motions can be repeated as desired (e.g., at various cycles and/or speeds) to provide agitation of the fluid within the containers.

0097One possible design for the agitation assembly is shown in conjunction with <figref idref="f0022">FIG. 26</figref>. As shown in <figref idref="f0022">FIG. 26</figref>, the agitation assembly 626 comprises one or more holding structures 600 comprising a plurality of holding wells 602 for holding a plurality of specimen containers 500. The agitation assembly 626 further comprises an agitation motor 628, an eccentric coupling 630, a first rotation arm 632, a second rotation arm or linkage arm 634 and a rack agitation bearing assembly 636. In operation, the agitation motor 628 rotates the eccentric coupling 630 in an off-center motion thereby moving a first rotation arm 632 in an off-center circular or off-center rotational motion. The off-center rotational movement of the first rotation arm 632 moves a second rotation arm or linkage arm 634 in a linear motion (as represented by arrow 635). The linear motion of the second rotation arm or linkage arm 634 rocks the rack agitation bearing assembly 636 in a back-and-forth rocking motion, thereby providing a back-and-forth rocking agitation motion (represented by arrow 638 of <figref idref="f0022">FIG. 26</figref>) to the holding structures 600.

0098In another possible design configuration, as shown in <figref idref="f0008">FIGS. 9A and 9B</figref>, the detection system 100 may includes upper and lower holding structures 800A and 800B in the form of cylindrical or drum structures containing a multitude of individual specimen container receiving structures or wells 802 for receiving one of the containers 500. In this embodiment, the cylindrical or drum holding structures 800A, 800B each rotate about a horizontal axis to thereby provide agitation of the containers 500. In accordance with this embodiment, each drum holding structure can comprise from about 8 to about 20 rows (e.g., from about 8 to about 20, from about 8 to about 18, or from about 10 to 1 about 6 rows), each comprising from about 8 to about 20 container receiving structures or wells 802 (e.g., from about 8 to about 20, from about 8 to about 18, or from about 10 to about 16 receiving structures of wells 802).

0099As described hereinabove, an automated transfer mechanism 820 is incorporated into the detection system 100 of <figref idref="f0008">FIGS. 9A-9B</figref> in order to grasp or pick-up a container 500 from the entrance location or port 110, and move or transfer the container 500 to a give receiving structure or well 802, of either the upper or lower drum holding structure 800, and deposit the container 500 therein. The automated transfer mechanism 820 in this embodiment can further operate to move a negative container 500 to a waste bin 146, or can operate to move a positive container to the positive container location 130, shown for example, in <figref idref="f0001">FIG. 1</figref>. Also, as previously described, the robotic head 820 of <figref idref="f0008">FIGS. 9A-9B</figref> can pick-up a container 500 from the entrance location or port 110 and load the container 500 head-first (i.e., top portion 502 first) into the receiving structures or wells 802 of the drum holding structures 800A, 800B. This orientation exposes the bottom or base 806 of the container 500 to a detection unit 810 which can read the sensor 514 located at the bottom of the container 500 to detect microbial or microorganism growth within the container.

0100As described elsewhere herein, positive and negative containers can be retrieved by the robotic transfer arm and transferred to other locations within the system. For example, a container determined "positive" for microbial growth can be retrieved and transferred via the transfer mechanism to a positive container location or port where a user or technician can easily remove the positive container. Similarly, a container determined "negative" for microbial growth after a designated time has passed can be transferred via the transfer mechanism to a negative container location or waste bin for disposal.

0101In one embodiment, the holding structure or rack 600 may further comprise a retention feature operable to hold or otherwise retain a specimen container 500 in the receiving structures or wells 602 of the rack 600. As shown in <figref idref="f0023 f0024">FIGS. 27A-27C</figref>, the retention device 860 comprises a canted coiled spring 864 and a v-shaped holding plate 862. In accordance with this embodiment, by using a canted coiled spring 868, multiple points of the coiled spring contact the container surface to retain the bottle in the rack well 602. The coils of the canted spring 864 are set at an angle relative to the vertical axis of the container, as shown in <figref idref="f0024">FIG. 27C</figref>, which shows exaggerated coils to demonstrate the coil angle relative to the vertical axis of the container. However, typically the canted spring 864 is a tightly coiled spring. For example the canted spring 864 can be at an angel of about 10 degrees to about 50 degrees, from about 20 degrees to about 40 degrees, or about 30 degree (as shown in <figref idref="f0024">FIG. 27C</figref>), relative to the vertical axis of the container. The v-shaped holding plate 862 is capable of holding and/or retaining said canted coiled spring 864 relative to, or adjacent to the holding structure 600. As shown, the holding plate 862 comprising a v-grooved retainer plate for retaining the canted coiled spring 864. The v-groove retainer plate 864 prevents any movement of the spring 864 relative to the container 500 and/or holding structure 600. Accordingly, unlike a traditional extension spring, which would typically contact a container at a single point (e.g., a flat leaf spring), the canted coiled spring 864 can be rigidly retained by the v-shaped groove 862 while the coils will deflect under pressure. The use of a canted spring 864 allows the load to be spread out, thereby providing uniform deflection.

0102As shown, e.g., in <figref idref="f0023">FIGS. 27A</figref> and <figref idref="f0024">27C</figref>, the receiving structures or wells 602 further comprise one or more ribs 868. In one design possibility, as shown in <figref idref="f0024">FIG. 27C</figref>, two of these ribs 868 are located directly opposite the canted coiled spring 864. These two ribs 868 form a groove that functions to self-center the container 500 within the well 602 along a vertical centerline (not shown). In operation, the canted coiled spring 864 applies force to the container 500 wall, thereby holding or retaining the container securely within the well 602 of the rack 600. In one embodiment, the two ribs 868 located opposite the coiled spring 864 can be spaced from 30 degrees to about 90 degrees apart, or from about 40 degrees to about 80 degrees apart. In another embodiment, the two ribs 868 located opposite the canted coiled spring 864 can be spaced about 60 degrees apart. Also, as shown in <figref idref="f0024">FIG. 27C</figref>, the holding structure may comprise a first row and a second row of parallel holding wells, the parallel holding rows being capable of, or operable for, holding a plurality of containers therein, and wherein the holding structure further comprises a first canted coiled spring located adjacent to the first row and a second canted coiled spring adjacent to the second row, wherein each of the canted coiled spring are operable for retaining the plurality of containers in said holding wells.

0103Using the canted coiled spring 864, v-groove retainer 862 and two ribs 868 located opposite said canted coiled spring 864, the bottle will always be held securely in the same location within the well 602, regardless of any sideloads applied through agitation or during rack cell insertion. The canted coiled spring 864 and v-groove retainer 862 also allow for the use of a shorter depth holding well 602 and holding structure 600. The shorter holding well 602 depth will allow for multiple container designs and container lengths to be retained equally well, as well as allow more of the container surface to be expose to the incubation air flow within the system.

0104As one of skill in the art would appreciate other possible designs or configurations for the holding structure or structures 600 and/or agitation assembly are possible and are considered part of present invention.

Detection Unit

0105The various possible design configurations of the detection system 100 for detecting microbial agent growth within a specimen container, as shown in <figref idref="f0001 f0002 f0003 f0004">FIGS. 1-6</figref>, <figref idref="f0008">9A-9B</figref>, <figref idref="f0017">21A-21B</figref> and <figref idref="f0023 f0024">27</figref>, can include the use of similar detection means. In general, any known means in the art for monitoring and/or interrogating a specimen container for the detection of microbial growth can be used. As previously mentioned, the specimen containers 500 can be monitored continuously, or periodically, during incubation of the containers 500 in the detection system 100, for the positive detection of microbial growth. For example, in one embodiment, a detection unit (e.g., 810 of <figref idref="f0008">Figure 9B</figref>) reads the sensor 514 incorporated into the bottom or base 506 of the container 500. A variety of sensor technologies are available in the art and may suitable. In one possible embodiment, the detection unit takes colorimetric measurements as described in the <patcit id="pcit0061" dnum="US4945060A"><text>U.S. patents 4,945,060</text></patcit>; <patcit id="pcit0062" dnum="US5094955A"><text>5,094,955</text></patcit>; <patcit id="pcit0063" dnum="US5162229A"><text>5,162,229</text></patcit>; <patcit id="pcit0064" dnum="US5164796A"><text>5,164,796</text></patcit>; <patcit id="pcit0065" dnum="US5217876A"><text>5,217,876</text></patcit>; <patcit id="pcit0066" dnum="US5795773A"><text>5,795,773</text></patcit>; and <patcit id="pcit0067" dnum="US5856175A"><text>5,856,175</text></patcit>, which are incorporated herein. A positive container is indicated depending upon these colorimetric measurements, as explained in these patents. Alternatively, detection could also be accomplished using intrinsic fluorescence of the microorganism, and/or detection of changes in the optical scattering of the media (as disclosed, for example, in co-pending <patcit id="pcit0068" dnum="US46060709A" dnum-type="L"><text>U.S. patent application serial no. 12/460,607, filed July 22, 2009</text></patcit> and entitled, "Method and System for Detection and/or Characterization of a Biological Particle in a Sample."). In yet another embodiment, detection can be accomplished by detecting or sensing the generation of volatile organic compounds in the media or headspace of the container. Various design configurations for the detection unit can be employed within the detection system. For example, one detection unit could be provided for an entire rack or tray, or multiple detection units could be provided per rack or per tray.

Climate-Controlled Interior Chamber

0106As previously described, the detection system 100 may include a climate-controlled interior chamber (or incubation chamber), for maintaining an environment to promote and/or enhance growth of any microbial agents (e.g., microorganisms) that may be present in the specimen container 500. In accordance with this embodiment, the detection system 100 may include a heating element or hot air blower to maintain a constant temperature within said interior chamber. For example, in one embodiment, the heating element or hot air blower will provide and/or maintain the interior chamber at an elevated temperature (i.e., a temperature elevated above room temperature). In another embodiment, the detection system 100 may include a cooling element or cold air blower (not shown) to maintain the interior chamber at a temperature below room temperature. In accordance with this embodiment, the interior chamber or incubation chamber will be at a temperature of from about 18° to about 45° C. In one embodiment, the interior chamber can be an incubation chamber and can be maintained at a temperature from about 35° C. to about 40° C., and preferably at about 37° C. In another embodiment, the interior chamber may be maintained at a temperature below room temperature, for example from about 18° C. to about 25° C., and preferably at about 22.5° C. A particular advantage provided is the ability to provide a more constant temperature environment for promoting and/or enhancing microbial growth within a specimen container 500. The detection system 100 accomplishes this by providing a closed system, in which automated loading, transfer and unloading of specimen containers 500 occurs without the need to open any access panels that would otherwise disrupt the incubation temperature (from about 30° to 40° C., preferably from about 37° C.) of the interior chamber 620.

0107In general, the detection system 100 can employ any known means in the art for maintaining a climate-controlled chamber for promoting or enhancing microbial growth. For example, to maintain a temperature controlled chamber, one or more heating element or hot air blower, baffles and/or other suitable equipment known in the art, can be used to maintain the interior of the detection system 100 at the appropriate temperature for incubating the container and promoting and/or enhancing microbial growth.

0108Typically, one or more heating element or hot air blower under control of the system controller are used to maintain a constant temperature within the interior chamber 620 of the detection system 100. As known in the art, the heating element or hot air blower can be employed in a number of locations within the interior chamber. For example, as shown in <figref idref="f0003">FIGS. 5</figref> and <figref idref="f0004">6</figref> one or more heating elements or hot air blowers 740 can be positioned at the base of the holding structures or racks 600, for directing warm air across the plurality of holding structures or racks 600. A similar arrangement can be provided in the embodiments of <figref idref="f0008">FIGS. 9A and 9B</figref> (see, e.g., 840). The details of the incubation features are not particularly pertinent, and are known in the art, therefore a detailed description is omitted.

Controller and User Interface

0109The detection system 100 will include a system controller (e.g., a computer control system) (not shown) and firmware for controlling the various operations and mechanisms of the system. Typically, the system controller and firmware for controlling the operation of the various mechanisms of the system can be any known conventional controller and firmware known to those of skill in the art. In one embodiment, the controller and firmware will performs all operations necessary for controlling the various mechanisms of the system, including: automated loading, automated transfer, automated detection and/or automated unloading of specimen containers within the system. The controller and firmware will also provide for identification and tracking of specimen containers within the system.

0110The detection system 100 may also include a user interface 150 and associated computer control system for operating the loading mechanism, transfer mechanism, racks, agitation equipment, incubation apparatus, and receiving measurements from the detection units. These details are not particularly important and can vary widely. When a container is detected as being positive, the user can be alerted via the user interface 150 and/or by the positive indicator 190 (see, e.g., <figref idref="f0001">Figure 1</figref>) becoming active (i.e., an indicator light turning on). As described herein, upon a positive determination, the positive container can be automatically moved to a positive container location 130, shown for example in <figref idref="f0001 f0002">FIGS. 1-3</figref>, <figref idref="f0009">10-11</figref> and <figref idref="f0018 f0019">22-24</figref> for retrieval by a user.

0111The user interface 150 may also provide an operator or laboratory technician with status information regarding containers loaded into the detection system. The user interface may includes one or more of the following features: (1) Touch screen display; (2) Keyboard on touch screen; (3) System status; (4) Positives alert; (5) Communications to other systems (DMS, LIS, BCES &amp; other detection or identification Instruments); (6) Container or bottle status; (7) Retrieve containers or bottles; (8) Visual and audible Positive Indicator; (9) USB access (back ups and external system access); and (10) Remote Notification of Positives, System Status and Error Messages. In another embodiment, as shown in <figref idref="f0018">FIGS. 22-23</figref>, a status update screen 152 can also be used. The status update screen 152 can be used to provide status information regarding containers loaded into the detection system, such as, for example: (1) container location within the system; (2) container information, such as, patient information, sample type, input time, etc.; (3) positive or negative container alerts; (4) interior chamber temperature; and (5) an indication that the waste bin is full and needs to be emptied.

0112The particular appearance or layout of the detection system and user interface 150, and/or status update screen 152, is not particularly important, and can vary widely. <figref idref="f0001 f0002">Figures 1-2</figref> show one possible embodiment, which is provided by way of illustration and not limitation. <figref idref="f0018">Figures 22-23</figref> show another possible embodiment, which is also provided by way of illustration and not limitation.

Automated Unloading

0113The detection system 100 may also provide for automated transfer or automated unloading of "positive" and "negative" specimen containers 500. As previously described, containers in which a microbial agent is present are termed "positive" containers, and containers in which no microorganism growth is detected after a given time period are termed "negative" containers.

0114Once a container is detected as positive, the detection system will notify the operator of the results through an indicator (e.g. visual prompt 190) and/or through notification at the user interface 150. Referring now to <figref idref="f0001 f0002">FIGS. 1-3</figref> and <figref idref="f0003">5A-5B</figref>, positive bottles can be automatically retrieved via the transfer mechanism 650 (e.g., robotic transfer arm) and placed in a designated positive container area, such as a positive container location or exit port 130. This positive container area will be located outside of the instrument housing for easy user access to the container. In a one embodiment, the container will be placed in a vertical orientation within the positive container area. In one design configuration, the automated unloading of a positive container will employ the use of a transfer tube (not shown) through which a positive container (e.g., a positive blood culture bottle) can travel to be relocated to a designated positive container location or exit port 130. In accordance with this design feature, the transfer mechanism (e.g., the robotic transfer arm) will drop or otherwise deposit the positive specimen container into a top end of the transfer tube, and the container will travel through the transfer tube via gravity to the positive container location or port 130. In one embodiment, the transfer tube (not shown) can hold one or more "positive" specimen containers therein. For example, the transfer tube (not shown) can hold from about 1 to about 5, from about 1 to about 4, or from about 1 to about 3 "positive" specimen containers. In another embodiment, for example as shown in <figref idref="f0018 f0019">FIGS. 22-24</figref>, the positive container location or exit port 130 may comprise holding wells for one or more "positive" specimen containers, for example, two holding wells for separately holding two "positive" specimen containers.

0115In another embodiment of the detection system 100, negative containers can be transferred by the transfer mechanism 700 (e.g., robotic transfer arm) from the holding structure or rack 600 to a negative container location, such as a waste bin 146. Typically, the containers will be released from the robotic transfer arm and dropped into the waste bin 146, however other embodiments are contemplated and should be apparent to one of skill in the art. In one design configuration, the automated unloading of a negative container will employ the use of a transfer tube (not shown) through which a negative container (e.g., a negative blood culture bottle) can travel to be relocated to a designated negative container location, such as a waste bin 146. In accordance with this design feature, the transfer mechanism (e.g., the robotic transfer arm) will drop or otherwise deposit the negative specimen container into a top end of the transfer tube, and the container will travel through the transfer tube via gravity to the negative container location or waste bin 146. The detection system 100 may also include an access door 140 or drawer 142 that opens to provide user access to the negative container location, such as a negative container waste bin 146. In another embodiment, the waste bin 146 may include a scale to weigh the waste bin 146. As one of skill in the art would appreciate, by monitoring the weight of the waste bin 146, the system controller (not shown) can determine how full the waste bin 146 is, and can optionally provide a signal (e.g., at the user interface 150) indicating to the user or technician that the waste bin 146 is full, and thus, needs to be emptied.

Automated Laboratory System

0116As noted above, the detection system 100 of this disclosure can take on a variety of different possible configurations. One such configuration, particularly suited for high volume implementations, is shown in <figref idref="f0019">FIG. 24</figref>. As shown in <figref idref="f0019">FIG. 24</figref>, the detection system 100A can be employed in an automated microbiology laboratory system. For example, the detection instrument 100 can be included as one component of an automated laboratory system. In this embodiment, the detection instrument 100A can be linked or "daisy chained" to one or more additional other analytical modules or instruments for additional testing. For example, as shown in <figref idref="f0019">FIG. 24</figref>, the detection instrument 100A can be linked or "daisy chained" to a second detection unit 100B. However, in other embodiments, the detection instrument can be "daisy chained" or otherwise linked to one or more other systems or modules. These other systems or modules can include, for example, identification testing systems such as the VITEK or VIDAS systems of the assignee bioMérieux, Inc., a gram stainer, a mass spectrometry unit, a molecular diagnostic test system, a plate streaker, an automated characterization and/or identification system (as disclosed in co-pending <patcit id="pcit0069" dnum="US60216339B"><text>US patent application no. 60/216,339</text></patcit>, entitled "System for Rapid Non-invasive Detection of a Microbial Agent in a Biological Sample and Identifying and/or Characterizing the Microbial Agent", which was filed May 15, 2009) or other analytical systems.

0117Referring now to <figref idref="f0019">FIG. 24</figref>, an automated laboratory system can comprise a first detection system 100A, and a second detection system 100B. In other embodiments, the automated laboratory system can comprise a first detection system 100A, a second detection system 100B, and an automated characterization/identification system (not shown). In accordance with this embodiment, positive containers can be moved or transferred from the first detection system 100A to the second detection system 100B, and/or subsequently to the automated characterization/identification system, using a system transfer device 440. In other embodiments, the first detection system 100A can be coupled to a microorganism identification module or an antimicrobial susceptibility module (not shown).

0118As shown in <figref idref="f0019 f0020 f0021">FIGS. 24-25C</figref> two detection systems 100A and 100B are "daisy chained" together by system transfer device 440. This allows containers to be transferred from one detection system to another in case the first one is full. A similar system transfer device may also be provided for subsequent transfer of the specimen container 500 from the second detection system 100B to a subsequent systems or modules, as described elsewhere herein. The system transfer mechanism 441 comprises a first container locator device 400A having a transfer station 420 for transferring a container to a second or downstream instrument. The system transfer mechanism 441 also comprises a pusher arm 444 operable controlled by a pusher motor 442 and a transfer bridge 446, as shown in <figref idref="f0019 f0020 f0021">FIG. 24-25C</figref>. As shown, the pusher arm 444 may comprise a pair of parallel arms. In operation, when a container to be transferred is moved by the transfer station 420 of the first container locator device 400A, a pusher arm 444 is activated to push or move the container from the transfer station 420, across a transfer bridge 446, to the down-stream detection system 100B. As shown, the pusher arm 444 is connected to a pusher motor 442 via a pusher arm support structure 445. <figref idref="f0020 f0021">Figures 25A-C</figref> show the transfer of a container from the transfer station 420 of the first detection system 100A to the conveyor belt 206B (see <figref idref="f0019">FIG. 24</figref>) of the second detection system 100B, and show the container in: (1) a first position (<figref idref="f0020">FIG. 25A</figref>) as the pusher arm 444 begins to push the container across the transfer bridge 446; (2) a second or intermediate position (<figref idref="f0020">FIG. 25B</figref>) as the container crosses the transfer bridge 446; and (3) a final position (<figref idref="f0021">FIG. 25C</figref>) as the container arrives at the conveyor belt (not shown) of the down-stream detection system 100B. Furthermore, as shown in <figref idref="f0020 f0021">FIGS. 25A-25C</figref>, the system transfer device 440 may further comprise one or more locator device guide rails 450 attached to a base plate of the locator device 404 via one or more guide rail supports 452, and/or bridge guide rails 446, 448, to guide the container from the first locator device 400A and across the bridge 446 to the conveyor belt 206B (see <figref idref="f0019">FIG. 24</figref>) of the automated loading mechanism 200B of the down-stream detection system 100B. As would be well known in the art, the transfer of a container from the first detection system 100A to the second or down-stream detection system 100B, via the operation of the first container locator device 400A and pusher arm 444, can be controlled by the system controller. Typically, as shown in <figref idref="f0019">FIG. 24</figref>, only the first detection system 100A needs to include a user interface 150. The first 100A and second 100B detection systems may further comprise status screens 152A, 152B, positive container ports 130A, 130B, lower access panels 140A, 140B, automated loading mechanisms 200A, 200B and conveyor belts 206A, 206B.

0119Further, in accordance with this embodiment, positive containers can be transferred to other systems in the automated laboratory system. For example, as shown in <figref idref="f0019">FIG. 24</figref>, a container 500 determined positive in the first detection system 100A can be transferred to the second detection system 100B and/or subsequently to an automated characterization/identification system 104 described in <figref idref="f0028">Figures 31</figref>, <figref idref="f0042">57</figref>, <figref idref="f0058">77</figref>) for automated characterization and/or identification of the microbial agent therein.

0120As one of skill in the art would appreciate other possible designs or configurations for the automated laboratory system are possible and are considered part of this invention.

Method of Operation

0121In one embodiment, a method for detection of microorganism growth in an automated detection system is described herein; the method comprising: (a) providing a specimen container comprising a culture medium for promoting and/or enhancing growth of said microorganism; (b) inoculating said specimen container with a test sample to be tested for the presence of a microorganism; (c) loading said inoculated specimen container into said detection system using an automated loading mechanism; (d) transferring said specimen container to a holding structure located within said detection system using an automated transfer mechanism, said holding structure comprising a plurality of wells for holding one or more of said specimen containers; and said holding structure optionally providing agitation of said specimen containers to promote and/or enhance microorganism growth therein; (e) providing a detection unit for detecting microbial growth in said specimen container by detecting one or more by products of microorganism growth within said container; and (f) detecting growth of a microorganism using said detection unit and thereby determining said container positive for microorganism growth.

0122The method of operation of the detection system 100 will now be described with reference to <figref idref="f0027">FIG. 30</figref>. After inoculation of a specimen container 500 with a sample to be tested (e.g., by a laboratory technician or doctor) the specimen container 500 is delivered to the automated loading mechanism 200, for automated loading of the specimen container 500 into the detection system 100.

0123At step 540, the specimen container 500 is loaded into the detection system 100, e.g., by placing the container onto a loading station or area 202 of a transport mechanism 204, as shown for example in <figref idref="f0001">Figure 1</figref>. The specimen container 500 is then moved by the transport mechanism 204 (e.g., a conveyor belt) to an entrance location or port 110, and subsequently through said entrance location or port 110 and into the detection system 100, thereby automatically loading the specimen container 500 into the detection system 100.

0124At step 550, an automated transfer mechanism 700, such as a robotic transfer arm, as shown for example in <figref idref="f0003">FIGS. 5A-5B</figref>, can then be used to transfer the container 500 to, and deposit the container in, a holding structure or rack 600 contained within the interior chamber 620 of the detection system 100.

0125At step 560, the specimen container 500 is incubated within the detection system 100. The detection system 100 optionally provides for agitation (e.g., using an agitation assembly) of the holding structures or racks 600, and/or one or more warm air blowers (see, e.g., 740 in <figref idref="f0003">FIGS. 5A-5B</figref>) to provide a temperature controlled environment, to promote and/or enhance microbial growth within the specimen container 500.

0126At step 570, the specimen container 500 is read by a detection unit (see, e.g., 810 in <figref idref="f0008">FIGS. 9A and 9B</figref>) to determine if the specimen container 500 is positive for microbial growth.

0127At step 580, the reading of the specimen container is analyzed to determine if the container is positive for the growth of a microbial agent (e.g., a microorganism) therein. If not, the processing proceeds along the NO branch 582 and a check is made if a timer has expired (step 584). If the timer has expired, the container is deemed negative and the container is transferred to the waste container 146 (see for example <figref idref="f0001">FIG. 1</figref>) at step 586. Otherwise, the incubation continues and the reading of the specimen container 500 (step- 580) continues periodically.

0128If at step 580, if the specimen container 500 is determined to be positive, the processing proceeds to the YES branch 590. In one embodiment, the specimen container 500 is moved or transferred using the automated transfer mechanism (e.g., the container is automatically unloading, as described elsewhere herein) to the positive container location or port 130 (see for example <figref idref="f0001">FIG. 1</figref>) at step 594 for user access to the container and/or further processing. In another embodiment, the specimen container can be transferred using a system transfer device to another detection instrument and/or another analytical system (e.g., to an automated characterization and/or identification system 104 of <figref idref="f0028">Figures 31</figref>, <figref idref="f0042">57</figref>, <figref idref="f0058">77</figref>) for further processing.

Part 2 Automated Identification and/or Characterization of a Microbial Agent

(Figures 31-108)

I. Overview

0129An automated instrument is described herein that provides a new architecture and method for automated identification and/or characterization of a microbial agent in a specimen sample, e.g., biological sample. The identification and/or characterization instrument 104 is shown in block diagram form in <figref idref="f0028">Figure 31</figref>. Two embodiments are described herein in great detail, a first embodiment described in conjunction with <figref idref="f0029 f0030 f0031 f0032 f0033 f0034 f0035 f0036 f0037 f0038 f0039 f0040 f0041">Figures 32-56</figref> and a second embodiment described in conjunction with <figref idref="f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057">Figures 57-76</figref>. The embodiments of the instrument 104 operate on a specimen container 500 (<figref idref="f0028">Figure 31</figref>) containing a sample. In one example, the specimen container 500 is a standard culture bottle, e.g., a blood culture bottle, for containing a specimen sample therein, e.g., a blood sample. The bottle may have been just tested positive by the detection instrument 100 of the previous section when it is delivered the identification and/or characterization instrument 104.

0130In general, any type of sample that may contain a microbial agent, e.g., bacterium, fungi or yeast species, can be tested in the instrument 104 such as for example biological samples. For example, the specimen sample can be a clinical or non-clinical sample suspected of containing one or more microbial agents. Clinical samples, such as a bodily fluid, include, but not limited to, blood, serum, plasma, blood fractions, joint fluid, urine, semen, saliva, feces, cerebrospinal fluid, gastric contents, vaginal secretions, tissue homogenates, bone marrow aspirates, bone homogenates, sputum, aspirates, swabs and swab rinsates, other body fluids, and the like. Non-clinical samples that may be tested include, but not limited to, foodstuffs, beverages, pharmaceuticals, cosmetics, water (<i>e.g.</i>, drinking water, non-potable water, and waste water), seawater ballasts, air, soil, sewage, plant material (<i>e.g.</i>, seeds, leaves, stems, roots, flowers, fruit), blood products (<i>e.g.</i>, platelets, serum, plasma, white blood cell fractions, <i>etc.</i>), donor organ or tissue samples, biowarfare samples, and the like.

0131One possible configuration for the instrument 104 of this disclosure is in a combined system which integrates detection of a microbial agent in a specimen container (instrument 100 of the previous discussion) with automated identification and/or characterization of the microbial agent. This combined approach is also described in conjunction with the embodiment of <figref idref="f0023 f0024">Figure 27</figref>.

0132In this configuration, a specimen container 500 (<figref idref="f0001">Figure 1</figref>) is inoculated with a specimen sample (e.g., clinical or non-clinical sample) and loaded/unloaded into/out of an automated detection instrument 102 (e.g. <figref idref="f0058">Figure 77</figref>). After a sufficient time interval to allow natural amplification of microorganism (this time interval varies from species to species), the specimen container is tested within the detection instrument 102 for the presence of a microorganism. The testing occurs on a periodic basis so that as soon as a specimen container is tested positive it can be transferred to the identification and/or characterization instrument 104 for further analysis of the specimen sample.

0133Detection can be accomplished using a variety of technologies such as the colorimetric sensor described in the patent literature (see <patcit id="pcit0070" dnum="US4945060A"><text>U.S. Patents 4,945,060</text></patcit>; <patcit id="pcit0071" dnum="US5094955A"><text>5,094,955</text></patcit>; <patcit id="pcit0072" dnum="US5162229A"><text>5,162,229</text></patcit>; <patcit id="pcit0073" dnum="US5164796A"><text>5,164,796</text></patcit>; <patcit id="pcit0074" dnum="US5217876A"><text>5,217,876</text></patcit>; <patcit id="pcit0075" dnum="US5795773A"><text>5,795,773</text></patcit>; and <patcit id="pcit0076" dnum="US5856175A"><text>5,856,175</text></patcit>). Detection could also be accomplished using intrinsic fluorescence of the microorganism, detection of changes in the optical scattering of the media, or detection in the generation of volatile organics in the media or headspace. These techniques are known in the art and described in previously cited patent literature in the Background section of this document.

0134Once a specimen container 500 is detected as positive in the automated detection instrument 102 (see <figref idref="f0058">Figure 77</figref>), the detection instrument 102 will notify the operator through an indicator (e.g., visual prompt), or via a notification at the user interface display, or by other means. The system may be set up to automatically analyze a positive specimen container or require end user acknowledgement prior to sample analysis in the identification/characterization instrument 104 described below. With automatic characterization, it would be possible to notify the physician immediately via electronic means of the results from the identification/characterization system.

0135Once a specimen container is determined to be positive in the detection instrument 102, the positive specimen container is handed off or transferred to the identification and/or characterization instrument 104 described below. See <figref idref="f0058">Figure 77</figref>. The manner in which this is accomplished can vary widely depending on the physical configuration of the detection and identification/characterization instruments 102 and 104. One example of how this can be accomplished is described below in conjunction with <figref idref="f0042">Figure 57</figref>.

0136Referring now in particular to <figref idref="f0028">Figure 31</figref>, a specimen container or bottle 500 is received in the identification and/or characterization instrument 104, either in an automated or manual fashion. The manner in which this occurs is not particularly important and can vary widely depending on the configuration of the instrument 104. The specimen container 500 is placed in a suitable holding structure or rack 1906 in the identification and/or characterization instrument 104. <figref idref="f0029">Figures 32</figref>, <figref idref="f0030">35</figref>, <figref idref="f0042">57</figref> and <figref idref="f0043">58</figref> show several possible configuration for the holding structure 1906. The holding structure 1906 is typically adapted for holding a multitude of specimen containers 500. The holding structure 1906 has a facility for rotating the specimen containers to inclined positions above and below horizontal to facilitate venting and sample removal, as described below and optionally agitation of the sample and thereby promoting microbial growth. In an alternative configuration, the positively declared specimen container could remain in the racks within the detection instrument 102 and the sampling could occur directly from the detection instrument.

0137The identification and/or characterization instrument 104 includes a sample removal apparatus 1912 coupled to a robotic transfer mechanism which holds or grasps a disposable sampling device 1902. Together, they operate to remove a test sample (i.e., a portion of the specimen sample in the positive specimen container 500) and subsequently add the portion to a separation device 1904 (see <figref idref="f0031">Figures 36-41</figref>). The separation device 1904 can take several forms, and one configuration is described herein in which the separation device includes a reservoir (<figref idref="f0031">Figure 38</figref>, item 2602) for receiving the sample and a capillary tube 2604 connected to the reservoir 2602. The identification/characterization instrument 104 further includes a separation and/or concentration station 1916, optionally in the form of a centrifuge, which operates on the separation device 1904 so as to separate the microbial agent from other components in the test sample and concentrate the microbial agent within the separation device 1904. In one example, the microbial agent is concentrated in the form of a pellet or pellet-like mass in the bottom of the capillary tube 2604 of the separation device 1904. The identification/characterization instrument further includes a identification and/or characterization module or read station (<figref idref="f0028">Figure 31</figref>, 1918) which interrogates the concentrated microbial agent to identify and/or characterize the microbial agent.

0138The instrument 104 receives a cassette 1900 of disposables. The disposables are of two types: (1) sampling devices 1902 for venting and removing a test sample from the specimen container 500, and (2) separation devices 1904 which receive a portion of the sample from the container 500 via the sampling device 1902 and in which the microbial agent in the test sample is concentrated. In alternative configuration of the instrument the functions of the sampling device 1902 and the separation device 1904 are combined into a single disposable device as shown in <figref idref="f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057 f0058">Figures 60-78</figref> in which case the cassette 1900 will only include a multitude of the combined sampling and separation devices.

0139The instrument 104 further includes a robotic transfer mechanism 1910 which operates to access the disposables 1902 and 1904, positive specimen containers 500 held in the holder or rack 1906, a waste container 1908, the separation and concentration device 1916, and the identification module 1918. The robotic transfer mechanism 1910 may also operate to receive a positive specimen container from a separate detection instrument, and load the positive specimen container into the holding structure or rack 1906. The robotic transfer mechanism 1910 accesses the waste container, separation and concentration station 1916, identification module 1918 and other modules or components in the instrument 104 as necessary to perform the functions described below. The manner of construction of the transfer mechanism 1910 can vary widely depending on the configuration of the instrument 104. In the present invention, the robotic transfer mechanism has coupled to it a sample removal apparatus and said robotic transfer mechanism moves the separation device from the separation and concentration station to the identification and/or characterization module.

0140The sample removal apparatus 1912 is preferably incorporated into, or coupled to, the robotic transfer mechanism 1910 as indicated by the dashed lines 1913. The apparatus 1912 further includes robot gripping and handling mechanisms to grasp one of the venting and sampling devices 1902, the separation device 1904 and/or the specimen container 500. The sample removal apparatus 1912 is connected to a pneumatic system 1914 which enables robotic gripping functions. The pneumatic system 1914 may include a vacuum pump, as described in the second embodiment below. The vacuum pump operates to provide vacuum to the venting and sampling device 1902 to draw a sample from the specimen container 500 and provide positive pressure to the sampling device 1902 to inject the sample from the sampling device 1902 into the separation device 1904. These aspects of the identification instrument 104 will all be described in greater detail below.

0141In one embodiment, the identification module 1918 includes a light source (e.g., an excitation light source) which illuminates the concentrated microbial agent in the separation device 1904. In response to the illumination, the concentrated microbial agent emits a detectable fluorescence signal, i.e., intrinsic fluorescence, as described below. In addition, the illumination of the concentrated microbial agent by the light source will generate a reflectance signal or Rayleigh scattering signal; this signal is of the same wavelength of the excitation light and provides additional information about the absorption of the microbial agent. The reflectance signal may also provide the basis of normalization of the fluorescence data The configuration of the identification module 1918 includes a means for spatially dispersing the reflectance/fluorescence spectrum, which may take the form of a spectrometer. These fluorescence and reflectance signals (spectrum) are captured by a sensor array 1920 which generates signals supplied to a computer 1924. The computer executes algorithms to process the reflectance/fluorescence signals and responsively identifies and/or characterizes the microbial agent. In one embodiment, a report containing the identification or characterization result is sent to an output device 1926 (e.g., display or associated computer workstation, pager, cell phone or e-mail server). The results can include clinical gram type, direct identification of the microbial agent (e.g., to the genus or species level in a taxonomic hierarchy), or other clinical information regarding the microbial agent in the sample.

First Embodiment (Figures 31-56)

Sample removal apparatus and sampling from the specimen container (e.g., blood culture bottle 500) (Figures 31-35, 45-46, items 1910 and 1912)

0142A sample removal apparatus, in the form of a sample head 1912, retrieves a sampling device 1902 (disposable) from a cassette 1900 of such devices (<figref idref="f0028">Figures 31</figref>, <figref idref="f0030">35</figref>). This sampling device 1902 (<figref idref="f0032">Figure 44</figref>, see also <figref idref="f0045">Figures 62, 63</figref>) may take the form of a sterile sheathed needle or other means to pierce a stopper or other closure member in the specimen container 500 and vent the specimen container (if necessary) so as to equilibrate the bottle pressure with atmospheric pressure. The sampling device (<figref idref="f0032">Figure 44</figref>, <figref idref="f0045">62</figref>, 1902) includes a sampling container or chamber 3204 to hold the withdrawn test sample. The test sample will include a portion of the specimen sample and any culture media present. Another possible embodiment is that the sampling device contains the sterile sheathed needle and is directly connected to or incorporated into to the separation device (i.e., a combined sampling and separation device, see <figref idref="f0071 f0072 f0073 f0074 f0075 f0076 f0077 f0078">Figures 90-108</figref>). The sample removal apparatus 1912 may optionally include features to decontaminate the surface of the bottle prior to sampling (if necessary).

0143The robotic transfer mechanism 1910 (<figref idref="f0030">Figure 35</figref>) can be moved in three mutually orthogonal translation axes in addition to one rotational axis around one of the orthogonal translation axes so as to be able to position the sample removal apparatus 1912 opposite the access point (e.g. stopper, or septum) of each specimen container/bottle 500 while the bottle is held in the racks 2310 of the specimen container holder 1906. Alignment of a sheathed needle 3202 of the sampling device 1902 to the bottle access point can either be accomplished by a docking feature built-in to the container 500, a vision system (e.g., camera) or using pre-programmed dimensional coordinates and precision motion controlling of the robot transfer mechanism 1910. The bottle 500 is preferably first tilted upward so that the space below the access point or stopper contains the headspace gases and not liquid media. The rationale for this step is that the container should first be vented so that the pressure in the bottle is close to atmospheric pressure. This would prevent venting of aerosols from the bottle and excess fluid transfer and overfill and possible spillage in the case of a bottle over-pressure situation.

0144Similarly, if the culture has not produced significant by-products (e.g. headspace gases) or the microorganism is not a "gas producer", there will be an under-pressure condition or the pressure inside the bottle will be below atmospheric pressure which would make sampling difficult. The aseptic venting will equilibrate the pressure so that a fluid sample can be removed from the bottle.

0145After proper venting, the bottle 500 is tilted so that the access port of the bottle is oriented downwards and a liquid sample can be transferred to the sampling device 1902. The sampling device withdraws for example a 0.5 ml, 1.0, or 2.0 ml sample of blood/media from the specimen container. Alternatively, a positive displacement syringe like device could be developed to provide sampling of specimen containers over a wide range of vacuum or pressure conditions.

Optional lysis of components in the test sample

0146After the test sample has been withdrawn from the specimen container 500, any cellular components contained therein (e.g., blood cells) may need to be lysed so that they do not interfere with separation and identification/characterization processes described below. The optional lysis step can be performed using a lysis buffer (which is a pH balanced surfactant solution) or can be accomplished using sonication. Both approaches cause disruption of the blood cell walls. The lysis operation can be performed by adding the lysis buffer to the disposable sampling device 1902 either off-line or within the identification and/or characterization instrument 104. Alternatively, the lysis buffer can be mixed with the blood/media sample during the loading of the sample into the separation device 1904. After the lysis buffer and blood/media sample are combined, some amount of agitation or mixing needs to be performed to ensure the lysis buffer contacts the blood cells and cell wall rupture occurs. In one possible embodiment, the robotic transfer mechanism may move up and down or otherwise to accomplish this mixing. In another embodiment, a mixing station (e.g., a vortexer as described in the second embodiment below) can be included in the instrument 104 for accomplishing this mixing.

0147As an alternative, the separation device 1904 could have two compartments separated by a thermoresponsive gel or other separation material that would allow the lysis buffer and the blood/media mixture to be combined, then pass through into the microorganism separation device.

0148Another approach could incorporate a filter to collect the microorganisms on a surface and then resuspend the microorganisms into an inoculum for testing.

0149It is envisioned the multiple separation devices 1904 could be provided in a format such as a cartridge, cassette, disk or strip to facilitate ease of user loading the system.

Separation and/or concentration station (Figures 31, 51, item 1916) and separation device (Figure 31, 36-41, 51, item 1904)

0150After withdrawal of the specimen from the specimen container, and after optional lysing of the cellular components (e.g., blood cells) in the sampling device 1902, the sample is then injected or otherwise introduced into one of the separation devices 1904. A microbial agent present in the sample is separated from other components and concentrated into a pellet or pellet-like mass within the separation device 1904.

0151The details of the separation and/or concentration of the microorganism in the separation device (1904) are described in related patent applications incorporated by reference into this application hereinabove, but the basic method will be described below. The separation is accomplished using a density solution or density cushion filtration. In one embodiment, the separation device 1904 is preloaded with the density cushion. Separation and concentration occurs by means of centrifugation of the separation device 1904.

0152The separation device 1904 (<figref idref="f0031">Figures 36-41</figref>) itself can take the form of a capillary tube design with a 1 - 2 mm diameter internal cross section capillary tube filled with the density solution. Above this capillary tube region is a fluted structure that opens up (i.e., opens to a larger cross sectional area) to provide a reservoir for the blood/media sample and the density solution. The bottom surface of the separation device is made of a material that has very good ultraviolet and visible light transmission. The top of the structure has a lid that is applied before centrifugation. In alternative configurations the separation device could be illuminated from the side in which case the lower portion of the separation device is made from a material that has very good ultraviolet and visible light transmission; the cross-sectional shape of the capillary tube may be circular or square.

0153The mixed or lysed sample contents (lysis buffer and test sample) are loaded into the separation device 1904 (see <figref idref="f0035">Figures 50A-C</figref> and the description below) by means of injecting the sample from the sampling device 1902 into the separation device 1904. The density solution is either loaded into the separation device 1904 on-line in the identification and/or characterization instrument 104 or, more preferably the separation device 1904 is shipped pre-filled with the density solution. After the mixed or lysed sample is loaded into the separation device 1904 and the device 1904 capped, the separation device 1904 is loaded into a centrifuge 1916. Alternatively, this lid is configured with a septum. The sample can be added to the device 1904 by piercing the septum, preventing the need for lid removal and replacement. The centrifuge is activated and spun, e.g. for several minutes at high rpm. This action causes the microbial agent (which is not lysed) to pass through the density solution and concentrate at the base of the capillary tube in the separation device 1904 into a pellet or pellet-like mass in the very bottom of the tube (see <figref idref="f0031">Figure 40</figref>, concentrated microbial agent pellet 2804). In one embodiment, the device 1904 loaded with density cushion is centrifuged prior to loading of the test sample to remove any air bubbles or the like that may otherwise interfere with the separation and/or concentration step.

Identification/characterization module (read station) for microbiological identification and/or characterization (Figure 31, 51, 52 item 1918)

0154After the separation device 1904 has been centrifuged as described above, the centrifuge 1916 can be rotated so that the separation device 1904 is in a reading position wherein a identification and/or characterization module (read station) 1918 can interrogate the separated and/or concentrated microbial agent (<figref idref="f0031">Figure 40</figref>, pellet 2804). Alternatively, the separation device 1904 can be removed from the centrifuge by the robotic transfer mechanism 1910 and placed in a read station in a separate location.

0155In one form, the read station 1918 includes an optical reader assembly for interrogating the concentrated microbial agent (pellet) within the separation device 1904. Since the microorganism/microbial agent in the blood/media sample is forced to the bottom surface of the capillary tube in the separation device 1904 (see <figref idref="f0031">Figures 40 and 41</figref>), the microbial agent will be in contact with the bottom surface. In one possible implementation, the optical reader assembly observes the fluorescence signal (e.g., intrinsic fluorescence signal) emitted from the concentrated microbial agent due to illumination from an excitation lights source.

0156The fluorescence signal (e.g., intrinsic fluorescence) results from excitation by a UV, visible spectrum or IR light source (see <figref idref="f0031">Figure 41</figref>). The light sources could be continuum lamps such as a deuterium or xenon lamp for UV and/or a tungsten halogen lamp for visible/IR excitation. Since these light sources have a broad range of emission, the excitation band can be reduced using optical bandpass filters. Other methods for emission wavelength spectral width that may be utilized include an acousto-optic tunable filter, liquid crystal tunable filter, an array of optical interference filters, prism spectrograph, and still others. Alternatively, lasers are available in discrete wavelengths from the ultraviolet to the near infra-red; additionally many multiplexing methods are known to those skilled in the art,

0157Alternatively, light emitting diodes can be used as narrowband excitation light sources. LED's are available from a peak wavelength of 240 nm to in excess of 700 nm with a spectral width of 20-40 nm. The same methods for the reduction of spectral width can be incorporated with the LED's to improve discrimination between excitation and emission spectra.

0158The emission from the sample may be measured by any suitable means of spectral discrimination, most preferably employing a spectrometer. The spectrometer may be a scanning monochromator that detects specific emission wavelengths whereby the output from the monochromator is detected by a photomultiplier tube and/or the spectrometer may be configured as an imaging spectrograph whereby the output is detected by an imaging detector array such as a charge-coupled device (CCD) detector array. In one embodiment, a discriminator allows the observation of the fluorescence and/or scattering signal by a photodetection means (such as a photomultiplier tube, avalanche photodiode, CCD detector array, a complementary metal oxide semiconductor (CMOS) area sensor array and/or electron multiplying charge coupled device (EMCCD) detector array (<figref idref="f0001">Figure 1</figref>, item 1920). An optical lens system (2904 in <figref idref="f0031">Figure 41</figref>) in front of the sensor array will magnify the 0.78 -2.0 mm² area forming the bottom of the capillary tube 2604 so that it fills the frame of the sensor array. Alternatively, coupling between the disposable separation device 1902 and the optical fiber is direct optical fiber coupling with no lens system; the optical fiber probe is a six around one configuration at the distal end, with the proximal end having a linear configuration for emission fibers to couple into the entry slit of a spectrometer. Fluorescence signal strength at several different wavelengths are acquired and saved in a computer memory.

0159An alternative configuration is to reduce the capillary tube 2604 to less than 1 mm in diameter to account for low biomass samples. Furthermore, the geometry of the capillary area may take other shapes, such as a rectangular-shaped internal cross-section. Another optional embodiment is to configure the reading of the capillary tube from the side instead of from the bottom. There are two possible benefits to doing so: (1) avoid debris or fibers that sediment to the base of the capillary tube and (2) provide the opportunity to optically identify the presence of polymicrobic agents. A rectangular shaped capillary tube may be preferred for this side read application.

0160The identification and/or characterization module 1918 includes a computer (<figref idref="f0028">Figure 31</figref>, item 1924) that operates on the fluorescence signal strength measurements which are stored in memory. The measurements are compared to experimentally-determined fluorescence spectra measurements for different types of microorganisms (i.e. Gram positive, Gram negative, yeast, etc.) that are also stored in memory. The computer executes a classification algorithm and generates a classification result for the microbial agent, e.g., gram classification, gram family, and species. In one configuration, further analysis of the spectra of the captured intrinsic fluorescence signal is accomplished so that species identification and/or characterization or at least the top three probabilities for species identification is achieved. Details on the methods executed by the computer for identification and/or characterization are explained below.

0161The identification of Gram type, gram family and species could also be accomplished using a micro-Raman evaluation. Raman spectroscopy is a noncontact technique where the sample is illuminated by laser radiation. The scattered light is either elastically or inelastically scattered by interaction with the molecules which comprise the microbial agent. The elastically scattered light is referred to as Rayleigh scattering and the inelastically scattered light is Raman scattering. Raman spectroscopy has been shown to be a potentially viable method of microorganism identification and/or characterization by examination of the vibrational spectra of the microorganism.

0162The laser illumination and scattering collection optics are designed to focus the beam to a near-diffraction limited spot size. This size ensures adequate laser signal on the microbe since Raman scattering is very inefficient. The collection optics are designed to efficiently capture scattered light and couple it into an optical spectrometer for analysis. The Raman signal can be acquired at one or more locations and the subsequent signal averaged.

0163Once the Raman spectra are obtained, it is analyzed for location and strength of key peaks in the spectra. This is compared to a stored reference data set of known microorganisms so that Gram type, morphological information and species identification can be obtained. The reference data set from known microorganisms can be obtained in the same instrument using the same methods and reading instrumentation.

0164The methods used for identification are described in greater detail in the co-pending applications filed on October 2009 cited an incorporated by reference herein at the beginning of this document, and the reader is directed to such patent applications for further details. The methods using intrinsic fluorescence and a taxonomic hierarchical classification method are also explained in detail below.

Disposal of sampling device 1902 and separation device 1904 (Figures 31, 53, item 1908)

0165After the test sample is injected from the sampling device 1902 into the separation device 1904, the sampling device 1902 is discarded into a biowaste container 1908 within the identification and/or characterization instrument 104. After the reading of the separation device 1904, the separation device 1904 is also discarded in the biowaste container 1908. The biowaste container is periodically removed from the identification/characterization instrument and emptied, and then replaced into the identification/characterization instrument.

User Interface

0166The identification instrument 104 preferably includes a user interface (not shown) which provides an operator with status information regarding specimen containers loaded into the identification instrument. The user interface may include some or all of the following features: <ul id="ul0005" list-style="bullet" compact="compact"><li>Touch screen display</li><li>Keyboard on touch screen.</li><li>System status</li><li>Positives alert</li><li>Communications to other systems (DMS, LIS, BCES &amp; other detection or identification Instruments).</li><li>Specimen Container status</li><li>Retrieve specimen containers</li><li>Visual and audible Positive Indicator</li><li>USB access (back ups and external system access).</li><li>Remote Notification of Identification and/or Characterization Results, System Status and Error Messages</li></ul>

0167The particular appearance or layout of the user interface is not particularly important.

0168The results are sent to an output device 1926 (<figref idref="f0028">Figure 31</figref>), which may be a computer memory, instrument display, printer, pager, cell phone, personal digital assistant, e-mail server, or other device. The results will typically include one or more of the following: clinical gram type of the microbial agent, identification and/or characterization of the species of the microbial agent, or other clinical information.

Specimen Container 500

0169The specimen container 500 shown in <figref idref="f0028">Figure 31</figref> is designed to hold and contain a sample and may take the form of a standard culture bottle, e.g., blood culture bottle. Preferred embodiments of the bottle incorporate a bar code (<figref idref="f0028">Figure 31</figref>) for automated reading of the bottle 500 within the identification/characterization instrument 104 or off-line equipment. The bottle 500 includes a stopper (not shown) sealing the container from the environment having a pierceable septum. Optionally, where the bottle is used for both detection and automated identification, the bottle includes a colorimetric sensor formed or placed in the bottom of the bottle for purposes of colorimetric detection of the presence of microbial growth in the bottle 500. Specimen containers of the type shown in <figref idref="f0001">Figure 1</figref> are well known in the art and described in the patent literature cited in the Background section of this document, therefore a further description is unnecessary.

0170The configuration of the bottle is not particular important and the inventive system and methods can be adapted to a variety of containers for containing a sample. Thus, the present description of blood culture specimen containers is offered by way of example and not limitation.

II. Detailed Description of First Embodiment (Figures 31-56)

0171<figref idref="f0029">Figure 32</figref> shows one possible configuration of the identification/characterization instrument 104, including the cassette of disposables 1900, a rack or holder 1906 for positive specimen containers, a waste container 1908, a robotic transfer mechanism 1910, a sample removal apparatus 1912 which is attached or otherwise coupled to the robotic transfer mechanism 1910, a separation and concentration station 1916, and the identification and/or characterization module 1918. <figref idref="f0029">Figure 33</figref> is a top plan view of the arrangement of <figref idref="f0029">Figure 32</figref>. The holder 1906 includes three racks that are oriented in one position for incubation and receiving new positive specimen containers, e.g., from a remote detection instrument or a manual loading door. In <figref idref="f0029">Figure 34</figref>, the racks are moved to a position for sample removal from the specimen containers, and loading of the sample into the separation device 1904.

0172<figref idref="f0030">Figure 35</figref> is a perspective view of the identification/characterization instrument in the position of <figref idref="f0029">Figure 34</figref>, showing the identification/characterization instrument 104 in further detail. The holder 1906 includes three separate racks 2310, each holding twenty specimen containers 500. The racks 2310 are rotatable as a unit about the horizontal axis to tilt the specimen containers into upward orientation (shown in <figref idref="f0030">Figure 35</figref>) for purposes of venting the specimen containers and to a downward orientation (see <figref idref="f0032">Figure 45</figref>) for sample removal.

0173The robotic transfer mechanism 1910 includes vertical guide rails 2320 and a horizontal guide rail 2324. The sample removal apparatus 1912 is moved from left to right and up and down by means of collars connected to the guide rails and a motor and belt driving subassembly (not shown, but conventional). Thus, the sample removal apparatus 1912 can move to any of the bottle positions in the three racks 2310, when the specimen containers are in either the upward or downward orientation. The sample removal apparatus 1912 can further move fore and aft by sliding along the guides 2322.

0174<figref idref="f0030">Figure 35</figref> also indicates that the instrument 104 includes electronics 2300, which includes a computer 1924 for processing fluorescence measurements, a memory 2302 storing results of the analysis and a further memory or processing units 2304 for storing program code for operation of the identification/characterization instrument 104. The electronics 2300 are preferably located behind suitable panels, which are not shown.

Cassette of disposables

0175<figref idref="f0030">Figure 35</figref> shows a cassette 1900 of disposable devices which is loaded into the identification/characterization instrument 104. The cassette 1900 includes a multitude of sampling devices 1902 and separation devices 1904.

0176The separation device 1904 is shown in <figref idref="f0031">Figures 36-41</figref>. Referring to these Figures, the separation device consists of a body 2402 that defines a reservoir 2602 and a capillary tube 2604 which is connected to the reservoir 2602. The body 2402 defines an axis 2608 and the capillary tube 2604 is oriented along the axis 2608. A first end of the capillary tube 2610 is connected to the reservoir 2602 and the second end 2612 of the capillary tube communicates with a tube portion 2702 of an end piece 2502. The reservoir is accessed via a removable cap 2404 that threads onto threads 2502 formed at the top portion of the body 2402. The lower portion of the body 2402 is closed off by an end piece 2502 which is affixed to the body by means of a ridge 2704 fitting into a corresponding recess 2606 in the body and welding or use of an adhesive. The bottom wall 2506 of the end piece 2502 is of reduced thickness as indicated in <figref idref="f0031">Figure 38</figref>. The end piece incorporates a capillary tube 2702 which is aligned with the capillary tube 2604 of the body 2402. The body 2402 proximate to the second end of the capillary tube is made from an optically transparent material; in the embodiment of <figref idref="f0031">Figure 37</figref> the end piece 2502 is optically transparent for facilitating optical interrogation of the concentrated microbial agent 2804 located at the bottom of the capillary tube 2604. The separation device 1904 is loaded with a density solution or "cushion" 2802 (<figref idref="f0031">Figure 40</figref>), either preloaded with the material or less preferably the material is added to the separation device within the identification/characterization instrument.

0177<figref idref="f0031">Figures 42 and 43</figref> show an embodiment of the separation device 1904 in which the body of the separation device 1904 is a one-piece construction. Walls 3002 provide support for the lower portion of the capillary tube 2602. The body proximate to the lower portion of the capillary tube 2604 is made from an optically transparent material.

0178<figref idref="f0031">Figure 41</figref> shows the operation of interrogation of concentrated microbial agent 2804 within the separation device 1904, an operation performed by the identification module 1918 of <figref idref="f0028">Figures 31</figref> and <figref idref="f0030">35</figref>. Light from a light source passes along an optical fiber 2902 and is directed by lens system 2904 to the base of the separation device 1904. The light stimulates the production of fluorescence from the microbial agent 2804 and the fluorescence is directed via the optical fiber 2906 through the lens 2904 and fiber 2902 to a spectral dispersion system in the identification module 1918 (<figref idref="f0028">Figure 31</figref>) to the sensor array (1920, <figref idref="f0028">Figure 31</figref>).

0179The sampling device 1902 is shown schematically and parts not to scale in <figref idref="f0032">Figure 44</figref>. The device 1902 can take the form of a syringe-like device having a body 3200 defining a chamber 3204 and a sheathed needle 3202. The chamber 3204 may be pre-loaded with a selective lysis buffer 3206. The top of the chamber 3204 is sealed. The chamber may have a port 3208 which allows the sampling device to be connected to a vacuum or pneumatic unit to facilitate venting or sampling of a sample from the bottle 500. The lysis buffer 3206 can be pre-loaded into the sampling device 1902, or it may be loaded into the device 1902 in the instrument at the time of use.

0180In one embodiment, the lysis buffer loaded into the sampling device 1902 may be tailored to the specie(s) expected to be found. In one possible configuration, several reservoirs of selective lysis buffers are present in the instrument 104 and one of the lysis buffers is loaded into the sampling device at the time of use which is selected to be most optimal for the sample contained in a given specimen container. Additionally, the sampling can be repeated with different sampling devices each containing a different selective lysis buffer.

Sample Removal Apparatus (Sampling Head) 1912

0181The sample removal apparatus 1912 of <figref idref="f0028">Figures 31</figref> and <figref idref="f0030">35</figref> operates to remove a portion of the biological sample in the positive detection container 500 from the detection container 500 and add the portion to a separation device 1904 obtained from the supply of separation devices 1900. The physical configuration of the sample removal apparatus 1912 can take a variety of forms, depending on the configuration of the specimen containers, the sampling device, and the separation device. In the illustrated embodiment the sample removal apparatus 1912 takes the form of articulating fingers that open and close so as to grasp the sampling device 1902 and the separation device 1904. The sample removal apparatus 1912 is moved to the required position for sampling and loading into the separation device by means of operation of the robotic transfer mechanism 1910.

Venting and sampling

0182With reference to <figref idref="f0032">Figure 45</figref>, the sample removal apparatus 1912 is moved to a position where it is placed directly over one of the sampling devices 1902 in the cassette 1900. The fingers of the sample removal apparatus 1912 grip the sampling device 1902 and the apparatus 1912 is raised upwards, removing the sampling device 1902 from the cassette 1900. As shown in <figref idref="f0033">Figure 46</figref>, the specimen containers 500 are tilted upwards. The stopper at the top of the bottle is sterilized using UV light or a disinfecting agent (e.g., bleach or alcohol). As shown in <figref idref="f0033">Figure 47</figref>, the bottle is vented by introducing the needle 3202 (<figref idref="f0032">Figure 44</figref>) of the sampling device through a pierceable septum in the stopper of the bottle 500, equalizing the pressure within the interior of the bottle to that of ambient conditions. The port 3208 of the sampling device may be connected to the pneumatic system (1914, <figref idref="f0028">Figure 31</figref>) during this process, e.g., a rolling diagram pump 1710 as shown in the second embodiment below.

0183As shown in <figref idref="f0014">Figures 18</figref> and <figref idref="f0015">19</figref>, the racks 2310 are then rotated to the downward orientation. The sample removal apparatus 1912, in conjunction the pneumatic system, withdraws a test sample (i.e., a portion of the specimen sample) from the bottle 500 into the sampling device 1902.

Lysis

0184The sampling device 1902 is optionally loaded with approximately 1 ml of a lysis buffer 3206 (<figref idref="f0032">Figure 44</figref>). In this embodiment, an approximately 2 ml test sample is removed from the bottle 500 and mixed with the lysis buffer in the sampling device 1902, e.g., by agitation of the device 1902 after loading of the test sample into the sampling device 1902. The lysis operation is selective to non-microorganism components, e.g., blood cells, i.e., the microbial agent cells are not lysed.

0185The lysis buffer 3206 selectively lyses undesired cells (i.e., non-microorganism cells) that may be present in the sample, <i>e.g.</i>, blood cells and/or tissue cells. The selective lysis of non-microorganism cells permits separation of microorganisms from other components that may be present in the sample. Accordingly, the lysis solution is one that is capable of selectively lysing cells, <i>e.g.</i>, non-microorganism cells (<i>e.g.</i>, by solubilizing eukaryotic cell membranes). The lysis solution may comprise one or more detergents, one or more enzymes, or a combination of one or more detergents and one or more enzymes.

0186Useful detergent may include one or more non-denaturing lytic detergent, such as Triton® X-100 Triton® X-100-R, Triton® X-114, NP-40, Genapol® C-100, Genapol® X-100, Igepal® CA 630, Arlasolve™200, Brij® 96/97, CHAPS, octyl β-D-glucopyranoside, saponin, and nonaethylene glycol monododecyl ether (C12E9, polidocenol). Optionally, denaturing lytic detergents can be included, such as sodium dodecyl sulfate, N-laurylsarcosine, sodium deoxycholate, bile salts, hexadecyltrimethylammonium bromide, SB3-10, SB3-12, amidosulfobetaine-14, and C7BzO. Optionally, solubilizers can also be included, such as Brij® 98, Brij® 58, Brij® 35, Tween® 80, Tween® 20, Pluronic® L64, Pluronic® P84, non-detergent sulfobetaines (NDSB 201), amphipols (PMAL-C8), and methyl-β-cyclodextrin. In one embodiment, polyoxyethylene detergent detergents may be preferred. The polyoxyethylene detergent can comprise the structure C_12-18/E_9-10, wherein C12-18 denotes a carbon chain length of from 12 to 18 carbon atoms and E9-10 denotes from 9 to 10 oxyethylene hydrophilic head groups. For example, the polyoxyethylene detergent can be selected from the group consisting of Brij® 97, Brij® 96V, Genapol® C-100, Genapol® X-100, nonaethylene glycol monododecyl ether (polidocanol), or a combination thereof. ethylenediaminetetraacetic acid (EDTA)

0187The lysis solution may also comprise one or more enzymes. Enzymes that can be used in the lysis solutions include, without limitation, enzymes that digest nucleic acids and other membrane-fouling materials (<i>e.g.</i>, proteinase XXIII, DNase, neuraminidase, polysaccharidase, Glucanex®, and Pectinex®).

0188In another embodiment, one or more additional agents can be used, including for example, reducing agents such as 2-mercaptoethanol (2-Me) or dithiothreitol (DTT), stabilizing agents such as magnesium, pyruvate, and humectants, and/or chelating agents such as ethylenediaminetetraacetic acid (EDTA). The lysis solution can be buffered at any pH that is suitable to lyse the desired cells, and will depend on multiple factors, including without limitation, the type of sample, the cells to be lysed, and the detergent used. In some embodiments, the pH can be in a range from about 2 to about 13, <i>e.g.</i>, about 6 to about 13, <i>e.g.</i>, about 8 to about 13, <i>e.g.</i>, about 10 to about 13. Suitable pH buffers include any buffer capable of maintaining a pH in the desired range, <i>e.g.</i>, about 0.05 M to about 1.0 M CAPS.

Dispense into separation device 1904 and separation/concentration

0189As shown in <figref idref="f0016">Figure 20A and 20B</figref>, the sample removal apparatus 1912 carries the sampling device 1902 (loaded with a mixed lysis buffer and sample solution) to the position of one of the separation devices 1902 in the cassette 1900. The sample removal apparatus pierces the cap of the separation device 1904 with the needle 3202 of the sampling device 1902 and injects 0.5 to 1.0 ml of the test sample + lysis buffer mixture into the reservoir of the separation device 1904. The dispensing could also be performed after uncapping the separation device 1904 and recapping the separation device 1904 after recapping. The sample removal apparatus then transfers the sampling device 1902 to the waste container 1908 as shown in <figref idref="f0035">Figure 50C</figref> and deposits it into the waste container.

0190In one embodiment, the separation is carried out by a centrifugation step in which the sample (<i>e.g.</i>, a lysed sample) is placed on top of an approximately 1 ml liquid phase density cushion 2802 (<figref idref="f0031">Figure 40</figref>) previously loaded in the separation device 1904 and the device 1904 is centrifuged under conditions (e.g., 10,000 <i>g</i>) which allow the microorganisms to be isolated and concentrated (e.g., the microorganisms form a pellet or pellet-like mass at the bottom and/or sides of the separation device 1904). "Density cushion" refers to a solution having a homogenous density throughout. The density of the cushion is selected such that the microorganisms in the sample pass through the cushion while other components of the sample (<i>e.g.</i>, blood culture broth, cell debris) remain on top of the cushion or do not pass all of the way through the density cushion.

0191The material for the density cushion 2802 can be any material that has the appropriate density range for the methods of this invention. In general, the density of the cushion is in the range of about 1.025 to about 1.120 g/ml. In one embodiment, the material is colloidal silica. The colloidal silica may be uncoated (<i>e.g.</i>, Ludox® (W.R. Grace, CT)) or coated, <i>e.g.</i>, with silane (<i>e.g.</i>, PureSperm® (Nidacon Int'l, Sweden) or Isolate® (Irvine Scientific, Santa Ana, CA)) or polyvinylpyrrolidone (<i>e.g.</i>, Percoll™, Percoll™ Plus (Sigma-Aldrich, St. Louis, MO)). The colloidal silica may be diluted in any suitable medium to form the proper density, <i>e.g.</i>, balanced salt solutions, physiological saline, and/or 0.25 M sucrose. Suitable densities can be obtained with colloidal silica at a concentration of about 15% to about 80% v/v, <i>e.g.</i>, about 20% to about 65% v/v. Another suitable material for density cushions is an iodinated contrast agent, <i>e.g.</i>, iohexol (Omnipaque™ NycoPrep™, or Nycodenz®) and iodixanol (Visipaque™ or OptiPrep™). Suitable densities can be obtained with iohexol or iodixanol at a concentration of about 10% to about 25% w/v. Sucrose can be used as a density cushion at a concentration of about 10% to about 30% w/v <i>e.g.</i>, about 15% to about 20% w/v, for blood culture samples. Other suitable materials that can be used to prepare the density cushion include low viscosity, high density oils, such as microscope immersion oil (<i>e.g.</i>, Type DF; Cargille Labs, New York), mineral oil (<i>e.g.</i>, Drakeol® 5, Draketex 50, Peneteck®; Penreco Co., Pennsylvania), silicone oil (polydimethylsiloxane), fluorosilicone oil, silicone gel, metrizoate-Ficoll® (LymphoPrep™), <i>e.g.</i>, at a concentration of about 75% to about 100% for blood culture samples, diatrizoate-dextran (PolymorphoPrep™), <i>e.g.</i>, at a concentration of about 25% to about 50% for blood culture samples, carboxymethyl cellulose, hydroxypropylmethyl cellulose, polyethylene oxide (high molecular weight), Pluronic® F127, Pluronic® F68, mixtures of Pluronic® compounds, polyacrylic acid, cross-linked polyvinyl alcohol, cross-linked polyvinyl pyrrolidine, PEG methyl ether methacrylate, pectin, agarose, xanthan, gellan, Phytagel®, sorbitol, Ficoll® (<i>e.g.</i>, Ficoll® 400 at a concentration of about 10% to about 15% for blood culture samples), glycerol, dextran (<i>e.g.</i>, at a concentration of about 10% to about 15% for blood culture samples), glycogen, cesium chloride (<i>e.g.</i>, at a concentration of about 15% to about 25% for blood culture samples), perfluorocarbon fluids (<i>e.g.</i>, perfluoro-n-octane), hydrofluorocarbon fluids (<i>e.g.</i>, Vertrel XF), and the like as are well known in the art. In one embodiment, the density cushion is selected from one or more of colloidal silica, iodixanol, iohexol, cesium chloride, metrizoate-Ficoll®, diatrizoate-dextran, sucrose, Ficoll® 400, and/or dextran in any combination. The density cushion can also be made up of a combination of materials, <i>e.g.</i>, a combination of colloidal silica and oil.

Transfer to Separation and concentration station (Centrifuge)

0192As shown in <figref idref="f0036">Figure 51</figref>, after loading of the separation device 1904 with the mixed or lysed test sample, the sample removal apparatus 1912 retrieves the loaded separation device 1904, lifts it out of the cassette 1900, and moves the separation device 1904 to the centrifuge 1916. The separator 1904 is then placed into a holder or loading position of the centrifuge 1916.

0193A separation and concentration of the microbial agent in the sample occurs within the separation device 1904 using the centrifuge 1916.

0194The separation step can be carried out to separate the microorganisms from other components of the sample (e.g., non-microorganisms or components thereof) and to concentrate the microorganisms into a pellet that can be interrogated for identification and characterization purposes. The separation does not have to be complete, <i>i.e.,</i> it is not required that 100% separation occur. All that is required is that the separation of the microorganisms from other components of the sample be sufficient to permit interrogation of the microorganisms without substantial interference from the other components.

0195The centrifuge spins the separation device 1904 at high speed in order to concentrate the microbial agent into the bottom of the capillary tube within the separation device 1904. The combination of the action of the lysis buffer on the non-microorganism cells (e.g., blood cells), the presence of the density solution within the separation device 1904, and the centrifugation, results in the separation of microbial agent from the lysed blood/broth mixture and the concentration of the microbial agent into a pellet or pellet-like mass in the bottom of the capillary tube, as shown in <figref idref="f0031">Figure 40 and 41</figref>.

0196In one embodiment, the separation device 1904 is centrifuged in station 1916 using a swing out rotor so that the microorganisms form a pellet directly on the bottom of the separation device 1904 (in the bottom of the capillary tube shown in <figref idref="f0007">Figures 8</figref>, <figref idref="f0009">10</figref> and <figref idref="f0011">13</figref>). The separation device 1904 is centrifuged at a sufficient acceleration and for a sufficient time for the microorganisms to be separated (e.g., a pellet formed) from other components of the sample. The centrifugation acceleration can be about 1,000 x <i>g</i> to about 20,000 x <i>g</i>, <i>e.g.</i>, about 2,500 x <i>g</i> to about 15,000 x <i>g</i>, <i>e.g.</i>, about 7,500 x <i>g</i> to about 12,500 x <i>g</i>, <i>etc.</i> The centrifugation time can be about 30 seconds to about 30 minutes, <i>e.g</i>., about 1 minute to about 15 minutes, <i>e.g.</i>, about 1 minute to about 5 minutes.

Reading

0197The identification and/or characterization module (read station 1918), which is shown positioned adjacent to the centrifuge then interrogates the concentrated microbial agent using fluorescence spectroscopy (e.g., intrinsic fluorescence and/or diffuse reflectance), Raman spectroscopy or other optical technique. In other embodiments, the microorganisms in the pellet can be interrogated using mass spectrometry techniques, such as MALDI-TOF mass spectrometry, desorption electrospray ionization (DESI) mass spectrometry, GC mass spectrometry , LC mass spectrometry, electrospray ionization (ESI) mass spectrometry and Selected Ion Flow Tube (SIFT) spectrometry. As shown in <figref idref="f0018">Figure 22</figref>, the identification and/or characterization module 1918 may be physically located proximate to the centrifuge 1916, in which case the separation device 1904 does not need to be moved further by the robotic transfer mechanism. Alternatively, the identification and/or characterization module 1918 could be located in a different location within the identification/characterization instrument and the robotic transfer mechanism operates to move the separation device to the location of the identification and/or characterization module 1918.

Transfer to Waste

0198After reading, as shown in <figref idref="f0018">Figure 23</figref>, the robotic transfer mechanism 1910 and sample removal apparatus 1912 operates to lift the separation device 1904 from the centrifuge 1916, transfers the separation device 1904 laterally and places it in the waste container 1908. <figref idref="f0019">Figure 24</figref> shows the waste container 1904 containing a multitude of the sampling devices 1902 and the separation devices 1908. When the waste container 1908 is full it is removed from the instrument and then replaced with an empty waste container. Prior to disposal of the separation device, a photographic image of the lower region of the separation device may be taken with a camera (not shown) to verify the separation process and provide valuable information on the identity of the isolate, such as pellet size, shape, color and density.

External processing of concentrated microbial agent

0199While in the above embodiment the concentrated microbial agent is interrogated while it is still located within the separation device 1904, it is possible to remove the concentrated microbial agent from the separation device and test it directly to identify and/or characterize the microbial agent.

0200In this variation, referring to <figref idref="f0038">Figure 55</figref>, the separation device 1904 is transferred to a removal device or station 4302. At the station 4302, the cap 2404 of the separation device 1904 is removed and the concentrated microbial agent 2804 is removed from the separation device 1904. The microbial agent is then subject to one or more additional tests. In one possible configuration, the microbial agent is supplied to a molecular diagnostic test unit 4310 which may include a disposable test strip or the like and processing instrument for identification of the agent. Alternatively, a sample of the microbial agent could be applied to a MALDI mass spectrometry plate 4314 and the plate inserted into a mass spectrometry unit 4312. Alternatively, the microbial agent could be delivered to a microbial identification and/or characterization test device 4318 (e.g., test card) and the card incubated and tested in a processing instrument 4316.

III. Method of Operation

A. Flow chart (Figures 56A, B, C)

0201The method of operation of the identification/characterization instrument 104 in an embodiment in which the specimen container 500 is subject to both detection and identification steps will now be described with reference to <figref idref="f0039 f0040 f0041">Figures 56A -56C</figref>.

0202The process starts at step 4402 with the loading of a sample into one of the containers 500 and delivery of the loaded container 500 to a detection instrument (as described above in conjunction with <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>). See <figref idref="f0058">Figure 77</figref>, instrument 102.

0203At step 4404, the container 500 is loaded into the detection instrument 102, e.g., by placing the detection container on conveyer which delivers the container to the detection instrument or by manually loading the container. (See <figref idref="f0058">Figures 77 and 78</figref> and the description of those figures below)

0204At step 4406, the container 500 is incubated within the detection instrument 102.

0205At step 4408 the detection container is read (by a detection unit in the instrument 102).

0206At step 4410, the reading of the detection container is analyzed to determine if the container is positive. If no, the processing branches along NO branch 4411 and a check is made if a timer has expired (step 4412). If the timer has expired, the bottle is deemed negative and the bottle is transferred to the waste container at step 4414. Otherwise, the incubation continues and steps 4406, 4408 and 4410 continue periodically.

0207If at step 4410 the detection container is positive, the processing proceeds to the YES branch 4416. The detection container is moved to the exit location in the detection instrument at step 4418. At step 4420 the detection container is transferred to the identification/characterization instrument 104, e.g., by moving the detection container 500 onto a conveyor and moving it into the entrance location of the identification/characterization instrument (see <figref idref="f0058">Figure 77</figref>). The transfer could occur by some other manner, the details of which can vary widely.

0208At step 4422 (<figref idref="f0040">Figure 56B</figref>), the detection container is placed into one of the racks 2310 of the identification/characterization instrument 104. The robotic transfer mechanism 1910 may be used in this process.

0209At step 4424, the detection container is aseptically vented. This step may occur prior to picking up of the sampling device or may occur after picking up the sampling device, see <figref idref="f0012">Figures 15</figref> and <figref idref="f0013">16</figref>.

0210At step 4426, one of the sampling devices 1902 is picked up from the cassette 1900. The sampling device 1902 is pre-loaded with a selective lysis buffer as shown in <figref idref="f0012">Figure 15</figref>; alternatively the lysis buffer is added to the sampling device at this time.

0211At step 4428, a protective cap (not shown), if fitted, covering the needle 3202 of the sampling device is removed.

0212At step 4430, the needle 3202 is inserted into a upright vented container 500 (see <figref idref="f0013">Figures 16</figref> and <figref idref="f0014">17</figref>).

0213At step 4432, the detection container is inverted (see <figref idref="f0034">Figures 48 and 49</figref>) and a small sample (e.g., a 2.0 ml sample) is removed from the container 500.

0214At step 4434, the container 500 is rotated to an upright orientation and the needle 3202 of the sampling device 1902 is removed.

0215At step 4436, a small volume (e.g., 0.5 ml sample) of air is introduced into the sampling device. This could be accomplished automatically using the pneumatic system 1914 connected to the sampling device.

0216At step 4438, a protective cap for the needle 3202, if fitted, is replaced.

0217At step 4440, the sampling device 1902 is inverted and agitated to thoroughly mix the test sample with the selective lysis buffer.

0218At step 4442, the protective cap for the needle 3202, if fitted, is again removed. (Note: a station fitted with appropriate gripping or grasping features could be provided for automatically removing and replacing the cap of the needle or alternatively the cap could remain on the needle as described in the second embodiment)

0219At step 4444, a small portion of the positive broth/lysis buffer mix is discarded into a waste container.

0220At step 4446, the sample removal apparatus moves the sampling device 1902 to the position above one of the separation devices 1904 (see <figref idref="f0057">Figure 76</figref>) and pierces the cap with the needle of the sampling device. The separation device 1904 is pre-loaded with the density cushion in this embodiment.

0221In one possible variation, the lysis buffer is also loaded into the separation device 1904 with the density cushion, and the mixing of the sample and the lysis buffer takes place within the separation device 1904.

0222At step 4448, the sample removal apparatus 1912 gently adds 0.5 to 1.0 ml of the sample/lysis buffer mixture (i.e., lysed sample) on top of the density cushion already present in the reservoir of the separation device 1904. See <figref idref="f0035">Figure 50A and 50B</figref>.

0223At step 4450, the sample removal apparatus 1912 is moved to the position of the waste container 1908 and the sampling device 1902 is discarded. See <figref idref="f0035">Figure 50C</figref>.

0224At step 4452, the sample removal apparatus returns to the separation device 1904 and picks it up out of the cassette 1900 and moves it to the location of the separation and concentration station 1916, and places the separation device 1904 into the centrifuge. See <figref idref="f0036">Figure 51</figref>.

0225At step 4454, the centrifuge cycle is started.

0226At step 4456, after completion of the centrifugation process, the separation device is moved to the identification and/or characterization module 1918 (reading station). Where the reading station is proximate to the centrifuge, the centrifuge is rotated to a reading position wherein the separation device 1904 is positioned for reading as shown in <figref idref="f0009">Figure 11</figref>.

0227At step 4458, the optical scan of the separation device 1904 in the identification and/or characterization module is started (See <figref idref="f0036">Figure 51, 52</figref>).

0228At step 4460, after completion of the reading operation, the separation device 1904 is placed into the waste container 1908 (see <figref idref="f0037">Figures 53, 54</figref>).

B. Interrogation step 4458, and the Identification and/or characterization of microorganisms in identification module 1918

0229Once the microorganisms present in the sample have been isolated and/or pelleted in the separation device 1904, the isolated sample or pellet can be interrogated (e.g., spectroscopically) to characterize and/or identify the microorganisms in the sample or pellet in step 4458. The interrogation can take place in a non-invasive manner, that is, the pellet can be interrogated while it remains in the separation device 1904. The ability to identify the microorganisms in a non-invasive manner, optionally coupled with keeping the container sealed (e.g., hermetically sealed) throughout the separation and characterization/identification process and automating the procedure avoids the constant handling of contaminated and/or infectious samples and greatly increases the safety of the entire process. Furthermore, the ability to characterize and/or identify microorganisms by direct interrogation without further processing of the sample or pellet (<i>e.g.</i>, resuspension, plating, and growth of colonies), greatly increases the speed with which identification/characterization can be made.

0230In one embodiment, optical spectroscopic methods can be used to analyze one or more intrinsic properties of the microorganisms, <i>e.g.</i>, a property present within the microorganism in the absence of additional agents, such as stains, dyes, binding agents, <i>etc.</i> In other embodiments, the optical spectroscopic methods can be used to analyze one or more extrinsic properties of the microorganisms, <i>e.g.</i>, a property that can only be detected with the aid of additional agents. The interrogation can be carried out using, for example, fluorescence spectroscopy, diffuse reflectance spectroscopy, infrared spectroscopy, terahertz spectroscopy, transmission and absorbance spectroscopy, Raman spectroscopy, including Surface Enhanced Raman Spectroscopy (SERS), Spatially Offset Raman spectroscopy (SORS), transmission Raman spectroscopy, and/or resonance Raman spectroscopy or combination thereof.

0231The spectroscopic interrogation can be carried out by any technique known to those of skill in the art to be effective for detecting and/or identifying one or more intrinsic or extrinsic properties of microorganisms. For example, front face fluorescence (where the exciting and emitted light enters and leaves the same optical surface, and if the sample is generally optically thick, the excitation light penetrates a very short distance into the sample (<i>see, e.g.,</i><nplcit id="ncit0001" npl-type="s"><text>Eisinger, J., and J. Flores, "Front-face fluorometry of liquid samples," Anal. Biochem. 94:15 (1983</text></nplcit>)) can be used for identification of microorganisms in pellets. Other forms of measurement, such as epifluorescence, reflectance, absorbance, and/or scatter measurements, can also be employed in step 4458.

0232Typically, the light source, or excitation source, results in the excitation of the sample, followed by measurement of the emission of fluorescence of the sample at predetermined time points or continuously. Similarly, the reflected light from interaction of the excitation source with the sample may be measured to provide pertinent data for identification and/or characterization. The emission from the sample may be measured by any suitable means of spectral discrimination, most preferably employing a spectrometer.

0233In a presently preferred embodiment, control measurements (e.g., fluorescence spectra) are taken for known microorganisms, thus allowing for correlation of measured test data with characterization of the microorganisms of interest using various mathematical methods known to those skilled in the art. The measured test data from known microorganisms is stored in machine-readable memory, e.g., within the instrument 104 itself or within an associated data processing device, such as connected workstation. For example, the data from samples being tested by the instrument 104 may be compared with the baseline or control measurements utilizing software routines known to or within the ability of persons skilled in the art to develop. More particularly, the data may be analyzed by a number of multivariate analysis methods, such as, for example, General Discriminant Analysis (GDA), Partial Least Squares Discriminant Analysis (PLSDA), Partial Least Squares regression, Principal Component Analysis (PCA), Parallel Factor Analysis (PARAFAC), Neural Network Analysis (NNA) and/or Support Vector Machine (SVM). These methods may be used to classify unknown microorganisms of interest in the sample being tested into relevant groups (e.g., species) based on existing nomenclature, and/or into naturally occurring groups based on the organism's metabolism, pathogenicity and/or virulence in designing the system for monitoring, detecting and/or characterizing the organism as described previously.

0234To enhance Raman (SERS) and fluorescence signals, microorganisms could either be coated with gold and/or silver nanoparticles prior to centrifugation, and/or the inner optical surface could be pre-coated with metal colloids of particular size and shape (refs: <nplcit id="ncit0002" npl-type="s"><text>Lakowicz, Anal. Biochem. 337:171 (2005</text></nplcit>) for fluorescence; <nplcit id="ncit0003" npl-type="s"><text>Efrima et al., J. Phys. Chem. B. (Letter) 102:5947 (1998</text></nplcit>) for SERS). In another embodiment, the nanoparticles are present in the density cushion prior to centrifugation and associate with microorganisms as the microorganisms pass through the density cushion.

0235The sample illumination source (See <figref idref="f0031">Figure 41</figref>), or excitation source, may be selected from any number of suitable light sources as known to those skilled in the art. Any portion of the electromagnetic spectrum that produces usable data can be used. Light sources capable of emission in the ultraviolet, visible and/or near-infrared spectra, as well as other portions of the electromagnetic spectrum, can be utilized and are known to those skilled in the art. For example, light sources may be continuum lamps such as a deuterium or xenon arc lamp for generation of ultraviolet light and/or a tungsten halogen lamp for generation of visible/near-infrared excitation. These light sources provide a broad emission range and the spectral bandwidth for specific excitation wavelengths may be reduced using optical interference filters, prisms and/or optical gratings, as are well known in the art.

0236Alternatively, a plurality of narrowband light sources, such as light emitting diodes and/or lasers, may be spatially and/or temporally multiplexed to provide a multi-wavelength excitation source. For example, light emitting diodes are available from 240 nm to in excess of 900 nm and the sources have a spectral bandwidth of 20-40 nm (full width at half maximum). Lasers are available in discrete wavelengths from the ultraviolet to the near-infrared and can be employed using multiplexing methods well known to those skilled in the art.

0237The spectral selectivity of any of the light sources may be improved by using spectral discrimination means such as a scanning monochromator. Other methods of discrimination may be utilized, as known to those of skill in the art, such as an acousto-optic tunable filter, liquid crystal tunable filter, an array of optical interference filters, prism spectrograph, <i>etc.,</i> and in any combination. A consideration in selecting the spectral discriminator takes into the account the range of tunability as well as the level of selectivity. By way of illustration, for example, a discriminator might utilize the wavelength range of 300 - 800 nm with a selectivity of 10 nm. These parameters generally determine the optimum technology necessary to achieve the tunability range as well as the selectivity.

0238Typically, the light source results in the excitation of the sample, followed by measurement of the emission of fluorescence of the sample at predetermined time points or continuously. Similarly, the reflected light from interaction of the excitation source with the sample may be measured to provide pertinent data for detection and/or characterization.

0239The emission from the sample may be measured by any suitable means of spectral discrimination, most preferably employing a spectrometer. The spectrometer may be a scanning monochromator that detects specific emission wavelengths whereby the output from the monochromator is detected by a photomultiplier tube and/or the spectrometer may be configured as an imaging spectrograph whereby the output is detected by an imaging detector array such as a charge-coupled device (CCD) detector array. In one embodiment, a discriminator allows the observation of the fluorescence and/or scattering signal by a photodetection means (such as a photomultiplier tube, avalanche photodiode, CCD detector array, and/or electron multiplying charge coupled device (EMCCD) detector array).

0240The spectroscopic technique is used to obtain measurements that are preferably provided as Excitation-Emission Matrix (EEM) measurements. As used herein, EEM is defined as the luminescent spectral emission intensity of fluorescent substances as a function of both excitation and emission wavelength, and includes a full spectrum or a subset thereof, where a subset may contain a single or multiple excitation/emission pairs(s). Additionally, a cross section of the EEM with a fixed excitation wavelength may be used to show the emission spectra for a specific excitation wavelength, and a cross section of the EEM with a fixed emission wavelength may be used to show the excitation spectra for a sample. In one embodiment, multiple EEMs are measured at more than one specific excitation-emission wavelength pair, <i>e.g.</i>, at least at 2, 3, 4, 5, 6, 7, 8, 9, 10, or more specific excitation-emission wavelength pairs.

0241It has been found that a front-face fluorescence spectroscopy provides an advantage in measuring the fluorescence and/or reflectance properties of highly scattering and highly quenching samples. In one embodiment, the front-face method may be particularly useful. For example, front-face fluorescence may be particularly useful in highly absorbent samples because the excitation and emission beam does not need to travel through the bulk of the sample, and thus, may be less affected by the interfering components that may be contained therein (e.g., blood cells and microbiological culture media). The optical surface of the separation device 1904 may be illuminated at such an angle as to provide acceptable results as known to those skilled in the art, (<i>e.g.</i>, <nplcit id="ncit0004" npl-type="s"><text>Eisinger, J., and J. Flores, "Front-face fluorometry of liquid samples," Anal. Biochem. 94:15-21 (1983</text></nplcit>)). In one embodiment, the system is designed such that the spectroscopic system measures diffuse reflected light at a minimum of one fixed angle in addition to measuring emitted fluorescence at a minimum of one fixed angle.

0242In yet another embodiment, non-spectroscopic measurements from the detection system that detected the specimen container as "positive" (item 102 in <figref idref="f0058">Figure 77</figref>), such as detection times and growth rates can be used to assist in the characterization and/or identification of microorganisms from the isolated sample or pellet. Additionally, measurements taken from a photographic image of the lower region of the separation device can provide valuable information on the identity of the isolate, such as pellet size, shape, color and density.

0243In some embodiments, characterization and/or identification of the microorganisms in the isolated sample or pellet need not involve identification of an exact species. Characterization encompasses the broad categorization or classification of biological particles as well as the actual identification of a single species. Classification of microorganism from an isolated sample or pellet may comprise determination of phenotypic and/or morphologic characteristics for the microorganism. For example, characterization of the biological particles may be accomplished based on observable differences, such as, composition, shape, size, clustering and/or metabolism. In some embodiments, classification of the biological particles of interest may require no prior knowledge of the characteristics of a given biological particle but only requires consistent correlations with empiric measurements thus making this method more general and readily adaptable than methods based on specific binding events or metabolic reactions. As used herein "identification" means determining to which family, genus, species, and/or strain a previously unknown microorganism belongs to. For example, identifying a previously unknown microorganism to the family, genus, species, and/or strain level.

0244In some instances, characterization encompasses classification models which provide sufficient useful information for action to be taken. As used herein, the preferred classification models comprise grouping into one or more of the following: (1) Gram Groups; (2) Clinical Gram Groups; (3) Therapeutic Groups; (4) Functional Groups; and (5) Natural Intrinsic Fluorescence Groups.

0245(1) <u>Gram Groups</u>: Within the Gram Groups classification, microorganisms may be placed into one of three broad classification categories based on their Gram staining reaction and overall size, said groups selected from one or more of the following: (a) Gram positive microorganisms that stain dark blue with Gram staining; (b) Gram negative microorganisms that stain red with Gram staining; and (c) yeast cells that stain dark blue with Gram staining, but are very large rounded cells that are distinguished from bacteria by their morphological characteristics and size.

0246(2) <u>Clinical Gram Groups</u>: The Gram Groups may be further divided into several sub-categories representing distinguishing morphological features. These sub-categories comprise all the relevant clinical information reported by an experienced laboratory technologist, and thus provide a higher level of identification than a positive or negative Gram reaction. This particular classification is very helpful because it eliminates concerns about relying on the quality of a Gram stain and/or the skill level of the technician reading the smear by providing the equivalent clinically relevant information with an automated system. More specifically, subcategories of microorganisms based on this classification model may be selected from one or more of the following: (a) cocci, which are small rounded cells; (b) diplococci, which are two small rounded cells joined together; (c) rods, which are rectangular shape; and (d) bacilli, which are rod shaped. Examples of these sub-categories that can be ascertained by additional morphological information include: (i) Gram positive cocci; (ii) Gram positive cocci in chains; (iii) Gram positive cocci in clusters (<i>i.e.</i>, "grape-like" clusters); (iv) Gram positive diplococci; (v) Gram positive rods; (vi) Gram positive rods with endospores; (vii) Gram negative rods; (viii) Gram negative coccobacilli; (ix) Gram negative diplococci; (x) yeast; and (xi) filamentous fungi.

0247(3) <u>Therapeutic Groups</u>: The therapeutic groups comprise multiple microbial species that, when isolated from particular specimen types, are treated with the same class of antibiotics or mixture of antibiotics (<i>e.g.</i>, as described in <i>"</i><nplcit id="ncit0005" npl-type="s"><text>Sanford Guide to Antimicrobial Therapy 2008</text></nplcit><i>"</i>). In many cases, identity to the species level is not required by the clinician to enable a change from initial empiric therapy to a more targeted therapy because more than one species can be treated with the same choice of antibiotic(s). This classification level correctly places these "same-treatment" microorganisms into single therapeutic categories. Examples of this characterization level include the ability to distinguish highly resistant Enterobacteriacae (EB) species from sensitive EB species (<i>Enterobacter</i> spp. from <i>E. coli</i>), or fluconazole-resistant <i>Candida</i> species (<i>C. glabrata</i> and <i>C. kruzei</i>) from sensitive <i>Candida</i> species (<i>C. albicans</i> and <i>C. parapsilosis</i>), and so on.

0248<u>(4) Functional Groups</u>: According to the invention, microorganisms may also be placed into several groups based upon a mixture of metabolic, virulence and/or phenotypic characteristics. Non-fermentative organisms may be clearly distinguished from fermentative ones. Furthermore, microorganism species that produce hemolysins may be grouped separately from non-hemolytic species. In some cases, these groups represent broader categories than genus level (<i>e.g.</i>, coliforms, Gram negative non-fermentative rods), some at the genus level (<i>e.g</i>., <i>Enterococcus, Candida</i>), and some with closer to species-level discrimination (<i>e.g.</i>, coagulase-negative staphylococci, alpha-hemolytic streptococci, beta-hemolytic streptococci, coagulase-positive staphylococci, <i>i.e., S. aureus</i>).

0249<u>(5) Natural Intrinsic Fluorescence ("IF") Groups</u>: Microorganisms may also be placed into categories based on their natural tendency to group together by their innate and/or intrinsic fluorescence characteristics. Some of these groups may be common to Therapeutic and Functional Group categories. These groupings may comprise individual species, such as <i>E. faecalis, S. pyogenes,</i> or <i>P. aeruginosa</i> that have characteristic IF signatures and/or may contain small groups of organisms with relatively conserved IF signatures such as the <i>K. pneumoniae- K. oxytoca</i> or <i>E. aerogenes-E. cloacae</i> groups.

0250In addition to measuring intrinsic properties of microorganisms (such as intrinsic fluorescence) for identification purposes, the methods may use additional identifier agents to aid in the separation and/or identification process. Agents that bind to specific microorganisms, such as affinity ligands, can be used to separate microorganisms, to identify a class or species of microorganism (<i>e.g.,</i> through binding to a unique surface protein or receptor) and/or to identify a characteristic of the microorganism (<i>e.g.</i>, antibiotic resistance). Useful identifier agents include, without limitation, monoclonal and polyclonal antibodies and fragments thereof (<i>e.g.</i>, anti-Eap for <i>S. aureus</i> identification), nucleic acid probes, antibiotics (<i>e.g</i>., penicillin, vancomycin, polymyxin B), aptamers, peptide mimetics, phage-derived binding proteins, lectins, host innate immunity biomarkers (acute phase proteins, LPS-binding protein, CD14, mannose binding lectin, Toll-like receptors), host defense peptides (<i>e.g.</i>, defensins, cathelicidins, proteogrins, magainins), bacterocins (<i>e.g</i>., lantibiotics, such as nisin, mersacidin, epidermin, gallidermin, and plantaricin C, and class II peptides), bacteriophages, and dyes selective for nucleic acids, lipids, carbohydrates, polysaccharides, capsules/slime or proteins, or any combination thereof. If the agent does not itself give out a detectable signal, the agent can be labeled to provide a detectable signal, such as by conjugating the agent to a marker (<i>e.g.</i>, visible or fluorescent). Markers include, without limitation, fluorescent, luminescent, phosphorescent, radioactive, and/or colorimetric compounds. The agent can be added to the microorganisms at any step in the methods of the invention, <i>e.g.,</i> when the sample is obtained, during lysis, and/or during separation. In some embodiments, the presence of the agent in the pellet can be determined during interrogation of the pellet. Other useful identifier agents include substrates for microbial enzymes, chelating agents, photosensitizing agent, quenching agent, reducing agent, oxidizing agent, buffer, acid, base, solvent, fixative, detergents, surfactants, disinfectants (eg. alcohols, bleach, hydrogen peroxide) and toxic compounds (eg. sodium azide, potassium cyanide) and metabolic inhibitors such as cyclohexamide, etc. Similarly, many fluorescent compounds for measuring microbial cell viability, metabolism and/or membrane potential may be used as an identifier agent in the present invention. As would be readily appreciated by one of skill in the art, the sensitivity of a particular microorganism to any compound affecting its physical state or metabolism, such as an antibiotic, could be rapidly ascertained by adding the compound to the sample, lysis buffer, density cushion or any mixture thereof.

0251An embodiment of a method for performing identification and/or characterization of microbial agents in samples using intrinsic fluorescence will now be described in conjunction with <figref idref="f0062 f0063 f0064 f0065 f0066 f0067 f0068 f0069 f0070">Figures 81-89</figref>. Basically, the method can be embodied as a sequence of processing instructions stored in memory and executed using a conventional data processor or computer. The method executes an algorithm shown in <figref idref="f0060 f0061 f0062">Figures 81A-81C</figref> which is designed to provide the identification of a blood culture isolate (concentrated pellet) given an intrinsic fluorescence (IF) scan of the isolate from a predefined set of emission wavelengths.

0252In preferred embodiments, the method is encoded as software instructions implementing a multi-level identification algorithm, the different levels corresponding to different levels of a taxonomic hierarchy. Traditional classification algorithms that take input data and determine the identification of a microorganism use a single classification model. Given data from an intrinsic fluorescence scan at a predefined set of wavelengths of an unknown organism, the multi-leveled identification algorithm classifies the organism following the branches of a taxonomic hierarchy - Gram class, family, and species. A unique feature is the use of separate classification models at each identification step from highest, Gram class, to lowest, species. Additionally, the approach incorporates the use of parallel classification models to evaluate consistency between results. Thus, the probability of accurate identification and/or characterization is maximized, and generation of incorrect identification or characterization results is minimized. The multi-level taxonomic hierarchical classification method is applicable to other data sets besides intrinsic fluorescence data (e.g. it could be used to Raman spectral data or mass spectral data).

0253The identification method includes a set of data pre-processing steps (shown as blocks 5102, 5104 and 5106 of <figref idref="f0060">Figure 81A</figref>, and a set of analysis steps (the remaining blocks 5108, 5110, etc. in <figref idref="f0061">Figures 81B</figref>, <figref idref="f0062">81C</figref>). The method determines the identification of the organism at multiple levels of the taxonomic hierarchy. The pre-processing steps are designed to acquire IF scan data and perform data transformations that minimize variation between different strains of a microbial agent within a given organism group or species. The data analysis steps implement a multi-level identification using parallel classification models, as will be understood from the following discussion.

0254As noted above, preferred embodiments provide an organism identification at the Gram, family, and species levels. Organisms commonly found in blood cultures that can be identified by the algorithm include, but not necessarily limited to, those listed in Table 1. Obviously, for different applications (e.g., food, water, environmental samples, etc.) the organisms may differ from those listed in Table 1, however the methodology is the same. <tables id="tabl0001" num="0001"><table frame="all"><title><b>Table 1: Intrinsic Fluorescence Algorithm Identification Organism List</b></title><tgroup cols="3"><colspec colnum="1" colname="col1" colwidth="27mm" /><colspec colnum="2" colname="col2" colwidth="44mm" /><colspec colnum="3" colname="col3" colwidth="38mm" /><thead><row><entry valign="middle"><b><u>Gram Class</u></b></entry><entry align="center" valign="middle"><b>Family</b></entry><entry align="center" valign="middle"><b>Species</b></entry></row></thead><tbody><row><entry rowsep="0" align="center" valign="middle" /><entry morerows="11" align="center" valign="middle">Enterobacteriaceae</entry><entry align="center" valign="middle">C. freundii</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">E. aerogenes</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">E. cloacae Complex</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">E. coli</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">K. oxytoca</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">K. pneumoniae</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">M. morganii</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">P. mirabilis</entry></row><row><entry rowsep="0" align="center" valign="middle">Gram-negative</entry><entry align="center" valign="middle">P. stuartii</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">P. vulgaris</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. enteritidis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. marcescens</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">Moraxellaceae</entry><entry align="center" valign="middle">A. baumanii</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">Neisseriaceae</entry><entry align="center" valign="middle">N. meningitidis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">Pasteurellaceae</entry><entry align="center" valign="middle">H. influenzae</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">Pseudonomadaceae</entry><entry align="center" valign="middle">P. aeruginosa</entry></row><row><entry /><entry align="center" valign="middle">Xanthomonadaceae</entry><entry align="center" valign="middle">S. maltophilia</entry></row><row><entry rowsep="0" align="center" valign="middle" /><entry morerows="1" align="center" valign="middle">Enterococcaceae</entry><entry align="center" valign="middle">E. faecalis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">E. faecium</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">Listeriaceae</entry><entry align="center" valign="middle">L. monocytogenes</entry></row><row><entry rowsep="0" /><entry morerows="5" align="center" valign="middle">Staphylococcaceae</entry><entry align="center" valign="middle">S. aureus</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. capitis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. epidermidis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. hominis</entry></row><row><entry rowsep="0" align="center" valign="middle">Gram-positive</entry><entry align="center" valign="middle">S. lugdunensis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. warneri</entry></row><row><entry rowsep="0" /><entry morerows="4" align="center" valign="middle">Streptococcaceae</entry><entry align="center" valign="middle">S. agalactiae</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. bovis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. mitis / S. oralis</entry></row><row><entry rowsep="0" /><entry align="center" valign="middle">S. pneumoniae</entry></row><row><entry /><entry align="center" valign="middle">S. pyogenes</entry></row><row><entry morerows="4" align="center" valign="middle">Yeast</entry><entry morerows="4" align="center" valign="middle">Ascomycetes</entry><entry align="center" valign="middle">C. albicans</entry></row><row><entry align="center" valign="middle">C. glabrata</entry></row><row><entry align="center" valign="middle">C. krusei</entry></row><row><entry align="center" valign="middle">C. parapsilosis</entry></row><row><entry align="center" valign="middle">C. tropicalis</entry></row></tbody></tgroup></table></tables>

0255The processing steps or modules shown in <figref idref="f0060 f0062">Figures 81A-C</figref> will now be described in detail.

Pre-processing

0256Step 5102: Obtain a fluorescence value, n_ij, for each excitation value, i = 1,2, ..., x, and each emission, j = 1,2, ..., y, combination. The ratio, emission value/excitation value, must fall within the interval (1.05, 1.95).

0257Step 5104: For each fluorescence value, n_ij, calculate the natural logarithm value, ln (n_ij).

0258Step 5106: Calculate the 1^st derivative of the natural log transform (from step 5104) for each emission value, j = 2, 3, ..., y-1, across a given excitation wavelength, i.

0259It is advantageous to transform the raw fluorescence data to minimize strain-to-strain variation within each organism group, using both steps 5104 and 5106. Additionally, the transformation process tends to create similar variance across organism groups. <figref idref="f0063">Figures 82</figref>, <figref idref="f0064">83</figref> and <figref idref="f0065">84</figref> illustrate by way of example the effects of performing the described pre-processing for multiple strains of <i>Staphylococcus aureus</i> evaluated across the emission range at excitation 315. In <figref idref="f0063">Figure 82</figref>, each line represents the fluorescence signal from a single strain. The line 5202 indicates the mean fluorescence signal at each emission value. <figref idref="f0064">Figure 83</figref> shows the strain-to-strain variation in the fluorescence signal after application of the natural logarithm transformation (step 5104); note that the curve for all of the strains are close together. <figref idref="f0065">Figure 84</figref> shows the strain-to-strain variation at excitation of 315 nm after calculation of the first derivative of the natural logarithm transform (step 5106). Again, note that the curve for all the strains are very close together, particularly at the emission range of 400-610 nm.

0260As another example, <figref idref="f0066">Figure 85</figref> shows the strain-to-strain variation in the fluorescence signal at excitation of 415 nm for <i>Candida parapsilosis,</i> prior to performing the transformation steps. Note the wide variation in emission in the range of 400-650 nm. Strain-to-strain variation for this organism at excitation of 415 nm after performing the natural logarithm transformation is shown in <figref idref="f0067">Figure 86</figref>. Strain-to-strain variation after performing the first derivative transformation is shown in <figref idref="f0068">Figure 87</figref>. Note that in <figref idref="f0068">Figure 87</figref> the strain-to-strain variation is much reduced.

Analysis

0261Step 5108: The first level of classification in the analysis after performing the pre-processing steps is gram classification 5108. At this step, the processing includes two branches, one represented by steps 5110 and 5112 and another represented by steps 5114 and 5116. <figref idref="f0060">Figure 81A</figref> is not meant to imply that the branches could not be performed sequentially; the branches could be performed either sequentially or in parallel.

0262Step 5110: Gram Classification Distance Calculation. Using the 1^st derivative transforms for a predefined set of excitation / emission pairs, calculate the distance, <maths id="math0001" num=""><math display="block"><msub><mi mathvariant="normal">d</mi><mi>a</mi></msub><mo>=</mo><msup><mfenced open="[" close="]" separators=""><msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced><mi mathvariant="normal">t</mi></msup><msup><mi mathvariant="normal">Σ</mi><mrow><mo>−</mo><mn>1</mn></mrow></msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced></mfenced><mrow><mn>1</mn><mo>/</mo><mn>2</mn></mrow></msup></math><img file="EP2430461B2_D0001.tif" /></maths> for each Gram class defined in the model where <ul id="ul0006" list-style="dash" compact="compact"><li><i>a</i> = 1, 2, 3, represents the Gram classes defined in the model</li><li><i>m</i> represent the vector of calculated values of the 1^st derivative, <i>m_ij</i>, for each excitation / emission pair <i>i, j</i></li><li><i>m_a</i> represent the vector of mean values <i>m_a(ij)</i> from a distribution for each class <i>a</i> at excitation / emission pair <i>i</i>, <i>j</i></li><li>t represent the transpose of the vector</li><li><i>(m - m_a)</i> represent the vector of differences <i>m_ij</i> - <i>m_a(ij)</i> for each excitation / emission pair <i>i,j</i></li><li>Σ^-<i>1</i> represents the inverse of the covariance matrix for the predefined set of excitation / emission pair. The set of excitation and emission pairs are experimentally determined from fluorescence measurements (with preprocessing performed) of known microorganisms (see <figref idref="f0069">Figures 88</figref> and <figref idref="f0070">89</figref> and the discussion below).</li></ul>

0263The term "model" is used to refer to a set of known microbial agents for which IF measurements (including transforms) at the predetermined excitation wavelengths have been previously obtained and for which a specimen is a candidate for classification, e.g., the agents listed in Table 1.

0264Step 5112: Gram Classification Interpretation. <ul id="ul0007" list-style="dash" compact="compact"><li>Let u_g represent the maximum distance threshold</li><li>If all distances, d₁, d₂, and d₃, are greater than u_g, the classification result is <i>Unknown</i></li><li>Else, determine the value of d_min, the minimum value of d₁, d₂, and d₃</li><li>Let w_g represent the low discrimination threshold factor</li><li>If more than one distance, d₁, d₂, and d₃, is less than (d_min ∗ w_q), the classification result is Low Discrimination between the Gram classes having distances less than (d_min ∗ w_q)</li><li>If only one distance, d₁, d₂, and d₃, is less than (d_min ∗ w_q), the classification result is the corresponding Gram class.</li></ul>

Step 5114: All Families Classification Distance Calculation

0265Using the 1^st derivative transforms for a predefined set of excitation / emission pairs, calculate the distance, <maths id="math0002" num=""><math display="block"><msub><mi mathvariant="normal">d</mi><mi>a</mi></msub><mo>=</mo><msup><mfenced open="[" close="]" separators=""><msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced><mi mathvariant="normal">t</mi></msup><msup><mi mathvariant="normal">Σ</mi><mrow><mo>−</mo><mn>1</mn></mrow></msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced></mfenced><mn>½</mn></msup></math><img file="EP2430461B2_D0002.tif" /></maths> for each organism family defined in the model where <ul id="ul0008" list-style="dash" compact="compact"><li><i>a</i> = 1, 2, ...,k, represents all of the organism families defined in the model</li><li>∑<i>^-1</i> represents the inverse of the covariance matrix for the predefined set of excitation / emission pairs (same remark as above, the set of excitation and emission pairs are experimentally determined)</li><li><i>m</i> represent the vector of calculated values of the 1^st derivative, <i>m_ij,</i> for each excitation / emission pair <i>i, j</i></li><li><i>m_a</i> represent the vector of mean values <i>m_a(ij)</i> from a distribution for each class <i>a</i> at excitation / emission pair <i>i, j</i></li><li><i>t</i> represent the transpose of the vector</li><li><i>(m - m_a)</i> represent the vector of differences <i>m_ij</i> - <i>m_a(ij)</i> for each excitation / emission pair <i>i, j</i></li></ul> Note: The predefined set of excitation / emission pairs can be unique for the gram classification versus all species classification.

0266Step 5116: All Families Classification Interpretation <ul id="ul0009" list-style="dash" compact="compact"><li>Let u_f represent the maximum distance threshold</li><li>If all distances, d₁, d₂, ..., d_a, are greater than u_f, the classification result is <i>Unknown</i></li><li>Else, determine the value of d_min, the minimum value of d₁, d₂, ..., d_a</li><li>Let w_f represent the low discrimination threshold factor</li><li>If more than one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_f), the classification result is Low Discrimination between the organism families having distances less than (d_min ∗ w_f)</li><li>If only one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_q), the classification result is the corresponding family.</li></ul>

0267Step 5118: Pooling gram and all families classification interpretations for final gram classification result.

0268If the Gram classification is a single choice and the all families classification is a single choice, the pooled classification result is the indicated Gram class if the family classification falls under the taxonomic hierarchy of the Gram class.

0269If the Gram classification is a single choice and the all families classification is a single choice, the pooled classification result is <i>Unknown</i> if the family classification does not fall under the taxonomic hierarchy of the Gram class.

0270If the Gram classification is a single choice and the all families classification is a low discrimination, the pooled classification is the indicated Gram class if the family associated with the shortest distance falls under the taxonomic hierarchy of the Gram class.

0271If the Gram classification is a single choice and the all families classification is a low discrimination, the pooled classification is <i>Unknown</i> if the family associated with the shortest distance does not fall under the taxonomic hierarchy of the Gram class.

0272If the Gram classification is a low discrimination and the all families classification is a single choice, the pooled classification result is the Gram class that corresponds to the Gram class under which the family resides on the taxonomic hierarchy.

0273If the Gram classification is a low discrimination and the all families classification is a single choice, the pooled classification result is <i>Unknown</i> if none of the Gram classes correspond to the Gram class under which the family resides on the taxonomic hierarchy.

0274If the Gram classification and the all families classification are both <i>Unknown,</i> the pooled classification result is <i>Unknown.</i>

0275The processing then proceeds to step 5120, Gram Family Classification, a second level of classification. This step consists of sub-steps 5122, 5124 and 5126.

Step 5122: Gram family classification distance calculation.

0276Using the 1^st derivative estimates for a predefined set of excitation / emission pair that are specific to the Gram classification result, calculate the distance, <maths id="math0003" num=""><math display="block"><msub><mi mathvariant="normal">d</mi><mi>a</mi></msub><mo>=</mo><msup><mfenced open="[" close="]" separators=""><msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced><mi mathvariant="normal">t</mi></msup><msup><mi mathvariant="normal">Σ</mi><mrow><mo>−</mo><mn>1</mn></mrow></msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced></mfenced><mn>½</mn></msup></math><img file="EP2430461B2_D0003.tif" /></maths> for each organism family defined in the model, where <ul id="ul0010" list-style="dash" compact="compact"><li><i>a</i> = 1, 2, ..., k, represents the number of organism families defined in the model</li><li>∑<i>^-1</i> represents the inverse of the covariance matrix for the predefined set of excitation / emission pairs (same remark as before regarding the pairs)</li><li><i>m</i> represents the vector of calculated values of the 1^st derivative, <i>m_ij</i>, for each excitation / emission pair <i>i, j</i></li><li><i>m_a</i> represent the vector of mean values <i>m_a(ij)</i> from a distribution for each class <i>a</i> at excitation / emission pair <i>i, j</i></li><li><i>t</i> represent the transpose of the vector</li><li><i>(m</i> - <i>m_a)</i> represent the vector of differences <i>m_ij</i> - <i>m_a(ij)</i> for each excitation / emission pair <i>i</i>, <i>j</i></li></ul>

0277Step 5124: Gram Family Classification Interpretation Let u_t represent the maximum distance threshold If all distances, d₁, d₂, ..., d_a, are greater than u_t, the classification result is <i>Unknown</i> Else, determine the value of d_min, the minimum value of d₁, d₂, ..., d_a Let w_t represent the low discrimination threshold factor If more than one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_t), the classification result is Low Discrimination between the organism families having distances less than (d_min ∗ w_t) If only one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_t), the classification result is the corresponding family.

Step 5126 Gram Family Classification Result.

0278If the Gram family classification result is <i>Unknown,</i> the test organism classification is finalized at the Gram level.

0279If the Gram family classification result is Low Discrimination, the test organism classification is finalized as the Gram and families included in the low discrimination.

0280If the Gram family classification result a single family, the IF data from the test organism are further analyzed to determine if a species level identification can be determined.

0281Step 5128 Gram family Species Classification. The processing instructions proceed to a gram family species classification level, consisting of substeps 5130, 5132, and 5134.

Step 5130 Gram family species classification distance calculation.

0282Using the 1^st derivative estimates for a predefined set of excitation / emission pair that are specific to the Gram family classification result, calculate the distance, <maths id="math0004" num=""><math display="block"><msub><mi mathvariant="normal">d</mi><mi>a</mi></msub><mo>=</mo><msup><mfenced open="[" close="]" separators=""><msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced><mi mathvariant="normal">t</mi></msup><msup><mi mathvariant="normal">Σ</mi><mrow><mo>−</mo><mn>1</mn></mrow></msup><mfenced separators=""><mi>m</mi><mo>−</mo><msub><mi>m</mi><mi>a</mi></msub></mfenced></mfenced><mn>½</mn></msup></math><img file="EP2430461B2_D0004.tif" /></maths> for each organism species defined in the model, where <ul id="ul0011" list-style="dash" compact="compact"><li><i>a</i> = 1, 2, ..., k, represents the number of organism species defined in the model</li><li>Σ^-<i>1</i> represents the inverse of the covariance matrix for the predefined set of excitation / emission pairs (same remark as before)</li><li><i>m</i> represents the vector of calculated values of the 1^st derivative, <i>m_ij</i>, for each excitation / emission pair <i>i</i>, <i>j</i></li><li><i>m_a</i> represent the vector of mean values <i>m_a(ij)</i> from a distribution for each class <i>a</i> at excitation / emission pair <i>i</i>, <i>j</i></li><li><i>t</i> represent the transpose of the vector</li><li><i>(m - m_a)</i> represent the vector of differences <i>m_ij</i> - <i>m_a(ij)</i> for each excitation / emission pair <i>i, j</i></li></ul>

0283Step 5132 Gram family species classification interpretation. <ul id="ul0012" list-style="dash" compact="compact"><li>Let u_s represent the maximum distance threshold.</li><li>If all distances, d₁, d₂, ..., d_a, are greater than u_t, the classification result is <i>Unknown.</i></li><li>Else, determine the value of d_min, the minimum value of d₁, d₂, ..., d_a.</li><li>Let w_s represent the low discrimination threshold factor.</li><li>If more than one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_s), the classification result is Low Discrimination between the organism species having distances less than (d_min ∗ w_s)</li><li>If only one distance, d₁, d₂, ..., d_a, is less than (d_min ∗ w_t), the classification result is the corresponding species.</li></ul>

0284Step 5134 Gram family species classification result.

0285If the Gram family species classification result is <i>Unknown,</i> the test organism classification is finalized at the Gram and family level.

0286If the Gram family species classification result is Low Discrimination, the test organism classification is finalized as the Gram, family, and species included in the low discrimination.

0287If the Gram family species classification result a single species, the test organism classification is finalized at the Gram, family, and species level.

0288At step 5136, the results determined at steps 5134, 5118, and 5126 are returned and reported to the user, e.g., on a user interface for the identification instrument, transmitted to an attached workstation, returned to another software module, or otherwise generated for the user.

0289In regards to organism identification (steps 5134, 5118 and 5126), discrimination between species is possible only if the values of the first derivative (of the natural logarithm transform of the emission value) are unique for each species in the model at some portion of the emission range for at least one excitation wavelength. <figref idref="f0069">Figures 88</figref> and <figref idref="f0044">59</figref> illustrate the discrimination potential between a subset of species for excitation wavelengths 315 nm (<figref idref="f0069">Figure 88</figref>) and 415 nm (<figref idref="f0070">Figure 89</figref>). Referring to <figref idref="f0069">Figure 88</figref>, it is apparent that several of the species can be discriminated from the others based on the first derivative at excitation wavelength 315. The mathematical model uses the first derivative values for emissions where visual differences exist as inputs to discriminate between species. Using selected sections of values across the emission range the following species can be clearly discriminated from the others: <i>E. coli, H. influenzae, P. aeruginosa,</i> and <i>S. pneumoniae.</i> In addition, <i>S. aureus</i> and <i>S. epidermidis</i> can be discriminated from other species but not each other. The sections of values across the emission range at a given excitation wavelength are the predefined pairs in the inverse matrices Σ<i>^-1</i> in the distance calculations in the processing steps described above. These pairs may for example be excitation at 315 nm and the range of emission values indicated by the circles shown in <figref idref="f0069">Figure 88</figref>, i.e., (315/300-450), (315, 485-500), (315/570-580).

0290Referring to <figref idref="f0070">Figure 89</figref>, it is apparent that the emissions at excitation wavelength 415 nm has the ability to discriminate between species. Using selected sections of values across the emission range <i>C. parasilopsis</i> and <i>P. aurginosa</i> can be clearly discriminated from the other species. It is also of interest to note the difference between first derivative values for <i>S. aureus</i> and <i>S. epidermidis</i> that occurs around emission 450 nm. When the information from the selected sections of values across the emission range for wavelengths 315 and 415 (<figref idref="f0069">Figures 88</figref> and <figref idref="f0070">89</figref>) is combined, all of the species in the model can be discriminated from each other at a high rate (> 97% reliability).

IV. Second Embodiment (Figures 57-76)

0291A second embodiment of the identification system 104 will be described in conjunction with <figref idref="f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057">Figures 57-76</figref>. This embodiment is similar to the first embodiment of <figref idref="f0028 f0029 f0030 f0031 f0032 f0033 f0034 f0035 f0036 f0037 f0038 f0039 f0040 f0041">Figures 31-56</figref> in terms of overall function and operation; the main differences are (1) a different construction of the robotic transfer mechanism 1910; (2) a provision for vortexing of the sample and lysis buffer in the sampling device 1902, and (3) inclusion of optional detection features in the rack holding the specimen containers 500 (see <figref idref="f0043">Figure 58</figref>) for detecting microbial growth within the container 500 so that the identification system is intimately combined with a detection system for detecting whether a specimen container is positive for presence of a microbial agent. A few other points of differentiation in the details of the configuration of the second embodiment will also be noted in the following description.

0292However, the second embodiment, like the first embodiment of <figref idref="f0028 f0029 f0030 f0031 f0032 f0033 f0034 f0035 f0036 f0037 f0038 f0039 f0040 f0041">Figures 31-56</figref>, shares the same overall goals and design objectives. That is, the second embodiment of <figref idref="f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057">Figures 57-76</figref> automates the removal of a test sample from a specimen container (preferably soon after a positive determination has been made), automates lysing of non-microorganism cells in the test sample, automates loading of the lysed sample into a disposable separation device, automates separation and concentration of the microbial agent present in the lysed sample in the separation device, and automates interrogation of the microbial agent to identify and/or characterize the microbial agent.

0293The culture bottles/specimen containers 500 are loaded into racks or holding structures of the identification instrument 104 either manually or automatically. In an optional configuration, the specimen containers 500 are tested for the presence or microorganisms by a detection subsystem which is incorporated into the racks. In a manual, prior art method, without automation, a technician would remove a bottle from a separate detection instrument after the bottle is deemed "positive". This could be several hours after the diagnostic determination, especially if the determination is made in the middle of the night or when the lab is understaffed. However, with the automated identification instrument in this embodiment, the steps of automated identification and/or characterization of the microbial agent can proceed immediately, and automatically, after the specimen container is deemed "positive" .

0294In the case of lytic centrifugation and intrinsic fluorescence measurement, features of both of the illustrated embodiments, it may be desirable that the sample be processed for purposes of identification and/or characterization shortly after a positive call by an associated detection instrument. As the bottle is called positive the microorganisms are in an exponential stage of growth. This growth phase is distinguished from the lag phase and death phase which are both before and after, respectively, the exponential phase. Microorganisms in this exponential phase have different physical and genetic expression characteristics than the lag and death phase.

0295By automating this process of identification and/or characterization, the technician is removed from the system. Identification and/or characterization of the microbial agent can occur much more rapidly in the present embodiments as compared to prior approaches.

A. System layout

0296The identification instrument 104 in accordance with a second embodiment is shown in <figref idref="f0042">Figure 57</figref>. The instrument 104 includes a first cassette 1900A containing a plurality of disposable sampling devices 1902 and a second cassette 1900B containing a plurality of disposable separation devices 1904. A rack or holding structure 1906 includes receptacles for holding a multitude of containers 500 containing samples for identification testing. The rack 1906 is shown contained within an insulated incubation enclosure 1812. The enclosure 1812 includes a door 1810 that is opened to expose the bottles 500 and allow venting of the bottles and removal of a test sample via a robotic transfer mechanism 1910, sample removal apparatus 1912, and the sampling device 1902.

0297The robot transfer mechanism 1910 includes a rotating base and movable joints and segments between the joints so as to allow the robotic transfer mechanism 1910 and in particular gripping structures included in the sample removal apparatus or sampling head 1912 to access the various components in the instrument 104. These components include a separation and concentration device (centrifuge 1916), the cassettes 1900A and 1900B, a vortexer 1814 for mixing a lysis buffer and test sample within the sampling device 1902, a read station 1918, and various containers 1802, 1804, 1806 containing different lysis buffers and/or density cushions in the situation where the lysis buffers and density cushions are added to the sampling device or separation device at the time of use. The robotic transfer mechanism 1910 is able to access each of the bottles 500 and optionally grip and hold the bottles 500. Thus, the robotic transfer mechanism 1910 may optionally be the device to automatically load the bottles 500 into the holding structure or rack 1906. Alternatively, the bottles 500 could be loaded into the rack manually via an access door positioned on the opposite side of the enclosure 1812 from the door 1810. See <figref idref="f0058">Figure 79</figref>, door 4902.

0298In the configuration of <figref idref="f0042">Figure 57</figref>, a centrifuge cup holder 1800 holds a small cup-like holder 1801 into which the separation device 1904 is placed (see <figref idref="f0057">Figure 76A</figref>); the combination of the separation device 1904 and cup-like holder 1801 are placed into the centrifuge 1916 for separation and concentration of the microbial agent in the separation device 1904. After centrifugation, the cup-like device 1801 is returned to the cup holder 1800. The sample removal apparatus 1912 grips the separation device and the robotic transfer mechanism places it into the reading/identification module 1918. The concentrated microbial agent in the separation device 1904 is interrogated by the reading/identification module 1918. The reading step may include the features described above, such as measuring intrinsic fluorescence spectra of the sample and, with the aid of a computer, comparison of the measured spectra to a data set containing spectra from known microbial agents and classification using a classification algorithm. After reading, the separation device 1904 is placed into a waste container (see <figref idref="f0028">Figures 31</figref>, <figref idref="f0032">45</figref>, item 1908).

0299<figref idref="f0043">Figure 58</figref> is an illustration of an alternative arrangement for the identification instrument 104. In this embodiment, the walls or panels from the incubation enclosure are removed to show one embodiment of the racks 1906 that hold the bottles 500. The racks 1906 are incorporated into a rotating turret which rotates about a vertical axis. Detection instrumentation for noninvasively detecting whether a bottle is positive is incorporated in the racks 1906. These aspects are described in more detail in co-pending application serial no.___________, attorney docket no. 01145/MBHB 09-271-E, filed on the same date as this application, the content of which is incorporated by reference herein. Accordingly, in this embodiment the racks 1906 and associated detection instrumentation function as an automated detection system 102 for determining the presence of a microbial agent in a specimen container.

0300<figref idref="f0044">Figure 59</figref> is another perspective view of the embodiment of <figref idref="f0042">Figure 57</figref>, showing the centrifuge 1916, vortexer 1814 and sample removal apparatus 1912 included in the robotic transfer mechanism 1910.

0301<figref idref="f0044">Figure 60</figref> shows the cassettes 1900A and 1900B of disposables in more detail. While each cassette is shown holding twenty-five disposable sampling devices 1902 or separation devices 1904, the number or arrangement of the devices 1902 and 1904 within a replaceable cassette 1900 is not important.

B. Robot Transfer Mechanism 1910 and sampling removal apparatus 1912

0302<figref idref="f0045">Figure 61</figref> is a perspective view of the robotic transfer mechanism 1910. The transfer mechanism 1910 is shown in a form of a six-axis robot. The robot includes six rotational joints 1700 indicated by the arrows and segments 1702 between the robot joints that expand or contract linearly in order to extend or contract or otherwise move the position of the sample removal apparatus 1912 placed at the tooling end of the robot arm in three-dimensional space. A rolling diaphragm pump assembly 1710 is fitted to the robot transfer mechanism 1910 to apply vacuum or positive pressure to the sampling device 1902 via a connecting tube 3402 to facilitate venting and sampling the containers 500 as described below. The pneumatic system 1914 (<figref idref="f0028">Figure 31</figref>) provides pneumatic controls for the gripping tooling forming the sample removal apparatus 1912.

0303A six axes robot is chosen to allow for flexibility especially the ability to vent and sample the bottle. A pneumatic gripper 1954, see <figref idref="f0046">Figures 64</figref> and <figref idref="f0047">65</figref>, is placed at the tooling end of the robot on the last rotary joint. Plates attached to the gripper 1954 hold three end effectors; that is, there are three separate gripping components: one 1956 for the sampling device 1902, one 1958 for the separation device 1904 and specimen containers 500, and one (not shown) for a vacuum tube which may be used in future configurations. A connector 1952 is used to attach the free end of the tube 3402 to the fitting 3208 (<figref idref="f0029">Figure 33</figref>) on the proximal end of the sampling device 1902. A pneumatically operated linear slide 1950 is moved forward to advance the connector 1952 to engage with the sampling device 1902 and backward to disengage from the sampling device when the device 1902 is deposited in the waste container.

0304The gripper 1954 and linear slide 1950 are pneumatic driven, with the gripper and linear slide controlled from the same air line (3602 <figref idref="f0047">Figure 66</figref>). Flow control valves (not shown) control the rate movement on the gripper and linear slide. When the sampling device 1902 is to be picked up, the gripping component 1956 is positioned around the sampling device 1902 with the component 1956 open and the linear slide 1950 retracted. An air valve (not shown) is activated to close the gripper 1954 and close the gripping component 1956 and advance the linear slide 1950. Through flow controls, the gripper closes first, grabbing the sampling device 1902. Shortly after, the linear slide 1950 advances and engages the connector (1952 in <figref idref="f0046">Figure 64</figref>) with the sampling device 1902. Tubing 3402 connects the pump assembly 1710 with the connector 1952 in <figref idref="f0046">Figure 64</figref> and sampling device 1902, thereby establishing a connection from the sampling device 1902 to the pump 1710 (<figref idref="f0047">Figure 66</figref>) via the tubing 3402.

C. Sampling device 1902

0305The sampling device 1902 in this embodiment is shown in <figref idref="f0045">Figures 62 and 63</figref>. The operation of the device 1902 for venting and sampling a specimen container 500 is described below in conjunction with <figref idref="f0047">Figures 66</figref> and <figref idref="f0048">67</figref>. The operation of the device 1902 for injecting the sample into the separation device 1904 is described below in conjunction with <figref idref="f0055 f0056 f0057">Figures 73-76</figref>.

0306Referring now to <figref idref="f0045">Figures 62 and 63</figref>, the sampling device 1902 includes a 18-gauge needle 3202 having a rubber sheath 3214. A luer fitting 3212 connects the needle 3202 to a 5 ml syringe body or tube 3200. A 0.2 µm hydrophobic filter 3218 is coupled to the syringe body 3200 with an elastomeric fitting 3210. A port or fitting 3208 receives the tube 3402 (<figref idref="f0029">Figure 34</figref>) which is connected to the rolling diaphragm pump 1710 fitted on the robot transfer mechanism 1910 of <figref idref="f0045">Figure 61</figref>.

0307The sheath 3214 has four functions: 1) sheath the needle 3202 to avoid needle stick injuries, 2) keep needle 3202 sterile, 3) prevent leaking of components out of tube 3200, and 4) act as spring to push back on components during sampling from the specimen container 500 and the injection of the separation device 1904 (see <figref idref="f0056">Figures 74</figref> and <figref idref="f0032">45</figref>). The sheath prevents the needle 3202 from sticking or binding to a septum or stopper fitted on the end of the specimen container 500. As the needle is withdrawn from the septum the rubber sheath pushes against the septum preventing the binding of the needle and septum. Similarly, during injection of the separation device the spring-like compression of the sheath 3214 pushes against the screw cap of the separation device 1904 and prevents the needle for sticking or binding to the cap.

0308The hydrophobic filter 3218 (<figref idref="f0045">Figure 63</figref>) prevents microbes from contaminating the pumping system and tubing. Since this filter is hydrophobic, liquid is prevented from passing to the pump 1710 of <figref idref="f0045">Figure 61</figref>. Another function of the filter besides preventing contamination, is repeatable fluid withdrawal. Once liquid touches the filter 3218 no more air can be evacuated from the tube 3200 since the water blocks the flow of air. Thus, the pump 1710 can continue pumping but the volume of liquid extracted will be a function of the tubing volume and not the precision of the pump.

D. Vacuum pump assembly 1710

0309The vacuum pump assembly 1710 of <figref idref="f0028">Figure 31</figref> is shown isolated in perspective view in <figref idref="f0031">Figure 36</figref>. The pump 1710 contains a rolling diaphragm 1712 connected to a linear actuator 1714. Solenoid valves 1716 and 1718 switch the pump from input to output. During the venting step, in which the bottles 500 are vented to atmosphere using the sampling device 1902, the solenoid valves 1716 and 1718 are actuated to let positive pressure vent through the system (input). Also, during sampling the pump draws in fluid from the bottle 500 into the sampling device 1902. The fluid is ejected (output) to the separator device 1904 (<figref idref="f0055 f0056">Figures 73-74</figref>). For both input and output modes, the linear actuator 1714 continues to operate, moving the rolling diaphragm 1712 back and forth. Check valves (not shown in <figref idref="f0031">Figure 36</figref>) take part in controlling the direction of the fluid.

E. Venting and Sampling

0310The venting and sampling steps are shown in <figref idref="f0048">Figures 67</figref> and <figref idref="f0049">68</figref>. The robot 1910 first picks up one of the sampling devices 1902 from the cassette 1900A. The robot 1910 moves into the position shown in <figref idref="f0048">Figure 67</figref>. The door 1810 is opened. The racks 1816 of <figref idref="f0048">Figure 67</figref> are rotated to an upwards pointing position and venting occurs by means of inserting the needle of the sampling device 1902 into the specimen containers 500. The racks 1816 are then rotated to a downward pointing position shown in <figref idref="f0048">Figure 67</figref> and the pump 1710 operated to draw a small a test sample (e.g., 0.5 to 1.0 ml) from the specimen container 500 into the sampling device 1902. The sampling device 1902 is either pre-loaded with lytic agent or alternatively the lytic agent is added to the sampling device 1902 prior to the venting and sampling steps. In the case where the sampling device is loaded with lytic agent in-situ, the robotic transfer mechanism grasps one of the sampling devices, accesses lytic agent solutions stored in containers 1802, 1804, 1806 etc., see <figref idref="f0042">Figure 57</figref>, and withdraws 1.0 to 2.0 ml of lytic agent into the sampling device 1902 and then proceeds with the venting and sampling steps.

F. Mixing of Lytic agent and Sample in Sampling Device 1902

0311As noted previously, the embodiment of <figref idref="f0024 f0025 f0026 f0027 f0028 f0029 f0030 f0031 f0032 f0033">Figures 27-46</figref> includes features for agitating the sampling device 1902 in order to mix the test sample withdrawn from the specimen container with the lytic agent present in the sampling device 1902, e.g., by means of vortexing.

0312The vortexing will now be described in conjunction with <figref idref="f0044">Figures 59</figref>, and <figref idref="f0050 f0051 f0052 f0053">69-72</figref>, showing the vortexer 1814. A unique feature of this system is a vortex cup 3900 which holds the sampling device 1902. The robotic transfer mechanism 1910 first places the sampling device 1902 in the vortex cup 3900 (see <figref idref="f0050">Figure 69</figref>), releases the sampling device 1902, and then moves upward into the position shown in <figref idref="f0051">Figure 70</figref>. The robot gripper fingers 3450 then closes loosely around the above the hydrophobic filter 3218 (<figref idref="f0045">Figures 62, 63</figref>) of the sampling device 1902. The sampling device 1902 is held loosely in the vortexer cup 3900 so that the vortexer 1814 can be free to agitate the sampling device 1902. If it is held tightly the vortexer 1814 is not free to agitate the sample/lysis buffer mixture which is present in the sampling device 1902. The bottom surface 1957 of the gripper tooling 1956 retains the sampling device 1902 in the vortexer 1814 during vortexing.

0313The vortexer 1814 includes a base 3902 that the cup or holder 3900 is mounted to as via fasteners extending through holes 4202 in the flange 4204 of the holder 3900 as shown in <figref idref="f0052 f0053">Figures 71-72</figref>. The interior channel 4200 of the holder 3900 is sized to fit the sampling device 1902 as shown in <figref idref="f0051">Figures 70</figref> and <figref idref="f0052">71</figref>. The vortexing sufficiently mixes the sample and the lysis buffer with a 5 second cycle at 3000 rpm.

0314In one optional configuration, the vortex cup 3900 include heating elements to maintain the sample in the sampling device 1902 at 37 degrees C. The heating may take the form of a coil resistive heater 3910 shown in <figref idref="f0050">Figure 69A</figref>. The agitation frequency, duration and temperature of the vortex process may change for particular samples and buffers.

G. Injection of mixed sample into separation device 1904

0315It may be desirable to first load the separation device into the centrifuge to pre-spin the lytic buffer and insure no trapped air is present in the capillary tube of the separation device. Also, if the optics system is configured in the centrifuge a quality check (e.g., a pre-read of the separation device before adding lysed sample) can be performed. Quality control checks could include inspection for debris or fibers that may be present in the separation device, scratches to the optic surfaces, or other optic defects. After the vortexer 1814 completes the mixing of the sample and lysis buffer in the sampling device 1902, an approximately 1 ml portion of the mixed sample and lysis solution (lysed sample) is then injected into the disposable separation device 1904. This operation may occur while the separation device 1904 is still contained within the cassette 1900B of <figref idref="f0039 f0040 f0041">Figures 56</figref> and <figref idref="f0048">67</figref>. The mixed sample and lysis buffer is shown as mixture 4302 in <figref idref="f0031">Figure 43A</figref>. (<figref idref="f0055">Figure 73D</figref> shows the rubber sheath 3214 shown partially removed from the needle 3202 but this is only to better illustrate the sheath and the needle; the needle is covered by the sheath during use as shown in <figref idref="f0054">Figures 73B</figref> and <figref idref="f0055">73C</figref>).

0316To accomplish the injection of the sample into the separation device 1902, the robotic transfer mechanism positions the (loaded) sampling device 1902 over one of the separation devices 1904 as shown in <figref idref="f0054">Figure 73A</figref> and then proceeds to lower the sampling device 1902 so that the needle 3202 is forced through both the rubber sheath 3214 and the septum 4300 provided in the cap 2404 of the separation device 1904 so as to place the tip of the needle 3202 into the interior chamber 2602 of the separation device. See <figref idref="f0056">Figures 74, 75</figref> and <figref idref="f0057">76</figref>. This action compresses the rubber sheath 3214 as shown in <figref idref="f0056">Figures 74, 75</figref> and <figref idref="f0057">76</figref>, with the sheath 3214 acting on a spring and applying force to the cap 2404. As shown in <figref idref="f0057">Figure 76</figref>, the roller diaphragm pump 1710 operates to pump air into the sampling device 1902, creating positive pressure in the interior of the sampling device and thereby forcing the test sample/lysis buffer mixture 4302 to be injected via the needle into the separation device 1904 as shown in <figref idref="f0057">Figure 76</figref>. The mixture 4302 is dispensed on top of the 1.0 ml density cushion 2802 already present in the separation device 1904.

H. Transfer of loaded separation device 1904 into centrifuge 1916

0317After loading of the separation device 3202 in this manner, the robotic transfer mechanism 1910 proceeds to transfer the sampling device 1902 to a waste container, and then pick up the loaded separation device 1904 and place it in the cup 1801 held by the cup holder 1800 (<figref idref="f0043">Figure 58</figref>, <figref idref="f0057">Figure 76A-76C</figref>). Then, the combination of the cup 1801 and separation device 1904 is picked up and lifted off the holder 1800 (<figref idref="f0057">Figure 76A</figref>) by the robotic transfer mechanism 1910 and placed in the centrifuge 1916 (<figref idref="f0043">Figure 58</figref>) for separation and concentration of the sample in the separation device 1904.

0318In one possible embodiment, the centrifuge 1916 is not an indexed centrifuge, i.e., it does not come to the exact same position after spinning. The centrifuge lid is open and closed by a pneumatic cylinder. The position of the centrifuge is found by a camera (not shown) on the robot transfer mechanism 1910. A picture of the centrifuge is taken and machine vision software determines the position of the centrifuge so that the separation device 1902 can be correctly placed in the centrifuge. In particular, the camera looks for a fiduciary mark on the rotor and the robot moves to the appropriate position in the centrifuge rotor. The separation device 1904 is inserted into the proper location to maintain balance in the centrifuge 1916.

0319The centrifuge could be configured to just spin one separation device at a time (as in the case of the first embodiment), or multiple devices at a time as shown in <figref idref="f0042 f0043 f0044">Figures 57-59</figref>.

0320The machine vision component (camera) could be eliminated by using an indexed centrifuge rotor. In this configuration, the centrifuge rotor would stop at the same position after centrifugation. This could be accomplished by using a mechanical clutch to engage the rotor and moving it past an optical sensor to the correct position. This method could eliminate complexities (e.g. lighting, complex software algorithms) and costs associated with machine vision, and thus for some implementations may be preferred.

I. Separation and concentration of microbial agent in Separation device 1904

0321The centrifuge operates to spin the separation device 1902 at high revolutions per minute for sufficient time to concentrate the microbiological specimen within the separation device into a pellet or pellet-like mass, as described in conjunction with the first embodiment, e.g., 10,000 g for 2 minutes. During centrifugation the lysed red blood cells separate to the top of the density cushion and the intact microbes form a pellet at the bottom of the 1 mm capillary tube 2604 in the separation device 1902 (see <figref idref="f0054">Figure 73A</figref>). The centrifuge lid is opened using a pneumatic cylinder and the robot removes the separation device 1902 and cup 1801. The position of the capillary tube and holder is determined by machine vision as in the placement step above. The separation device 1902 and cup 1801 are removed as a unit from the centrifuge 1918 and placed on the cup holder 1800 (using pin 1805 as a locating mechanism, see <figref idref="f0057">Figure 76C</figref>), and then the robot 1910 picks up the separation device 1902 and moves it to the reading unit 1918.

J. Reading of concentrated microbial agent in separation device 1904

0322The reading unit 1918 interrogates the concentrated microbial agent forming the pellet within the separation device 1902 in the manner described at length above. The results (characterization and/or identification information for the microbial agent) are output to the user interface of the instrument, a connected workstation, a printer, or other output device depending on the configuration of the instrument.

K. Sterilization of specimen container 500 stopper

0323In some biological applications for the present instrument 104, the specimen container 500 is inoculated with a specimen sample such as human body fluids or other normally-sterile body fluids. This is accomplish by injecting the specimen sample via a needle through a stopper formed at the top of the container 500. There is a chance that the sample may contain biohazardous material. Often a small drop of the specimen sample, such as blood, may be left on the surface of the stopper. It is desirable to sterilize this surface before sampling and processing to avoid contamination of the container 500 with airborne or surface microbes.

0324Several methods could be developed to sterilize this surface in an automated manner. These include: <ol id="ol0004" compact="compact" ol-style=""><li>1) UV sterilization of the stopper surface. Ultraviolet light is a standard method of sterilizing surfaces. Automation could be accomplished by attaching a UV light source to a second robot or automation mechanism provided in the instrument that would move to the stopper surface for sterilization before venting the bottle or removing a test sample.</li><li>2) Misting the surface with a disinfectant such as isopropyl alcohol or other chemical and then wiping the surface clear. Presently this is the most common manual method of sterilizing inoculation sites. Normally, swabs are soaked in a disinfectant and a technician wipes the surface before inoculating the bottle or removing a sample. Mechanical wiping is necessary in the case of dried blood spots on the surface since a chemical mist may not penetrate through the blood. The misting of the surface can be automated by pressurizing a disinfectant reservoir with air and spraying this onto the surface of the stopper. The mechanical wipe can be accomplished by picking up a swab or fabric wipe and wiping the stopper surface. Other mechanical methods of wiping the surface include a rolling fabric soaked in the disinfectant. Again, these methods could be accomplished by means of a separate robotic mechanism in the instrument 104, or by providing the existing robot transfer mechanism 1910 with additional gripping/wiping/misting/UV sterilization components as the case may be.</li></ol>

L. Other configurations for robotic transfer mechanism 1910

0325While the second embodiment shown in <figref idref="f0042 f0043 f0044">Figures 57-59</figref> uses a six-axes robot for the automation robot transfer mechanism 1910 to accomplish transfer and positioning of components or materials in the instrument, it is but one of a variety of choices that could be made and the scope of the present disclosure is intended to encompass other robotic transfer mechanisms. A multi-axis robot arm was chosen because it is flexible. New automation steps can be easily programmed without requiring major mechanical tooling redesigns. Once the process is established, the robot could be replaced by a simpler and more compact robot, with fewer axes, or a Cartesian (x,y,z) automation system. The Cartesian system would be more inexpensive than the six-axes robot. A Cartesian system is used for example in the first embodiment (see <figref idref="f0030">Figure 35</figref>).

M. Electric actuators

0326A few of the actuators of the second embodiment (and in particular the gripper and slide aspects of the sample removal apparatus 1912) are operated by pneumatics (compressed air). Pneumatic mechanisms are simple to program and design, however they are not amenable to clinical or some laboratory settings where compressed air is not available. These actuators can be replaced by electrical/mechanical systems such as linear drives, stepper and servo motor connected to linear drives and solenoids.

N. Alternative mixing methods

0327In the second embodiment, a vortexer 1814 is used to vigorously mix the sample and lytic buffer. A different mixing method such as sonication or reciprocal mixing could be used in place of vortexing.

O. Other applications for identification system

0328We have described in detail a method and instrument for automatically vent and sample a specimen container, e.g., blood culture bottle. The sample is lysed and centrifuged to process the microbial agent present in the sample for further analysis. The features of the instrument can be applicable to other diagnostic systems and other types of culture bottles. These systems could include molecular biology tests or automated culture bottles for industrial samples. Industrial samples could include sterility testing of drugs or food.

0329In the case of molecular biology tests it may be very important to perform a microbial test during exponential growth of a microorganism. During the exponential growth phase the genetic expression of microbes is different than during the lag phase. In the lag phase, which is prior to the exponential growth phase, microbes are converting their genetic machinery to express proteins to consume the media nutrients which may be different from their previous environment. As the microbes enter exponential phase the genetic expression has become set.

0330An automated detection instrument (102), such as that described here and in our prior provisional application or the BacT/ALERT system, can determine when the microbes begin exponential phase and the automated identification method above can process a sample soon after exponential phase begins. In a manual culture method it would be difficult to determine when exactly the microbes enter into exponential phase since this would entail checking the bottles frequently for turbidity. Should the beginning of the exponential phase be missed by the technician, there is a risk that microbes would pass into death phase as the limited nutrients are consumed. Hence, in preferred embodiments the present identification instrument automatically processes the positive specimen containers soon or immediately after the container is deemed "positive."

0331In some other non-clinical embodiments of the identification system, the lysis step is optional or not preformed. Hence, the provision of a lytic buffer in the sampling device and vortexing the sampling device are not required in every possible configuration of the present inventive instrument.

P. Re-Sampling of Specimen Containers

0332The process of venting, sampling, separation and interrogation described above can be repeated on the same specimen container 500 as needed. In one possible variation, a given specimen container 500 is sampled successively using sampling devices 1902 loaded with different lytic buffers (e.g., loaded in situ from the supply of lytic buffers in the instrument) and loaded into different separation devices 1904 which are then subject to separation and concentration steps and then reading.

0333The instrument 104 may also perform identification and/or characterization testing without first performing the detection step; possibly shortening the time to identification. This mode of operation could be employed when other clinical data are available that are predictive of infection. Patient condition, biomarkers (e.g., PCT) etc. are examples of data that could be predictive of infection. In this mode, specimen containers are loaded into the identification instrument 104 (e.g., using the rack designs of either embodiment), the bottles are incubated in racks provided in the identification instrument, and every bottle is periodically sampled and subject to the separation and concentration step and the interrogation step. If a given sample is not able to be identified or characterized at the first iteration, the specimen container can be re-sampled, e.g., every 30 minutes, until sufficient microbial agent growth has occurred within the specimen container such that the reading step for that subsequent iteration returns an identification and/or characterization result. Incubation of the specimen container occurs prior to and during the sequential sampling of the specimen container.

Q. Coupling to automated detection instrument.

0334In some embodiments, the automated identification instrument 104 of the first and second embodiments is tightly coupled to an automated detection instrument configured to determine whether a specimen container 500 is positive for presence of a microbial agent. This tight coupling preferably provides for automated hand-off of positive specimen containers 500 from a detection instrument to the automated identification instrument 104 as soon as the specimen container is tested "positive."

0335A variety of instrument configurations for achieving such coupling are described in our prior <patcit id="pcit0077" dnum="US61216339A" dnum-type="L"><text>U.S. provisional application serial. 61/216,339 filed May 15, 2009</text></patcit> and above. A few options are shown in <figref idref="f0058">Figures 77 and 78</figref>. In <figref idref="f0058">Figure 77</figref>, an automated detection instrument 102 is linked via conveyer 4702 to the automated identification and/or characterization instrument 104. Bottles arriving at the automated identification and/or characterization instrument 104 are picked up by the robotic transfer mechanism 1910 and loaded into the racks. In <figref idref="f0058">Figure 78</figref>, the bottles are provided to a combined detection and automated identification and characterization instrument (e.g., as set forth above for the second embodiment, see <figref idref="f0043">Figure 58</figref> and the above discussion). In this configuration, the racks holding the incoming specimen containers 500 include detection instrumentation for interrogating colorimetric sensors incorporated in the bottom of the bottles. Further, the combined instrument 102 + 104 is provided with incubation features, such as providing the incubation enclosure 1812 of <figref idref="f0042">Figures 57</figref> and <figref idref="f0048">67</figref>.

0336Still other configurations are possible, as described above in Part 1. <figref idref="f0058">Figure 79</figref> shows an embodiment in which the combined instrument 102 + 104 includes a door 4902 for manual loading of bottles into the racks of the combined detection and identification/characterization instrument.

0337In the embodiments of <figref idref="f0058">Figure 77-79</figref>, a drawer 4702 is provided to provide access to remove waste from the instrument, e.g., specimen containers, sampling devices and separation devices.

0338The physical configuration of the external panels for the instruments of <figref idref="f0058">Figures 77-79</figref> are not particularly important and can vary widely. The instruments include a graphical user interface and display 4704 which can also vary widely.

R. Computer system schematic

0339<figref idref="f0059">Figure 80</figref> is schematic block diagram showing the identification and/or characterization instrument 104 and its associated computer control system. The details shown in <figref idref="f0059">Figure 80</figref> can vary widely and are not particularly important, and therefore are provided here by way of example and not limitation.

0340A computer 4902 running LabVIEW (National Instruments) is connected to two computers: (1) a computer 4904 via a serial connection, and (2) a robot control computer 4906 via an Ethernet connection. The computer 4904 controls the racks 1906 and associated detection subsystem for detecting whether bottles are positive, controls the stepper motors which agitates (oscillates) the rack 1906 to provide agitation during incubation via a motion controller 4908. A stepper motor (not shown) allows for the rack to be precisely put in position for venting and sampling by the robot transfer mechanism 1910.

0341The LabVIEW 4902 computer queries the computer 4904 for positive bottles. The computer 4904 computer replies through the serial connection and the bottle ID, time of positive and bottle position are parsed by the LabVIEW computer 4902. The bottle position is sent to the robot controller 4906 which opens the door to the racks (<figref idref="f0023 f0024">Figure 27</figref>, 1810) through a digital signal to a relay controlling pneumatic cylinders connected to the door. The robot 1910 acquires a sampling device 1902 and vents the bottle and samples as described above.

0342A digital signal from the robot controller 4906 is sent to relays to open and close the lid of the centrifuge 1916, start the centrifuge 1916 and control the vortexer 1816. Motion control of the linear actuator on the rolling diaphragm pump is controlled by the LabVIEW computer 4902 via a motion controller 4908.

0343Interrogation measurements (e.g., intrinsic fluorescence and/or diffuse reflectance measurements) captured by the identification module 1918 are sent to the LabVIEW computer 4902. The computer 4902 compares the measured spectra with stored reference spectra from known samples to identify and/or characterize the microbial agent in the sample as described above. To do this comparison, the computer 4902 includes a memory (e.g., hard disk) containing the reference spectra data and machine-readable code storing software instructions to perform the comparison, e.g., the algorithms described previously. The computer 4902 includes a conventional central processing unit which operates on the acquired data and stored reference data using the algorithm(s) to generate a result for the sample under test and provides a report e.g., via a user interface on the instrument or attached peripherals 4910. The computer 4902 can communicate over an Internet Protocol network 4914 with other remotely located computers 4912, e.g., to share identification and/or characterization results, store the results in a remote database, or interface to other laboratory information systems.

S. Combination of separation and sampling devices into a single disposable device.

0344As described previously, the identification and/or characterization instrument 104 includes a sample removal apparatus 1912 which holds or grasps a disposable sampling device 1902. Together, they operate to remove a portion of the biological sample in the positive detection container 500 and add the portion to a separation device 1904. The functions of separation and sampling could be performed in a single disposable device.

0345Referring to <figref idref="f0071 f0072">Figures 90-94</figref>, a separation device 6000 includes a body 6002, generally in the shape of a block, a top plate 6004 and a base plate 6006. The body contains an optical window used for intrinsic fluorescence measurements; the material forming the window optically clear and non-fluorescing. In general, the body 6002 can be molded or otherwise formed from any known plastic material known in the art. As shown in <figref idref="f0045 f0046">Figures 62-64</figref>, the body 6002 of the separation device 6000 encloses a lytic chamber 6020, a venting channel 6030, a fluid transfer channel 6034 and a separation chamber 6040. The lytic chamber 6020 and separation chamber 6040 are orientated along two parallel and adjacent vertical axes 6022, 6042, defined in the body 6002, each chamber having top and bottom terminal ends. The venting channel 6030 provides a first fluid communication channel connecting the bottom end of the lytic chamber to a vent or pump port 6018 in the top plate 6004. As shown in <figref idref="f0072">Figures 93-94</figref>, the first fluid communication channel further comprises a venting fluid flow groove 6032 contained in the upper surface 6034 of the body 6002 and providing fluid communication between the lytic chamber 6020 and the venting channel 6030. The fluid transfer channel 6036 provides a second fluid communication channel connecting the bottom end of the lytic chamber 6020 to the top end of the separation chamber 6040 for transferring a lytic buffer and sample from the lytic chamber 6020 to the separation chamber 6040. As shown in <figref idref="f0072">Figures 93</figref> and <figref idref="f0073">95</figref>, the second fluid communication channel further comprises a venting fluid flow groove 6038 contained in the upper surface 6034 of the body 6002 and providing fluid communication between the lytic chamber 6020 and the separation chamber 6040. The lytic chamber 6020, venting channel 6030 and fluid transfer channel 6036 are open to a bottom surface 6010 of the body 6002 of the device 6000, as shown in <figref idref="f0071">Figure 91</figref>. The bottom surface 6010 of the body 6002 may further comprise a lower fluid flow groove 6024 providing fluid communication between the bottom of the lytic chamber 6020 and the venting channel 6030 and fluid transfer channel 6036 through a valve well 6026 (described further below). The top plate 6004 and base plate 6006 can be attached to the body 6002 by any known means in the art to close of or otherwise seal the chambers 6020, 6040 and channels 6030, 6034. For example, the top plate 6004 and/or base plate 6006 can be affixed to the body by welding or by the use of an adhesive.

0346As shown in <figref idref="f0071">Figure 91</figref>, the separation device 6000 includes a valve 6012 and a valve actuator port 6008 that runs through the top plate 6004. The valve 6012 is contained within a valve well 6026 in the bottom surface 6010 of the body 6002, and is operable between a first position and a second position via an external actuator (not shown). When the valve 6012 is in a first position, a first fluid communication channel is "open" from the bottom of the lytic chamber 6020 through the venting channel 6030 to the vent or pump port 6018. This open first fluid communication channel is operable to vent excess pressure from the device 6000 or to provide a vacuum to the lytic chamber 6020 through the use of a pump (not shown). When the valve 6012 is in a second position, a second fluid communication channel is "open" from the bottom of the lytic chamber 6020 through the fluid transfer channel 6036 to the separation chamber 6040. This open second fluid communication channel is operable for transferring the lytic buffer and sample from the lytic chamber 6020 to the separation chamber 6040. As shown in <figref idref="f0072">Figure 92</figref>, the vent or pump port 6018 and sample entry port 6016 comprise open channels through the top plate 6004. In one possible embodiment, the sample entry port 6016 further comprises a pierceable septum (not shown). In another embodiment, a syringe needle (not shown) can be attached or affixed to the sample entry port 6016, thereby allowing the lytic and separation device to operate as the sampling device for directly obtaining a sample from a specimen container 500.

0347As shown in <figref idref="f0072">Figure 93</figref>, the separation chamber 6040 may further comprise an upper reservoir, a middle tapered section and a lower capillary tube 6048 all arranged around a central vertical axis. As shown, the middle tapered section connects the wider diameter upper reservoir and the smaller diameter capillary tube 6048. In one embodiment, the bottom wall of the capillary tube 6048 is made of an optically transparent material for facilitating optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6048. In another embodiment, the separation device 6000 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6048. As shown, the bottom wall opposite the capillary tube 6048 may be of a reduced thickness to facilitate optical interrogation as indicated in <figref idref="f0072">Figure 92</figref>. In yet another embodiment, optical interrogation can occur from the side of the device 6000. In accordance with this embodiment, the block will comprise a notch section 6010 and a reduced thickness side wall juxtaposed the capillary tube 6048. In accordance with this embodiment, the separation device 6000 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6048.

0348In operation, the lytic chamber 6020 can be loaded with a lysis buffer and a sample taken from a positive culture container. For example, a sampling device 1902, as described elsewhere herein, can be used to deposit separately or in combination a lysis buffer and a sample from a positive culture container into the lytic chamber 6020. In another embodiment, the lysis buffer can be added to the lytic chamber 6020 of the separation device 6000 within the characterization/identification subsystem. For example, the sampling device 1902 can be used to obtain an aliquot of lysis buffer (e.g., from a lysis buffer reservoir) that can be subsequently deposited into the lytic chamber 6020 through the sample entry port 6016 (e.g., a pierceable septum) in the body 6002. Next, the sampling device 1902 can be used to obtain a sample from a positive specimen container 500 and deposit that sample into the lytic chamber 6020 through the lytic chamber port 6016. The lysis buffer and sample are then mixed within the lytic chamber 6020, e.g., by agitation and/or vortexing of the sampling device 6000. The selective lysis step is allowed to proceed for a sufficient time to allow the lysis reaction to be substantially completed (e.g., from 1 to 5 minutes). This selective lysis step selectively lyses undesired cells (i.e., non-microorganism cells) that may be present in the sample, e.g., blood cells and/or tissue cells. In another embodiment, the lytic chamber 6020 can be pre-loaded with a lysis buffer and the sample loaded to the lytic chamber prior to agitation and/or vortexing. In one embodiment, the sampling device 6000 can optionally be incubated to allow the selective lysis step to proceed more quickly.

0349After the lysis step, the lysed sample and lysis buffer can be transferred to the separation chamber 6040 through the a fluid flow channel 6030 for the separation of any microorganisms over a pre-loaded a density cushion, as described herein. The valve 6012 is pressed down externally by a mechanical actuator (not shown), thereby opening the fluid flow channel 6030 between the lytic chamber 6020 and the separation chamber 6040. A pump above the separation chamber 6040 draws the mixture through the fluid flow channel 6030 to the top of the separation chamber 6040. In one embodiment, by holding the separation device 6000 at an angle, the fluid can flow gently down the interior wall of the separation chamber 6040 and onto the density gradient.

0350The identification/characterization instrument 104 further includes a separation and/or concentration station, optionally in the form of a centrifuge, which operates on the separation device 6000 so as to separate the microbial agent from other products in the portion of the biological sample and concentrate the microbial agent within the separation device 6000. In one example, the microbial agent is concentrated in the form of a pellet or pellet-like mass in the bottom of the capillary tube 6060 of the separation device 6000.

0351The identification/characterization instrument further includes a identification and/or characterization module or read station (see, e.g., <figref idref="f0028">Figure 31</figref>, 1918) which interrogates the concentrated microbial agent to identify and/or characterize the microbial agent.

0352Another embodiment having a stacked chamber design is shown in <figref idref="f0074 f0075 f0076 f0077 f0078">Figures 98-108B</figref>.

0353<figref idref="f0073 f0074">Figures 95-99</figref> illustrate a combined sampling and separation device 6100. As shown in <figref idref="f0073 f0074">Figures 95-96</figref> and <figref idref="f0074">98</figref>, the combined sampling and separation device 6100 includes an upper housing 6102, a lower housing 6104, and a flexible pinch valve 6108 connecting the upper housing 6102 and lower housing 6104. As shown in <figref idref="f0074">Figures 96 and 97</figref>, the upper housing encloses an upper lytic chamber 6120, the lower housing encloses a lower separation chamber 6140, and the flexible pinch valve 6108 defines a fluid transfer channel 6130 therethrough. The upper lytic chamber 6120, fluid transfer channel 6130 and lower separation chamber 6140 can be orientated around a central axis 6122.

0354The combined sampling and separation device 6100 further includes a pair of opposable compression tabs 6110, a valve actuator block 6106 and opposable actuator arms 6118 operable to "open" and "close" the flexible pinch valve 6110. In operation, the valve actuator block 6106 can be moved in a first direction (e.g., towards the compression tabs 6110, as represented by arrow 6107) to "open" the valve 6100. By moving the actuator block 6106 towards the compression tabs 6110 the actuator arms 6118 push up the compression tabs 6110 moving the compression tabs 6110 away from the flexible pinch valve thereby open the valve 6108. In the open position, the fluid flow channel 6130 is opened allowing fluid communication between the upper lytic chamber 6120 and the lower separation chamber 6140 (as shown in <figref idref="f0074">Figure 97</figref>). The valve actuator block 6106 can also be moved in a second direction (e.g., away from the compression tabs 6110, as represented by arrow 6109) to "close" the valve 6108. When the actuator block 6106 is moved away from the compression tabs 6110 the actuator arms 6118 move the pair of opposable compression tabs 6110 to a "closed" position, thereby pinching closed the flexible pinch valve 6108 (as shown in <figref idref="f0074">Figure 99</figref>).

0355As shown in <figref idref="f0073 f0074">Figures 95-96</figref> and <figref idref="f0074">98</figref>, the combined sampling and separation device 6100 also includes a syringe needle 6112 for obtaining a sample from a specimen container, and a vacuum port 6114 for pulling a vacuum within the lytic chamber 6120, thereby assisting with loading of the device 6100. Optionally the syringe may further comprise a sheath (not shown) to protect the syringe needle from damage and/or contamination. Also, as shown in <figref idref="f0073 f0074">Figures 95-96</figref> and <figref idref="f0074">98</figref>, the combined sampling and separation device 6100 includes a vacuum port 6114. The vacuum port will include a gas permeable filter or hydrophobic membrane 6116 that allows gases to pass but prevents contamination. In operation, the vacuum port can be connected to a pump (not shown) that can apply a vacuum to the sampling and separation device 6100 for the uptake of a sample from a positive specimen container.

0356As shown in <figref idref="f0074">Figures 97 and 99</figref>, the separation chamber 6140 includes an upper reservoir 6142, a middle tapered section 6144 and a lower capillary tube 6146 all arranged around axis 6122 below the lytic chamber 6120. As shown, the middle tapered section 6144 connects the wider diameter upper reservoir 6142 and the smaller diameter capillary tube 6146. In one embodiment, the bottom wall 6150 of the capillary tube 6146 is made of an optically transparent material for facilitating optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6146. In another embodiment, the separation device 6100 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6146. As shown, the bottom wall 6150 opposite the capillary tube 6146 may be of a reduced thickness to facilitate optical interrogation as indicated in <figref idref="f0031">Figure 41</figref>.

0357In operation, with the flexible pinch valve 6108 in the closed position, the lytic chamber 6120 can be loaded with a lysis buffer and a sample taken from a positive culture container. In one embodiment, the lysis buffer can be added to the lytic chamber 6120 of the separation device 6100 using the syringe needle 6112. For example, the syringe needle 6112 can be used to obtain an aliquot of lysis buffer (e.g., from a lysis buffer reservoir), depositing the lysis buffer into the lytic chamber 6120. Next, the syringe needle 6112 can be used to obtain a sample from a positive specimen container 500, depositing that sample into the lytic chamber 6120. The lysis buffer and sample are then mixed within the lytic chamber 6120, e.g., by agitation and/or vortexing of the sampling device 6100. The selective lysis step is allowed to proceed for a sufficient time to allow the lysis reaction to be substantially completed (e.g., from 1 to 5 minutes). This selective lysis step selectively lyses undesired cells (i.e., non-microorganism cells) that may be present in the sample, e.g., blood cells and/or tissue cells. In another embodiment, the lytic chamber 6120 can be pre-loaded with a lysis buffer and the sample loaded to the lytic chamber prior to agitation and/or vortexing. In still another embodiment, the sampling device 6100 can optionally be incubated to allow the selective lysis step to proceed more quickly.

0358After the lysis step, the lysed sample and lysis buffer can be transferred to the separation chamber 6140 through the a fluid flow channel 6130 for the separation of any microorganisms over a pre-loaded a density cushion, as described herein. To transfer the lysed sample and lysis buffer to the separation chamber 6140, the pair of opposable compression tabs 6110 are moved to the open position, thereby opening the flexible pinch valve 6108 and allowing fluid communication between the lytic chamber 6120 and the separation chamber 6140 through the fluid flow channel 6130. With the flexible valve 6108 in the open position, the lysed sample and lysis buffer will flow via gravity through the fluid flow channel 6130 and onto the density cushion (not shown) contained in the separation chamber 6140. In one embodiment, by holding the separation device 6100 at an angle, the fluid can flow gently down the interior wall of the separation chamber 6140 and onto the density gradient.

0359The identification/characterization instrument 104 further includes a separation and/or concentration station, optionally in the form of a centrifuge, which operates on the separation device 6100 so as to separate the microbial agent from other products in the portion of the biological sample and concentrate the microbial agent within the separation device 6100. In one example, the microbial agent is concentrated in the form of a pellet or pellet-like mass in the bottom of the capillary tube 6160 of the separation device 6100.

0360The identification/characterization instrument further includes a identification and/or characterization module or read station (see, e.g., <figref idref="f0028">Figure 31</figref>, 1918) which interrogates the concentrated microbial agent to identify and/or characterize the microbial agent as described previously.

0361Another embodiment of the combined sampling and separation device 6300 is shown in <figref idref="f0075 f0076">Figures 100-102</figref>. Like the combined sampling and separation device shown in <figref idref="f0073 f0074">Figures 95-99</figref>, the combined sampling and separation device 6300 includes an upper housing 6302 enclosing a lytic chamber 6320, a lower housing 6104 enclosing a separation chamber 6340, and a flexible pinch valve 6308 defining therethrough a fluid transfer channel 6130.

0362The combined sampling and separation device 6300 further comprises a pair of opposable compression tabs 6310, a valve actuator block 6306 and opposable actuator arms 6318 operable to "open" and "close" the flexible pinch valve 6308. In operation, the valve actuator block 6306 can be moved in a first direction (e.g., towards the compression tabs 6310, as represented by arrow 6307) to "open" the valve 6308. By moving the actuator block 6306 towards the compression tabs 6310 the actuator arms 6318 push up the compression tabs 6310 moving the compression tabs 6310 away from the flexible pinch valve thereby open the valve 6308. In the open position, the fluid flow channel 6330 is opened allowing fluid communication between the upper lytic chamber 6320 and the lower separation chamber 6140 (as shown in <figref idref="f0075">Figure 101</figref>). The valve actuator block 6306 can also be moved in a second direction (e.g., away from the compression tabs 6306) to "close" the valve 6308. When the actuator block 6306 is moved away from the compression tabs 6310 the actuator arms 6318 move the pair of opposable compression tabs 6310 to a "closed" position, thereby pinching closed the flexible pinch valve 6308 (not shown).

0363As shown in <figref idref="f0075 f0076">Figures 100-102</figref>, the combined sampling and separation device 6300 also comprises a syringe needle 6312 for obtaining a sample from a positive specimen container, a valve port 6314 for pulling a vacuum within the lytic chamber 6320, thereby assisting with loading of the device 6300. Optionally the syringe may further comprise a sheath (not shown) to protect the syringe needle from damage and/or contamination. The vacuum port will include a gas permeable filter or hydrophobic membrane 6116 that allows gases to pass but prevents contamination of the environment. The combined sampling and separation device further comprises a vacuum chamber, which is optionally pre-charged with a vacuum and operable connected to the sampling and separation device 6300 via a valve 6360 to apply a vacuum to the sampling and separation device 6300 for the uptake of a sample from a positive specimen container.

0364Referring to <figref idref="f0076">Figure 102</figref>, the valve mechanism 6360 of this embodiment comprises a pump port 6370 that allows a pump (not shown) to operate the plunger 6380 between a vacuum position and a venting position. The valve 6360 further comprises an interior chamber 6374, a vacuum port 6376, and a venting port 6378. In operation, the pump (not shown) can move the plunger to a first position or a vacuum position (as shown in <figref idref="f0076">Figure 104</figref>) thereby opening a fluid communication channel from said valve port 6372, through the interior chamber 6374 and through the vacuum port 6376 to the vacuum chamber 6362. In the first position or vacuum position, the valve 6360 allows a vacuum to be applied to the sampling and separation device 6300, thereby controlling the uptake of a sample from positive specimen container. The plunger 6380 can also be moved to a second position or venting position thereby opening a fluid communication channel from said valve port 6372, through the interior chamber 6374 and through the vacuum port 6378, thereby allowing the sampling and separation device to vent a specimen container prior to the uptake of a sample via the vacuum.

0365As shown in <figref idref="f0075">Figure 101</figref>, the separation chamber 6340 may further comprise an upper reservoir 6342, a middle tapered section 6344 and a lower capillary tube 6346 all arranged around axis 6322 below the lytic chamber 6320. As shown, the middle tapered section 6344 connects the wider diameter upper reservoir 6342 and the smaller diameter capillary tube 6346. In one embodiment, the bottom wall 6350 of the capillary tube 6346 is made of an optically transport material for facilitating optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6346. In another embodiment, the separation device 6300 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6346. As shown, the bottom wall 6350 opposite the capillary tube 6346 may be of a reduced thickness to facilitate optical interrogation as indicated in <figref idref="f0075">Figure 101</figref>.

0366As one of skill in the art would appreciate, the sampling and separation device 6300 of this embodiment operates in a similar manner as the sampling and separation device 6100 of the first embodiment. Accordingly, a detailed description of the operation of this specific embodiment is excluded. After the lysis step has been carried out, the sampling and separation device 6300 of this embodiment can be centrifuged for separation and/or pelleting of any microorganisms contained therein. The sampling and separation device 6300 of this embodiment may be pre-loaded with a lysis buffer and/or a density cushion.

0367Referring now to <figref idref="f0076">Figures 103-104</figref>, a third embodiment of a combined sampling and separation device 6200 is shown. The combined sampling and separation device 6200 includes an upper housing 6202, a lower housing 6204, and a rotary connection 6206 connecting the upper housing 6202 and lower housing 6204. As shown in <figref idref="f0076">Figure 104</figref>, the upper housing encloses an upper lytic chamber 6220, the lower housing encloses a lower separation chamber 6240, and the rotary connection 6206 defines a fluid transfer channel 6130 therethrough. The upper lytic chamber 6220, fluid transfer channel 6230 and lower separation chamber 6240 can be orientated around a central axis 6222, as shown in <figref idref="f0056">Figure 74</figref>.

0368In operation, the rotary connection 6206 can be rotated to an "open" position. In the open position, the fluid flow channel 6230 is opened allowing fluid communication between the upper lytic chamber 6220 and the lower separation chamber 6240 (as shown in <figref idref="f0076">Figure 104</figref>). The rotary connection 6206 can also be rotated to a "closed" position to close the fluid flow channel 6230. As shown in <figref idref="f0076">Figure 104</figref>, the fluid flow channel comprises an upper opening or channel 6232 through the upper portion of the rotary connection 6208 and a lower opening or channel 6234 through the lower portion of the rotary connection 6210. The rotary connection 6206 of this embodiment may further comprise a sealing gasket 6218 between the upper portion of the rotary connection 6208 and the lower portion of the rotary connection 6210, as shown in <figref idref="f0077">Figure 105</figref>, to prevent leaks.

0369As shown in <figref idref="f0076 f0077">Figures 103-105</figref>, the combined sampling and separation device 6200 also comprises a syringe needle 6212 for obtaining a sample from a positive specimen container, and a vacuum port 6214 for pulling a vacuum within the lytic chamber 6220, thereby allowing a sample to be loading into the lytic chamber 6260 of the device 6200. Optionally the syringe may further comprise a sheath (not shown) to protect the syringe needle from damage and/or contamination. The vacuum port 6214 will include a gas permeable filter or hydrophobic membrane 6216 that allows gases to pass but prevents contamination. In operation, the vacuum port 6214 can be connected to a pump (not shown) that can apply a vacuum to the sampling and separation device 6200 for the uptake of a sample from a positive specimen container.

0370As shown in <figref idref="f0076">Figure 104</figref>, the separation chamber 6240 may further comprise an upper reservoir 6242, a middle tapered section 6244 and a lower capillary tube 6246 all arranged around axis 6222 below the lytic chamber 6220. As shown, the middle tapered section 6244 connects the wider diameter upper reservoir 6242 and the smaller diameter capillary tube 6246. In one embodiment, the bottom wall 6250 of the capillary tube 6246 is made of an optically transparent material for facilitating optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6246. In another embodiment, the separation device 6200 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6246. As shown, the bottom wall 6250 opposite the capillary tube 6246 may be of a reduced thickness to facilitate optical interrogation as indicated in <figref idref="f0076">Figure 104</figref>.

0371As one of skill in the art would appreciate, the sampling and separation device 6200 of this embodiment operates in a similar manner as the sampling and separation device 6100 of the first embodiment. Accordingly, a detailed description of the operation of this specific embodiment is excluded. After the lysis step has been carried out, the sampling and separation device 6200 of this embodiment can be centrifuged for separation and/or pelleting of any microorganisms contained therein. The sampling and separation device 6200 of this embodiment may be pre-loaded with a lysis buffer and/or a density cushion.

0372Referring now to <figref idref="f0077 f0078">Figures 106-108B</figref>, another embodiment of a combined sampling and separation device 6400 is shown. The combined sampling and separation device 6400 includes an upper housing 6402, a lower housing 6404, and a rotary valve 6406 connecting the upper housing 6402 and lower housing 6404. As shown in <figref idref="f0078">Figures 107B and 108B</figref>, the upper housing encloses an upper lytic chamber 6420, the lower housing encloses a lower separation chamber 6440, and the rotary valve 6306 defines a fluid transfer channel 6430 therethrough. The upper lytic chamber 6420, fluid transfer channel 6430 and lower separation chamber 6440 can be orientated around a central axis 6422, as shown in <figref idref="f0058">Figures 77B and 78B</figref>.

0373In operation, the rotary valve 6406 can be rotated via a valve handle 6408 to an "open" position 6434 (see <figref idref="f0078">Figure 108B</figref>). In the open position, the fluid flow channel 6430 is opened allowing fluid communication between the upper lytic chamber 6420 and the lower separation chamber 6440 (as shown in <figref idref="f0078">Figure 108B</figref>). The rotary valve 6406 can also be rotated to a "closed" position 6434 (see <figref idref="f0078">Figure 107B</figref>) to close the fluid flow channel 6430.

0374As shown in <figref idref="f0077 f0078">Figures 106-108B</figref>, the combined sampling and separation device 6400 also comprises a syringe needle 6412 for obtaining a sample from a positive specimen container, and a vacuum port 6414 for pulling a vacuum within the lytic chamber 6420, thereby allowing a sample to be loading into the lytic chamber 6460 of the device 6400. Optionally the syringe may further comprise a sheath (not shown) to protect the syringe needle from damage and/or contamination. The vacuum port 6414 will include a gas permeable filter or hydrophobic membrane 6416 that allows gases to pass but prevents contamination. In operation, the vacuum port 6414 can be connected to a pump (not shown) that can apply a vacuum to the sampling and separation device 6400 for the uptake of a sample from a positive specimen container.

0375As shown in <figref idref="f0078">Figures 107B and 108B</figref>, the separation chamber 6440 may further comprise an upper reservoir 6442, a middle tapered section 6444 and a lower capillary tube 6446 all arranged around axis 6422 below the lytic chamber 6420. As shown, the middle tapered section 6444 connects the wider diameter upper reservoir 6442 and the smaller diameter capillary tube 6446. In one embodiment, the bottom wall 6450 of the capillary tube 6446 is made of an optically transparent material for facilitating optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6446. In another embodiment, the separation device 6400 is made of an optically transparent material to facilitate optical interrogation of a concentrated microbial agent (not shown) located at the bottom of the capillary tube 6446. As shown, the bottom wall 6450 opposite the capillary tube 6446 may be of a reduced thickness to facilitate optical interrogation as indicated in <figref idref="f0078">Figures 107B and 108B</figref>.

0376As one of skill in the art would appreciate, the sampling and separation device 6400 of this embodiment operates in a similar manner as the sampling and separation device 6100 of the first embodiment. Accordingly, a detailed description of the operation of this specific embodiment is excluded. After the lysis step has been carried out, the sampling and separation device 6400 of this embodiment can be centrifuged for separation and/or pelleting of any microorganisms contained therein. The sampling and separation device 6400 of this embodiment may be pre-loaded with a lysis buffer and/or a density cushion.

T. Further Advantages and Features

0377A number of further advantages and features are obtained by the systems and methods described herein: <ol id="ol0005" compact="compact" ol-style=""><li>1. The system detects the growth of microorganisms and facilitates sampling of a container once adequate microbial growth occurs so the microorganisms can be isolated, purified and characterized from blood (or other sample) and prepared for use in and tested in an ID, AST, molecular or other system.</li><li>2. The system can provide for: <ul id="ul0013" list-style="dash"><li>Automated loading and unloading</li><li>Automated incubation</li><li>Automated agitation of culture specimen containers to accelerate antibiotic neutralization</li><li>Automated detection system for improved time to detection,</li><li>Sampling of the positive detection container at the time of detection and automatically prepare a purified sample and present the sample to an optical interrogation unit.</li><li>Optional second detection technology for characterization of the purified sample,</li><li>Automated calibration of optical detection system</li><li>Automated waste disposal system</li></ul></li><li>3. Automated clinical Gram, species-level identification antibiotic resistance marker and/or characterization within 15 min of positive bottle detection, with attendant significant clinical benefits</li><li>4. Characterization and/or identification testing only performed on positive specimen containers.</li><li>5. More reliable characterization result (immediate sample during growth acceleration phase)</li><li>6. Characterization during exponential phase cultures is possible, as is characterization during a stationary or stable phase.</li><li>7. Rapid Blood Culture Possibilities: <ul id="ul0014" list-style="dash"><li>Opportunity/benefits for multiple samples of same bottle.</li><li>Incubate 4-8 hrs and then sample (stat mode)</li><li>Septicemia and/or screening negative specimen containers</li></ul></li><li>8. Major workflow improvement <ul id="ul0015" list-style="dash"><li>automate Gram result for blood cultures.</li><li>automated identification and/or characterization</li><li>possible to provide purified sample for AST or molecular testing</li></ul></li><li>9. Supply of disposables to the identification and/or characterization instrument in a cartridge for easy loading</li><li>10. Added disposable cost is only incurred for positive specimen containers (where there is clinical value)</li><li>11. Potential to save cost for negative samples via sensorless bottle.</li><li>12. Only one system for characterization and identification.</li><li>13. Low complexity blood culture detection system.</li><li>14. The identification and/or characterization system could be configured as an external, separate system but the advantage of being able to immediately sample positive specimen containers would be lost. Hence, the preferred embodiments couple the identification and/or characterization instrument to the detection instrument to enable automated transfer of positive specimen containers. The system can operate 24/7 with little or no human involvement.</li><li>15. Potential for complete characterization at time of detection (intrinsic fluorescence spectroscopy, Raman spectroscopy, mass spectroscopy or other technology)</li><li>16. Simplified manufacturing process for culture bottle.</li><li>17. A combined CO2 or other sensor could be included for: <ul id="ul0016" list-style="dash"><li>Compatibility with previous systems,</li><li>Contamination detection during manufacturing, transport or storage,</li><li>Accommodate delayed entry of specimen containers into a incubation/reading system.</li></ul></li><li>18. A memory device (such as RFID) could be included with the system to store: <ul id="ul0017" list-style="dash"><li>Data from an initial read of the bottle at time of sample collection (including time),</li><li>Information from a test (could be used for post characterization),</li><li>Manufacturing information (lot, date, expiration, initial readings, etc),</li><li>Patient and sample information at time acquired at the time of collecting the sample.</li></ul></li><li>19. Conveyer input/output facilitating automation and high capacity installations.</li><li>20. Automated loading/unloading (via robot transfer mechanism or conveyor).</li><li>21. Design of the detection instrument without drawers improves internal system thermal stability by not exposing the incubator area to ambient air.</li><li>22. Automatic moving of specimen containers from one position to another or from one rack to another if a rack fails (fault tolerance).</li><li>23. Video camera with image analysis on the robot transfer mechanism in either the detection instrument and/or the identification/characterization instrument to aid in: <ul id="ul0018" list-style="none" compact="compact"><li>-- location of specimen containers/disposables,</li><li>-- recovering from error conditions,</li><li>-- detecting spills,</li><li>-- for troubleshooting (field service can connect to the camera for remote diagnosis &amp; repair).</li></ul></li><li>24. Expandability: <ol id="ol0006" compact="compact" ol-style=""><li>a) Internal capacity/functionality by adding racks/modules.</li><li>b) External by adding other instruments</li></ol></li><li>25. Measuring volume of blood present in the detection container <ol id="ol0007" compact="compact" ol-style=""><li>a) by weight or optically</li><li>b) or acoustically</li><li>c) or ultrasound scanning</li><li>d) or other method.</li></ol></li><li>26. Automation promotes "Load and Go" operation of the system. Once the specimen containers are supplied to an input conveyer or robotic transfer mechanism, the rest of the operation is automated and the operator can attend to other tasks.</li><li>27. Presenting the bottle at input or output to a fixed point in space for interface to another system.</li><li>28. Automated preplanning before loading and rejecting error specimen containers to a return station.</li><li>29. Verifying authentication of a product to ensure counterfeit specimen containers are not being used. <ul id="ul0019" list-style="none" compact="compact"><li>-- using a specific authentication method</li><li>-- using the internal camera to look for manufacturer logo, label features, etc.</li></ul></li><li>30. Password protection for access to positive specimen containers.</li><li>31. Automated dispensing of negatives into bottle waste.</li><li>32. Safety: <ol id="ol0008" compact="compact" ol-style=""><li>a) Elimination of sharps exposure for venting and sampling specimen containers</li><li>b) Reduction in laboratory personnel to biohazardous materials</li><li>c) Manual/Automated decontamination of disposables and/or system</li><li>d) Automated decontamination of stoppers prior to sampling</li><li>e) Automated venting of specimen containers to eliminate exposure to risk to laboratory personnel handling specimen containers that have high internal pressure due to gas producing organisms.</li></ol></li></ol>

0378- From the foregoing description, it will be appreciated that we have disclosed an automated system for rapid detection of a microbial agent in a sample and identifying and/or characterizing the microbial agent, comprising, in combination: a detection instrument (100/102, <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>) receiving a specimen container 500 containing a sample, the detection instrument including a heated enclosure for incubating the specimen container and a detection unit interrogating the specimen container to detect whether the specimen container is positive for the presence of a microbial agent in the sample; a supply of disposable separation devices (1904, could also be one of the combined sampling and separation devices of <figref idref="f0071 f0072 f0073 f0074 f0075 f0076 f0077 f0078">Figures 90-108</figref>); and an identification/characterization instrument (104, <figref idref="f0028 f0029 f0030 f0031 f0032 f0033 f0034 f0035 f0036 f0037 f0038 f0039 f0040 f0041 f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057 f0058">Figures 31-77</figref>) receiving a specimen container detected positive by the detection instrument, the characterization/identification instrument comprising: (a) a sample removal apparatus (1912, <figref idref="f0028">Figure 31</figref>) coupled to a robotic transfer mechanism and operative to remove a portion of the sample from the specimen container and add the portion to a separation device (1904) obtained from the supply of separation devices; (b) a separation and concentration station (1916, <figref idref="f0028">Figure 31</figref>) operative on the separation device after receiving the portion of the sample so as to separate the microbial agent from other products in the sample and concentrate the microbial agent within the separation device; and (c) an identification and/or characterization module (1918, <figref idref="f0028">Figure 31</figref>) interrogating the concentrated microbial agent to identify and/or characterize the microbial agent, wherein the robotic transfer mechanism moves the separation device from the separation and concentration station to the identification and/or characterization module.

0379In another aspect, we have disclosed a method for rapid identification and/or characterization of a microbial agent present in a sample, the sample loaded into a specimen container, comprising performing the following steps in an automated manner: <ol id="ol0009" compact="compact" ol-style=""><li>(a) incubating the specimen container 500; (b) periodically interrogating the specimen container to determine whether it is positive for presence of a microbial agent within the specimen container; (c) when the specimen container is determined positive, withdrawing a portion of the sample from the specimen container with a sample removal apparatus coupled to a robotic transfer mechanism; (d) introducing the portion of the biological sample into a disposable separation device (1904); (e) lysing components in the portion of the biological sample, either before or after performing step (d); (f) transferring the separation device to a separation and concentration station using the robotic transfer mechanism; (g) separating and concentrating the microbial agent within the separation device; (h) transferring the separation device to an identification and/or characterization module using the robotic transfer mechanism; and (i) analyzing the concentrated microbial agent to identify and/or characterize the microbial agent, wherein steps (a)-(i) are performed automatically within an integrated detection and identification/characterization instrument 104 as described above.</li></ol>

0380In one embodiment the analyzing step (i) comprises the step of performing a spectroscopic analysis of the concentrated microbial agent. In another embodiment the spectroscopic analysis comprise one of (i) intrinsic fluorescence spectroscopy or (ii) Raman spectroscopy.

0381The method may further include step (g)(1) withdrawing the concentrated microbial agent from the separation device and wherein step (i) is performed on the concentrated microbial agent after withdrawal from the separation device.

0382The analyzing step (i) may include at least one of (i) performing a spectroscopic analysis on the concentrated microbial agent, (ii) performing mass spectrometry on the concentrated microbial agent, (iii) performing molecular testing of the concentrated microbial agent and (iv) introducing the concentrated microbial agent into a microbial characterization test device and subjecting the test device to analysis.

0383There is also discussed that steps (a) and (b) are performed in an automated detection instrument (100/102, <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>) and wherein steps (c), (d), (e) and (f) are performed in an automated identification and/or characterization instrument 104 (<figref idref="f0028 f0029 f0030 f0031 f0032 f0033 f0034 f0035 f0036 f0037 f0038 f0039 f0040 f0041 f0042 f0043 f0044 f0045 f0046 f0047 f0048 f0049 f0050 f0051 f0052 f0053 f0054 f0055 f0056 f0057 f0058">Figures 31-77</figref>).

0384In yet another aspect, an automated method for rapid characterization and/or identification of a microbial agent has been disclosed, comprising the steps of: <ol id="ol0010" compact="compact" ol-style=""><li>(a) providing a detection subsystem (100/102) having an entrance location for receiving specimen containers 500 containing samples to be tested, and detection apparatus for detecting when a specimen container has become positive for presence of a microbial agent in a sample within the specimen container; (b) when a specimen container has become positive, automatically moving the specimen container to an identification and/or characterization subsystem remote from the detection subsystem (<figref idref="f0058">Figure 77</figref>); (c) within the characterization and/or identification subsystem, automatically performing the steps of: (1) withdrawing a portion of the sample from the specimen container; (2) dispensing the withdrawn portion of the sample into a disposable separation device; (3) concentrating the microbial agent within the withdrawn portion of the sample within the separation device; and (4) analyzing the concentrated microbial agent to characterize and/or identify the microbial agent.</li></ol>

0385In yet another aspect, an automated method for rapid characterization and/or identification of a microbial agent has been disclosed, comprising the steps of: <ol id="ol0011" compact="compact" ol-style=""><li>(a) receiving a specimen container containing a sample to be tested in a detection instrument (100/102, <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>); (b) detecting when the specimen container has become positive for presence of a microbial agent in the sample; (c) when such detection has occurred, automatically removing a portion of the sample from the specimen container and placing the portion of the sample into a disposable separation device (1904); (d) separating and concentrating the microbial agent in a disposable separation device, and (e) analyzing the concentrated microbial agent to identify and/or characterize the microbial agent.</li></ol>

0386In still another aspect, a sample testing system has been disclosed, comprising, in combination: a detection subsystem (100/102, <figref idref="f0001 f0002 f0003 f0004 f0005 f0006 f0007 f0008 f0009 f0010 f0011 f0012 f0013 f0014 f0015 f0016 f0017 f0018 f0019 f0020 f0021 f0022 f0023 f0024 f0025 f0026 f0027">Figures 1-30</figref>) having an entrance location for receiving specimen containers containing samples to be tested, and detection apparatus for detecting when a specimen container has become positive for presence of a microbial agent in the sample; an identification and/or characterization subsystem receiving a positive specimen container and having modules for automatically characterizing and/or identifying the microbial agent in the positive specimen container; and apparatus for automatically transferring a positive detection container from the detection subsystem to the identification and/or characterization subsystem.

0387The apparatus for automatically transferring can take the form of a conveyor system as shown in <figref idref="f0058">Figure 77</figref>. The automatically transferring can also take the form of a a robotic arm assembly as shown in <figref idref="f0029">Figures 32</figref>, <figref idref="f0030">35</figref> and <figref idref="f0042">57</figref>. In still another embodiment, the conveyor system includes a first conveyor and a second conveyor, and wherein the system comprises two detection subsystems daisy chained and coupled to each other by the first conveyor, and wherein the one of the detection subsystems is coupled to the identification and/or characterization subsystem by the second conveyor, and wherein a positive specimen detected in either the two detection subsystems is moved to the identification and/or characterization subsystem by means of the second conveyor.