CA2138254A1 - Improved optical detection system for apparatus to culture and detect bacteria in human tissue - Google Patents

Abstract

An improved optical system for use in an instrument for culturing and detecting the presence of microorgan-isms in human tissue specimens is dis-closed. The improved optical detec-tion system is designed to reduce un-wanted noise by substantially blocking all light other than light from a sensor positioned on an inside wall of a culture bottle from reaching the photodetector.
A control circuit providing a "lock-in"
detection system designed to reduce un-wanted noise is also disclosed. The de-tection system is capable of rapidly and automatically detecting whether a spec-imen bottle has been inserted into the instrument.

Description

-~ 94/26874 2138 2 5 4 PCT~S94/05392 IMPROVED OPTICAL DETECTION 8Y~TEN
~OR APPARATU~ TO CULT~RE AND
DETECT BACTERIA IN HUMAN TI~8UE

This application is a continuation-in-part of application S.N. 07/887,627, filed May 22, 1992, pending, and is also a continuation-in-part of application S.N.
07/638,481, filed January 4, 1991, also pending, which, in turn, is a continuation-in-part of application S.N.
07,609,278, filed, November 5, 1990, now U.S. Patent No.
5,173,434, all of which prior applications are incorporated herein by reference and made a part hereof.-FIELD OF THE lNV~'~. .ION
This invention relates generally to analytical apparatus for detecting the presence of bacteria in human tissue, and is particularly directed to an improved optical detection system for use in automated apparatus for culturing and detecting viable bacteria in human blood specimens.
BAC~GROUND OF THE INVENTION
Bacteremia -- the prolonged presence of one or more viable bacteria in the blood -- is a serious and life-threatening infection. The most common symptom of 2~ bacteremia is a fever of unknown origin. Accordingly, hospitals routinely perform a large number of tests to determine whether patients exhibiting this symptom have bacteremia. Presently, the only way a definitive diagnosis can be made is by isolating bacteria in the blood by means of a so-called "blood culture." Because bacteremia is life-threatening, positive specimens must W094t26874 -- PCT~S94/05392 2138X~4 be detected as quickly as possible so that the patient can be treated with the correct antibiotics.
Currently, there are several methods of detecting positive blood cultures. The conventional manual method involves inoculating bottles containing a growth medium with blood specimens. The growth medium is formulated to provide nutrients for bacterial growth. The bottles are inspected daily for obvious signs of bacterial growth.
Samples from bottles suspected to be positive are then o further cultured to obtain isolated bacterial colonies which can then be identified. This method is very labor-intensive and costly, since daily inspections and subculturing of suspect bottles are required.
Various attempts have been made to improve the conventional manual method. For example, culture bottles have been made with added attachments containing solid media. The user inverts the bottle each day, thereby inoculating the solid media and enabling growth of isolated bacterial colonies, which can then be identified. Another improved process uses a "growth indicator" which detects the buildup of gases in the headspace of the bottle. A third method is to concentrate organisms in the specimen by centrifugation and then culture the concentrated bacteria on solid media. Despite such improvements, these methods still suffer from the drawback of being highly labor-intensive.
Attempts to automate the process of culturing blood specimens have also been made. Most automated processes rely on the fact that bacteria cultured in a medium including a carbon source, such as glucose, break down this carbon source to form CO2 as part of normal growth and metabolism. Early efforts at automation used culture V094/26874 PCT~S94/05392 ~13~2~

bottles containing radioisotope-labelled media. Blood specimens are inoculated into the bottle. Bacteria, if present in the specimen, metabolize the carbon-containing compounds in the media and give of radioactive-labelled C2 as a waste product. Gas in the headspace of the bottle is sampled by puncturing the seal at the top of the bottle with a needle and removing a portion of the gas. The radioactive C02 can then be detected by conventional radiometry.
0 A number of drawbacks have been reported with such systems. For example, EPO Patent Application No.
85302261.4, published October 16, 1985, states:
"Radioisotope labeled materials are expensive and require special handling during storage, use and disposal.
15 Moreover, although the levels of radioactivity encountered in using such systems are very low, prospective users may be deterred by personal fears of radioactivity." Moreover, some research has suggested that radiometric detection systems are less accurate than other methods and result in more false positive readings.
Second, such systems are "invasive," that is, they require the use of a needle to puncture the bottle seal to obtain gas for testing. Because sample gas must actually be removed from the bottle, fairly complex 25 pneumatic systems are needed to handle the gas and return it to the bottles. Further, if the needles are not properly sterilized, the specimens can be contaminated with bacteria on the needle, raising the potential for "false positive" readings. In addition, because the bottles are sampled and read invasively, automated instruments are generally more complex mechanically, since the bottles must be transported mechanically from W094/26874 PCT~S94/05392 2~38Z5~

an "incubation" station, where the bottles are maintained at the appropriate conditions for bacterial growth, to a "reading" station, where the headspace gas is sampled and read. Most significantly, the need to handle needles for 5 periodic testing is labor-intensive and, because the culture bottles contain blood, increases the risk of - disease transmission due to needle sticks and the like.
EP0 Application No. 83108468.6 (published August 27, 1983) summarizes the relative benefits of noninvasive o sampling over invasive methods:
"there is no possibility of contamination caused by needle or probe penetration of the vial septum;
the design of an automated apparatus is simplified, in that there is no need to provide provisions for a 15 needle-carrying head assembly or other invasive sampling apparatus;
the necessity of replacing flushed head space gas with sterile culture gas is eliminated;
the use of special culture gases is not required;
faster vial sampling is possible, since only vial positioning is involved;
no vertical head motion is necessary;
the cost of culture media raw materials is reduced due to the elimination of any radiolabeled substrate; and all radioisotopes are eliminated, which eliminates the problems of shipping, handling and storing low level radioisotopes."
(See EP0 Patent Application No. 83108468.5, pp. 8-9.) Early attempts to improve automated instruments 30 focused on improving the detection system. Thus, EP0 Application No. 85302261.4 describes a system in which radioisotope labelling has been replaced with direct "094l26874 PCT~S94/05392 2 5 ~ -detection of non-radioactive CO2 in the headspace gas by means of infrared spectroscopy. While this alleviated the problems associated with radiometric detection, the shortcomings of invasive sampling remain. In addition, 5 the use of infrared spectroscopy requires that culture bottles be made of special materials.
EPO Application No. 83108468.8 discloses a system which detects CO2 levels in the headspace gas by taking infrared readings directly through the culture bottle, lo i.e., noninvasively. However, the instrument disclosed is equipped with only a single light source and detector.
This, in turn, requires that the culture bottles be periodically cycled past the detector for readings, thus increasing the mechanical complexity of the instrument 15 and limiting the number of samples the instrument can rapidly process. Finally, problems can occur in calibrating the infra-red spectrometer to the many bottles which must be read.
More recently, improved instruments with non-invasive sampling systems have been developed. In these systems, the culture bottle is incubated and read in the same location within the instrument. Each bottle is held on a rack inside the incubation chamber. The bottles are periodically agitated (to increase the diffusion of CO2 25 and thereby shorten detection time) while being incubated at approximately 35 C.
EPO Patent Application No. 89200554.7, published September 20, 1989, describes the detection system used in such instruments. A colorimetric sensor (pH
indicator) is adhered to the bottom inside surface of each bottle. The sensor turns from green to yellow as the level of CO2 within the media increases. Individual W094/26874 PCT~S94/05392 ~1382~

optical units are provided for each bottle. These optical units include LEDs to illuminate the sensor, photodetectors, and associated electronics and signal conditioning equipment. The instrument periodically 5 "reads" each sensor using reflected light to monitor changes in the transmission of the sensor at a specific wavelength. When a level of CO2 consistent with microbial growth is reached, the instrument alerts the user of a positive blood culture.
lo While these improved systems have alleviated some of the problems of conventional blood culture instruments, several drawbacks still remain. First, these instruments have been equipped with enclosed, "oven-like" incubation chambers. This, in turn, requires that the instrument be 15 fairly large (particularly in height) to accommodate the number of culture bottles typically processed in a hospital laboratory. This is a significant disadvantage in many laboratories, since floor and bench space is typically at a premium. This arrangement is also undesirable from the standpoint of the user, since the topmost bottles may be out-of reach when the instrument is placed on a laboratory bench.
Second, because the detection system is based on changes in the light transmission of the sensor, the 25 light illuminating the sensor is the same wavelength as the light reflected from the sensor. This makes it possible for light which is not indicative of changes in the sensor (e.g., light reflected from the bottom of the glass or plastic culture bottle, as well as other reflective surfaces) to reach the detector. Because the detection system does not discriminate between light reflected from the sensor and such unwanted "noise," the ~094/26874 213 ~ 2 ~ ~ PCT~S94/05392 dynamic range of detection is generally more limited. In addition, it becomes critical to physically isolate the illuminating light source from the detector, placing further design constraints on the configuration of the s optical system.
Accordingly, a need exists for an automated blood culture instrument which is capable of incubating blood specimens under the appropriate conditions, but which has - a compact design, thereby reducing the laboratory floor lo space it occupies and making it more convenient for use by laboratory medical technicians. Further, a need exists for an instrument which uses non-invasive sampling and non-radiometric detection, but which has a highly accurate and sensitive detection system, which does not rely upon measuring changes in light transmission of monochromatic light.
In copending application S.N. 07/887,627, filed May 22, 1992, an improved blood culture instrument, which is designed to fulfill these needs, is disclosed. This instrument includes a unique optical system designed to optically interrogate a sensor located on the inside bottom wall of a blood culture bottle. As noted in copending application S.N. 07/887,627, it is preferred in the practice of the invention to make~use of a sensor made in accordance with the teachings of copending applications S.N. 07/638,481, filed January 4, 1991, and S.N. 07/609,278, filed November 5, l990 (now U.S. Patent No. 5,173,434), both of which are entitled "Measurement of Color Reactions by Monitoring a Change in 30 Fluorescence," are assigned to the assignee of the present application, and are incorporated herein by reference and made a part hereof.

W094/26874 PCT~S94/05392 21382~
, In particular, it is preferred to use a sensor made in accordance with the teachings of copending application S.N. 07/609,278. As disclosed in that application, the sensor preferably comprises a chromophore layer and a s fluorophore layer. The chromophore layer preferably consists of a pH sensitive chromophore encapsulated within a gas permeable, hydrogen-ion impermeable matrix, such as silicone. Positioned atop the the chromophore layer (when the culture bottle is in its upright lo position) is the fluorophore layer. The fluorophore layer preferably consists of a fluorescent dye encapsulated within a water and gas impermeable polymer, such as an acrylic polymer. When the culture bottle is placed within the blood culture instrument, the 15 chromophore layer is situated or sandwiched between the fluorophore layer and an optical unit housed within the instrument. The optical unit is designed to periodically interrogate the fluorescent signal emanating from the fluorescent layer, to determine whether bacterial growth is occurring within the culture bottle.
Although an instrument designed in this manner overcomes many of the drawbacks with conventional systems noted above, further drawbacks were encountered. The most significant problem was encountered in attempting to 2s use a commercial grade culture bottle in place of the specially fabricated bottles typically used in automated blood culture apparatus. Such specially fabricated bottles are made by welding relatively flat pieces of glass together, giving the bottle -- and, in particular, the bottom wall of the bottle to which the sensor is attached -- uniform and consistent optical characteristics. While such specially fabricated bottles --094/26874 PCT~S94/05392 ~13~5~

are desirable from an optical standpoint, they are generally more expensive than commercial grade bottles.
More importantly, because of the way in which they are manufactured, they tend to be somewhat fragile.
5 Naturally, fragility is generally undesirable in this context, since culture bottles contain human tissue samples and bottle breakage could potentially result in disease transmission from infected samples.
For these reasons, it was felt to be desirable to use lo less expensive and sturdier commercial grade bottles instead of the more conventional blood culture bottles.
Unfortunately, because of the way many commercial bottles are made, the bottom wall of the bottle is not substantially flat. Instead, this bottom wall is 15 generally concave on the outside and generally convex on the inside, creating a convex raised area or "mound" on the inside bottom wall. Since this is typically where the sensor is located, difficulties were encountered in the optical detection system. In particular, since the 20 sensor was now positioned a greater distance from the optical detection unit and the curved glass had different optical characteristics, one result was a significant decrease in sensitivity. For two reasons, this made it critical to reduce "noise" in the system. First, it was 25 necessary to maintain an acceptable signal-to-noise ratio so that sensitivity would not be impaired. Second, the increased noise made it difficult to construct relatively simple algorithms to determine whether a specimen bottle is truly "positive;" the noise would have made these algorithms unduly complex.
In attempting to solve these problems, several potential sources of noise were identified. A first W094/26874 PCT~S94/05392 21~2~

source of noise was thought to be light entering from the outside environment and reflecting off various optical surfaces in the instrument and bottle. This noise component seemed to be particularly great during the 5 early stages of bacterial growth. An additional noise component was also encountered. When so-called "hemolytic" organisms -- organisms which break down blood cells -- were cultured in the bottle, a temporary decrease in fluorescent emission was observed after lo initial bacterial growth was detected. Because this phenomenon was observed only in the case of hemolytic organisms, it was felt that the source of this noise component was reflected light interacting with the sample itself. (As a result, this phenomenon was referred to by 15 the inventors as the "blood blip.") This noise component was particularly troublesome, since it occurred during a critical time period for detection of bacterial growth.
In addition to solving the sensitivity problems noted above, it was felt desirable to overcome an additional drawback encountered in automated apparatus for tissue sample and culture. In a number of conventional apparatus, when a bottle is placed in the instrument the user must input information into the sytem computer to alert the system that a bottle has been added in a 25 particular location. In laboratories where a large number of tests are performed, this data entry process can become cumbersome, since the laboratory technician must either (a) maintain a separate list of where bottles were placed and then enter all of the information into the computer at once, or (b) alternate between entering the information and placing bottles in the instrument.
In either event, the process is often time-consuming and '-'094/26874 PCT~S94/05392 ._ ~138254 labor-intensive, and has the potential for increasing operator error.

In view of these additional drawbacks, a need exists for an improved optical detection system which can be 5 used with sturdier and less costly commercial grade blood culture bottles. A further need exists for an optical system which is highly accurate and sensitive and which reduces unwanted optical noise. Finally, a need exists for an optical system which can automatically detect when a bottle is placed in the instrument so that this information need not be manually entered into the system computer.

8UMMARY OF THE l~v~..lON

Accordingly, it is an object of the present invention 15 to provide an improved optical detection system for use in an automated apparatus for culturing and detecting bacteria in human tissue (in particular, blood) which substantially reduces unwanted optical noise and thereby has improved sensitivity.

It is a further object of the present invention to provide an improved optical detection system which is relatively inexpensive and which can be used with sturdier and less expensive commercial grade blood culture bottles.

It is a further object of the present invention to provide an improved optical detection system which is capable of automatically detecting when a bottle is placed within a blood culture instrument, thereby simplifying use of the instrument for laboratory technicians.

W094l26874 PCT~S94/05392 21382Sg ;, These and other objects are accomplished by providing an instrument for detecting the presence of microorganisms in human tissue in a specimen-containing vessel which comprises means for holding one or more s specimen-containing vessels and light emission means.
The light emission means is configured to permit emitted light to impinge upon a sensor positioned on an inside wall of a specimen-containing vessel held in the vessel holding means. Light detection means are also provided lo for converting light energy from the sensor into a detectable signal. Finally, light blocking means are provided for substantially covering all but a selected portion of the sensor which is to be optically interrogated. The light blocking means is designed to substantially prevent light other than light from the sensor from reaching the light detection means.
In another aspect of the invention, a control circuit for use in detecting the presence of microorganisms in tissue is also disclosed. The control circuit increases the sensitivity of the optical detection system and makes it possible for the system to easily and rapidly determine automotacally whether a bottle has been placed into a bottle-receiving opening in the instrument. The control circuit comprises power supply means; light emitting means for receiving power from said power supply means and producing a light emission in response thereto;
modulator means for providing a time-variant signal to said light emitting means causing the latter to replicate said time-variant signal; light responsive means responsive to a fluorophoric response produced by said light emission and producing an electrical response signal; demodulator means clocked to said time-variant - 094/26874 PCT~S94/05392 213825~

signal to selectively apply a first level and a different second level of amplification to said electrical response signal dependent on the value of said time-variant signal to provide a demodulated response signal; integrator means receiving said demodulated response signal and time-averaging this signal to provide an output voltage signal; whereby said demodulator applies an amplification to said response signal which is synchronized with and in phase with said time-variant signal to selectively pass a o portion of said electrical response signal to said integrator, which passed signal portion is characteristic of said time-variant signal.
The foregoing features and advantages of the present invention will be more readily understood upon consideration of the following detailed description, taken in conjunction with the accompanying drawings, in which:
BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a perspective view of an automated blood culture apparatus made in accordance with the present invention;
FIG. 2 is a side view of the apparatus, showing one of the specimen-holding drawers in its open position;
FIG. 3 is a view similar to that of FIG. 2 in 2s somewhat schematic form, with portions of the specimen-holding assembly removed to show the system for heating and circulating air within the specimen-holding drawers;
FIG. 4 is a side view of the specimen-agitating assembly used in one embodiment of the present invention, showing the specimen-containing racks in their lowermost agitation position;

W094/26874 ~ PCT~S94/05392 2 ~g~4 FIG.. 5 is a view similar to that of FIG. 4, showing the specimen-containing racks in their uppermost agitation position;
FIG. 6 is a top view of one of the specimen-5 containing drawers taken along the line 6--6 in FIG. 1;
FIG. 7 is a front view of one of an individual specimen holder;
FIG. 8 is a cross-sectional view taken along the line 7--7 in FIG. 7;
o FIG. 9 is a side view of an alternative bottle-gripping arrangement for retaining culture bottle within the bottle holding racks;
FIG. 10 is a perspective view of an assembly for moving the specimen-holding drawers between their closed 15 and open positions;
FIG. 11 is a perspective view of an assembly for agitating the specimen-containing racks;
FIG. 12 is a dwell chart showing the relative position of the specimen-containing racks during several 20 agitation cycles in graphical form;
.FIG. 13 is a graph of intensity as a function of wavelength, showing schematically the optical properties of the excitation light as well as the light emitted by the fluorescent sensor; and FIG. 14 is a side view of an alternative assembly which may be used to agitate the specimen-containing racks.
FIG. 15A is a view similar to that of FIG. 8, showing an improved optical system and sensor used to detect the growth of microorganisms in patient tissue specimens.

--~94/26874 ~1~ 8 2 ~ 4 PCT~S94/05392 FIG. 15B is an exploded perspective view of the improved optical system, showing a spatial filter which may be used to improve the sensitivity of the system.
FIG. 16 is a schematic diagram of a control circuit 5 which may be used in the practice of the present invention.
FIG. 17 is a graph of voltage as a function of time for various outputs of the control circuit depicted in FIG. 16.
o DETAILED DESCRIPTION
Figs. 1 and 2 show the general arrangement of an instrument 10 made in accordance with the present invention. This Specification describes a preferred form of the invention, in which the instrument is used to lS culture and detect bacteria in human tissue and, in particular, in human blood. However, although the instrument is described as being used for detection of microorganisms or bacteria in blood, it will be understood that the instrument may be used to detect microbial growth in any number of tissues, including urine, cerebral-spinal fluid, synovial fluid, and others.
Fig. 1 illustrates the instrument of the present invention generally. Instrument 10 includes a specimen-handling module 12 under the control of a microcomputer 14, which is preprogrammed to follow certain specimen-handling protocols in accordance with input from the user. A detailed description of the general types of software commands and processing steps which could be - used to program the microcomputer to perform such protocols is attached as an Appendix hereto.
- In the embodiment shown, each specimen-handling module 12 includes a housing 32 and two slide-out drawers W094/26874 ~ 5 4 PCT~S94/0~392 16, 18, each of which includes a plurality of racks 20, 22, 24, 26, 28, 30, which hold the specimen-containing vessels or bottles for processing. In Fig. 1, drawer 16 is shown in its open position, while drawer 18 is shown 5 in its closed position.
As described in greater detail below, each of the - slide-out drawers 16, 18 is equipped with a heating system (see Fig. 3) designed to warm the drawers to the appropriate temperature for bacterial growth and maintain them substantially at that temperature. Each of the drawers 16, 18 is also equipped with a mechanical agitation system (see Figs. 4 and 5) for periodically agitating the bottles. Such agitation is known to shorten the time to detection by causing CO2 generated by 15 bacteria within the bottle to diffuse more rapidly to the fluorescent sensor, which is preferably affixed to the bottom inside of the bottle. Finally, the drawers 16, 18 are also equipped with an optical detection system, including a plurality of optical units (see Figs. 7 and 20 8) which monitor CO2 production by optically interrogating the fluorescent sensors on each of the culture bottles. Optical readings for each bottle are transferred via a data link (not shown) to the microcomputer 14, where it is stored for later retrieval 25 and use.
As best seen in Figs. 1 and 2, in a preferred form a blood culture instrument module includes at least one, and preferably two or more, slide-out drawers 16, 18 slidably received in housing 32 for holding the blood specimen-containing vessels or bottles during processing.
By configuring the instrument in this manner in accordance with the present invention, the instrument has -~94/26874 ~1 3 ~ ~ 5 4 PCT~Sg4/05392 sufficient bottle-holding capacity for hospital laboratory use, while maintaining a compact size and a small "footprint" desirable for most users. This is because the bottles can be held within the instrument for 5 most processing steps, while still keeping them readily available and within easy reach of the laboratory technician upon opening the drawer. The compact size of the instrument made in accordance with the present invention is an important advantage in most settings, o particularly hospitals, since laboratory space is generally limited due to the large number of instruments and pieces of equipment housed within a typical microbiology laboratory.
Referring to Fig. 1, the front face of each drawer 5 includes an information panel/user interface for displaying information relating to the specimens held within that drawer and for enabling the user to control certain functions pertaining to that drawer. (In Fig. 1, the information panel for drawer 16 is designated by the reference numeral 17.) Information which may be displayed on the information panel by, for example, LED
or LCD displays, include the temperature within the drawer, the number of specimen bottles which have been read as "positive," and the number of available positions 2s for additional specimen bottles. Functions which may be controlled by the user may include opening and closing the drawer, as well as disabling an alarm designed to signal, for example, a positive reading within the drawer. However, it will be understood that other types of information may be displayed on the panel and other commands may be likewise be input from the user interface, as desired.

W094/26874 PCT~S94/05392 '~l3~2~ ~ -The system of the present invention is preferably designed so that multiple specimen-handling modules may be interfaced with a single microcomputer. In this way, the specimen-holding capacity of the system may be 5 substantially increased, as desired. The modules are also preferably designed so that they may be stacked one atop another if desired, to minimize the amount of floor space the system occupies.
Referring again to Fig. 1, the drawer 16 is slidably lo received within housing 32. In a preferred arrangement, a pair of integral slide extensions 34a, 34b are rigidly affixed to the drawer 16 by means of screws, bolts or the like at a position adjacent the top of drawer. The slide extensions are slidably received within tracks 36a 36b.
Tracks 36a, 36b are themselves slidably received within receiving guides (not shown) which are rigidly mounted to the inside of housing 32. Conventional ball bearing assemblies (not shown) permit the slide extensions 34a, 34b to slide freely within tracks 36a, 36b, and the tracks 36a, 36b to slide freely within the receiving guides. The slide extensions 34a, 34b, tracks, 36a, 36b, and receiving guides are commercially available in the form of a three-section ball bearing slide which permits the drawer 16 to slide in and out of housing 32. Success has been had with a three-section ball bearing slide Model No. ESBB manufactured by Barnes Engineering Company of Anaheim, California. Preferably, the slides are made of hardened steel which has been electro-plated such that they adequately support the drawers 16, 18 while maintaining their corrosion resistance under the temperature conditions prevailing within the drawers.

094/26874 PCT~S94/05392 ~13825~1 Fig. 10 illustrates the manner in which the bottom of drawer 16 is slidably mounted within the housing. A
single three-part ball bearing slide, positioned to lay flat (i.e., rotated clockwise 90 degrees relative to the slide extensions 34a, 34b of the three-part slides illustrated in Fig. 1) is used to prevent the drawer from "wobbling" from side to side within the housing. The slide extension (not shown), is rigidly attached to the underside of drawer 16 within a longitudinal recess lS0 o which runs substantially the length of the drawer 16.
This extension is received in a track 152, which, in turn, is received within receiving guide 154 mounted to the inside of the drawer housing. As in mounting the top of the drawer, ball bearing assemblies are used to enable the extension to slide freely within the track 152, and the track 152 to slide freely within the receiving guide 154.
Although Figs. 1 and 10 illustrate one method of slidably attaching the drawer to the housing 32 using three-part ball bearing slides, it will be understood that the drawers may be slidably mounted to the housing using any suitable means, such as, by way of example, conventional slides, tongue and groove configurations, and the like.
In a preferred arrangement also illustrated in Fig.
10, means are also provided to move the drawer 16 under power between a first, closed position, in which the drawer and its contents are substantially enclosed within the housing 32, and a second, open position, in which the 30 drawer and its contents are located substantially outside the housing 32. The drawer is moved in response to a command from the user, which can be input, for example, W094/26874 - PCT~S94/05392 2~3~2,5~ ~ -from microcomputer 14 or from the information display/user interface 17 in Fig. 1. As shown in Fig.
10, motor M, under the control of the microcomputer, powers an associated belt drive 156. The belt drive 156, 5 in turn, rotates a screw drive 158 which engages threaded drawer extension 160. The drawer extension 160 is rigidly attached adjacent a lower corner of the drawer 16. Upon actuation of the motor M, the rotating screw drive moves the drawer under power in or out of the o housing, as desired, in the directions of the double-headed arrow. Appropriate flags are used to signal the microcomputer to deactivate the motor M once the drawer 16 reaches its open or closed position.
It will also be understood that other means for 15 mechanically moving the drawer in or out of the housing, such as, by way of example, belt drives, gear assemblies, and the like, may also be used in practicing the present invention.
Referring now to Fig. 2, the drawer 16 also includes means for holding a plurality of specimen-containing vessels. This vessel-holding means may take the form of a plurality of racks 20, 22, 24, 26, 28, 30 which are adapted to hold or retain the specimen bottles during processing. Each rack has a plurality of bottle-25 receiving openings 38 which are sized to accommodatespecimen bottles. As will be described in greater detail below, at the base of each bottle-receiving opening 38 is an optical unit 46 for taking optical readings of a sensor affixed to the bottom inside of the bottle.
Although in Fig. 2 the bottle receiving openings are illustrated as being circular to accommodate a generally cylindrical specimen bottle, it will be understood that ~94/26874 ~ 13 8 2 S ~ PCT~S94/05392 apertures having a variety of shapes (e.g., rectangular, triangular, or polygonal), could also be used in appropriate circumstances. In addition, although the drawer 16 is illustrated with six racks accommodating 10 bottles each, it will be understood that other quantities may also be held within the racks. Indeed, it is preferred that each drawer accommodate as many bottles as possible in order to maximize the capacity of each module.
o When the drawer is in its closed position, the vessel-holding means should be substantially enclosed within, i.e., covered by, the housing. It will be understood that the vessel-holding means need not be completely enclosed within the housing, so long as the vessels are substantially located within the housing, thereby reducing the amount of space the instrument module occupies. Likewise, when the drawer is in its open position, the vessel-holding means should be located substantially outside the housing, i.e., in a position in which the vessels can be readily accessed or removed by the instrument operator.
It will be understood that the racks may be fastened together to form an integrated assembly, as illustrated in the drawings, or may be fabricated as individual units which can be removably attached within the drawer 16. It may be desirable in certain circumstances for individual racks to be removed so that specimen bottles can be inserted offsite, and then the racks can be reinserted into the instrument at a later time. It will be understood that this can be accomplished in any number of ways, including providing a frame within the drawer to which the racks may be removably attached.

W094/26874 PCT~S94/05392 8~

The face of each bottle holding rack is equipped with an LED (light emitting diode) panel 15, which includes an array of LEDs 19, two of which are associated with each bottle receiving opening 38. The LEDs associated with 5 each opening provide the user with information concerning the status of the optical readings for the bottle contained in that opening. For example, a red LED might indicate a bottle testing "positive," while a green LED
might indicate a bottle which has as yet tested o "negative." The panel 15 may take the form of a printed circuit board which includes the array of LEDs for all of the bottle receiving openings in that rack, as well as associated circuitry for transmitting on/off information and power to the LEDs under the control of the lS microcomputer. The panel 15 may then be removably mounted to its rack by means of Velcro~ fasteners or other similar means.
Fig. 7 depicts a portion of one of the bottle-holding racks in greater detail. Adjacent each bottle-receiving aperture is gripping means adapted to removably grip the specimen-containing vessel so that it may be repeatably held at a predefined, substantially fixed depth within the aperture. This depth is predefined and substantially fixed to allow the optical unit to interrogate the sensor affixed to the specimen-containing vessel from a well-defined and repeatable position, thereby ensuring more accurate optical readings when a vessel is removed and then reinserted. The gripping means may comprise one or more flexible arms positioned adjacent the periphery of the aperture. The gripping means may take the form of one or more arms. In Fig. 7, the gripping means includes three outwardly extending fingers 40a, 40b, 40c ~94l26874 PCT~S94/05392 ~13825~

positioned around the periphery of each cylindrical opening 38 in order to repeatably position and support the bottle within the rack. The fingers may be fastened to the base of the rack (shown in Fig. 9) or formed s integrally therewith so that they protrude upwardly adjacent the opening. In one form of the invention, the fingers 40a, 40b, 40c are molded integrally with the base of each rack from a suitable thermoplastic resin, such as an acrylonitrile-butadiene-styrene lABS) resin or an o acetal resin (e.g., Delrin~, a registered trademark of E.I. Du Pont de Nemours & Co.). Preferably, the fingers 40a, 40b, 40c are uniformly spaced at approximately 120 intervals around the periphery of the opening. Each of the fingers 4Oa, 4Ob, 40c includes a recessed portion 41a, 41c (the recessed portion of finger 40b is not visible in Fig. 7) which is shaped to engage an engagement area on the outside surface of a specimen bottle. A flanged end 42a, 42b, 42c on each finger is designed to engage the shoulder of a culture bottle inserted into the aperture 38.
Preferably, the fingers 4Oa, 4Ob, 40c are arranged to form an opening which is smaller than the diameter of the culture bottle. In that case, the fingers 4Oa, 4Ob, 40c should also be capable of flexing or deforming outwardly to admit the bottle and, in cooperation with the flanged ends 42a, 42b, 42c, to engage the shoulder of the culture bottle in a "snap-fittable" mechanical arrangement once the bottle has been inserted to the pre-defined depth within the aperture. Such an arrangement has several advantages. First, it helps to properly position the bottom of the bottle (and, as a result, the sensor affixed to the bottle) securely and repeatably against W094/26874 PCT~S94/05392 the optical unit 46 to ensure accurate and consistent optical readings. Second, such an arrangement preferably gives the instrument operator tactile and/or audible feedback when the bottle is properly seated within the 5 opening, helping to reduce errors in loading and positioning the bottles. In the absence of such tactile feedback, the operator could insert the bottle into the opening to varying degrees, causing inaccuracy and inconsistency in the optical readings.
lo An alternative means of gripping the bottle within the bottle receiving opening is illustrated in Fig. 9, which shows a portion of one of the bottle holding racks.
In this embodiment, the bottle gripping means includes springs 53 formed of a resilient metal, such as spring 15 stainless steel. Again, it is preferred that at least three, and preferably four, springs 53 be provided for each bottle and that they be equally spaced around the opening. However, it will be understood that two or even one spring could be used. The springs 53 are attached to base plate 57 (which, in this embodiment is made from aluminum or another suitable metal) by riveting, welding, or other conventional means. Base plate 57 has a plurality of apertures formed therein so that the sensor (not shown) affixed to the inside of the bottle 120 can be optically interrogated by the optical units 46. Each spring 53 has a crimp 55 formed in one end for gripping the bottle 120. The crimps 55 are shaped to engage a corresponding engagement area taking the form of an indentation or detent 47 in the bottle 120. The springs are flexible and resiliently deformable so that when the bottle 120 is inserted into the bottle receiving opening, the springs 53 are resiliently deformed in an outward V094/26874 21~ 8 2 S ~ PCT~S94/05392 direction to admit the bottle 120. Once the bottle is fully seated at the appropriate depth within its aperture, the springs 52 return substantially to their original position and engage the detent 47 in the bottle 120. This is evident to the operator by the tactile and audible feedback provided when the bottle "snap-fits"
into tight, mechanical engagement with the springs 53.
It will be understood by those skilled in the art that other similar ways of removably holding the bottles 0 within the racks may also be used, such as, by way of example, ball-spring plungers designed to engage a detent in the bottle, a plurality of springs arranged within the bottle receiving opening so as to grip the bottle, a deformable plastic or rubber O-ring, or a cam and lever gripping arrangement. Likewise, the engagement area on the bottle may take any number of shapes, such as a continuous detent around the entire circumference of the bottle (as illustrated in Fig. 8) or a more localized area. In this regard, as noted above, it is important to keep in mind that the purpose of such arrangements is (1) to hold the bottom of the culture bottle securely in a pre-defined position adjacent to, and substantially centered with respect to, the optical unit to help assure greater accuracy and predictability in the optical readings, (2) to provide the operator with some form of tactile and/or audible feedback once the bottle is properly seated within the rack, and (3) to assist the operator in positioning the bottle within the rack in a reproducible and repeatable fashion.
Fig. 9 also illustrates the manner in which the optical units and related circuitry are attached to the base plate 57 of the bottle holding racks. A plurality WOg4/26874 PCT~S94/05392 ~,~3~S 4 26 of PEM fasteners 59 are rigidly affixed to the base plate 57 at spaced intervals along its length. Each PEM
fastener has an annular base 54 and plurality of prongs 56 adjacent its opposite end. A plurality of optical 5 units 46 -- one for each bottle receiving opening -- are attached along the length of a printed circuit board (PCB) 41. The PCB 41 is equipped with the necessary circuitry for providing power to the optical units and for transmitting the optical readings (which, as explained in greater detail below, are converted into a voltage by the optical unit) to the microcomputer for storage and later use. The PCB 41 also has a plurality of holes formed along its length. To attach the PCB 41 to its bottle holding rack, the prongs 56 on the PEM
15 fasteners 59 are inserted into the holes in the PCB 41 until the PCB engages the annular bases 54. The prongs 56 deform inwardly so that they can pass through the apertures in the PCB 41 and then spring back to their original position so that they retain the PCB 41 in 20 engagement with the annular bases 54. In this way, the PCBs 41 are easily assembled to the bottle holding racks, and can easily be removed for repair or replacement.
As best seen in Figs. 1 and 2, the inside of each drawer is preferably equipped with a bar-code reader 162 25 centrally positioned within a V-shaped channel 164, which extends longitudinally across the drawer 16. The channel 164 is sized to accommodate specimen bottles which are to be inserted into one of the bottle receiving openings 38.
Preferably, a bar-code label is placed on the side of each specimen bottle to identify the patient from whom the specimen was taken. It will be understood that many hospitals now employ systems in which detailed - ~o 94,26874 2 i 3 8 2 S ~ PCT~S94/05392 information about a patient is associated with a unique bar-code for that patient. Labels containing that bar-code are then used to track and identify treatments and procedures pertaining to that patient. It is intended that the instrument of the present invention should be capable of interfacing with the hospital bar-code system, if available. Alternatively, bar-code labels could be generated solely for use with the instrument of the present invention to track specimens and identify them as o having come from a particular patient.
When the user wishes to insert a specimen bottle into the drawer, he or she places the area of the specimen bottle bearing the bar-code label in the V-shaped channel 164 and draws the bottle across the bar-code reader 162 to scan the patient information into the microcomputer.
The system automatically detects where the bottle is placed within the drawer so that the patient information can be associated with the optical readings for that bottle. The optical readings and associated patient information are stored for later retrieval and use.
As also seen in Figs. 1 and 2, the interior face of the drawer is equipped with a second user interface/
information panel 166. This user interface enables the user to perform certain additional operations, and provides certain additional information, such as instructions for inserting a new bottle into an available bottle-receiving aperture.
Another significant feature of the present invention is a system for controlling and maintaining the temperature of the specimen bottles while they are being held within the slide-out drawers of the instrument.
Because the optimal temperature for encouraging growth of W094/26874 PCT~S94/05392 3~S~

many bacteria is approximately 35-37 C and, more preferably, close to 35 C, for many blood culture applications it is important to maintain the bottles near or at this temperature so that any bacteria in the s specimen will multiply as rapidly as possible, thereby decreasing the time it takes to detect a positive - culture. Accordingly, the present invention includes means operably associated with the slide-out drawers for (1) warming the interior of the drawer to an elevated lo temperature suitable for encouraging growth of microorganisms, and (2) maintaining the interior of the drawer substantially at or near that elevated temperature, when the drawer is in its closed position.
In a preferred form, such means comprises a forced air convection system which will now be described in detail.
Fig. 3 illustrates the interior of one of the slide-out drawers 16 with the bottle-holding racks removed.
Adjacent the interior front end of the drawer 16 is a forward duct 60 positioned vertically within the drawer 16. The forward duct 60 is substantially hollow and open at side 61, which faces the interior of the drawer 16.
Forward duct 60 is attached at its base to base plate 62, which is positioned transversely to the forward duct 60 adjacent the interior bottom of the drawer 16. Adjacent the interior rear end of the drawer 16 is a vertically positioned rear duct 64, which is open at side 63 facing the interior of the drawer 16 and which is also attached to base plate 62. Preferably, the ducts are formed of punched sheet metal, which is then bent and welded, or by other conventional methods of metal forming. It will be understood, however, that the ducts may be formed of -'094/26874 PCT~S94/05392 21~8254 - other materials, such as molded plastic, and may be formed in a variety of shapes and configurations.
- When the drawer 16 is in its closed position within the specimen-handling module, the upper openings 63, 65 of the vertically extending forward and rear ducts 62, 64 are brought into alignment with corresponding openings in upper duct 66, located within the module in the following manner. Upper duct 66 forms a passageway which is generally in the shape of an inverted U. When the drawer lo 16 is closed, the vertical segments of this inverted U-shaped passageway are brought into alignment with the upper openings 63, 65 of the forward and rear ducts located within the drawer 16, so that air may circulate from this upper passageway into the forward and rear ducts 60, 62.
Located within the upper duct 66 are a blower fan 68 and a heating coil 70. In response to direction from the microcomputer, the fan 68 is energized and forces air in the direction of the arrows in Figure 3. The air passes over the heating coil 70, where it is warmed. The heated air then passes downwardly in the direction of the arrows into the interior of the drawer 16 through the upper opening 65 in the rear duct 64 located within the drawer 16. The rear duct 64 is equipped with a plurality of louvres 72, which are sloped in order to direct and channel the heated air over, around, and across the culture bottles held within the racks. The openings between the louvres 72 coincide generally with the position of the bottle-holding racks. (A representative bottle, illustrated without its holding rack, is identified by reference numeral 76 in Figure 3.) W094/26874 PCT~S94/05392 ~13~2S~ :

As shown in Fig. 3, the louvres also increase in size (and, in particular, width) from the top to the bottom of the rear duct 64. Because the air flow decreases at greater distances from the fan 68, this configuration 5 assists in distributing the heated air in a substantially equal manner to each of the bottle holding racks in the drawer.
After the heated air circulates within the closed drawer, passing over the bottles and thereby warming the o specimens and media contained inside, it passes under the force of fan 68 into the forward duct 60. The air then passes upwardly (in the direction of the leftmost arrows in Figure 3) past a temperature probe 67 which monitors the air temperature. Temperature information is conveyed to the microcomputer, which is programmed to energize the fan 68 and heating coil 70 as needed in order to maintain the temperature of the interior of the drawer at about 35-37 C and, more preferably, at 35 ~2/-1 C, in order to encourage bacterial growth within the specimen bottle.
Although this is the preferred temperature for most microorganisms, it will be understood that the instrument may be designed to maintain the internal temperature in other appropriate temperature ranges. For example, the preferred temperature for culturing many types of fungi 2s is approximately 31 C. In general, the instrument should be designed to maintain a temperature which is optimal for the particular type of microorganism to be detected. It will also be understood that some fluctuation in the temperature of the drawer interior is permissible, as long as the temperature of the culture vessels is kept within acceptable limits for encouraging growth of microorganisms.

~094/26874 ~ 2 5 ~ PCT~S94/05392 To prevent heated air from escaping from the drawers in substantial quantities, thereby permitting the bottles to become unacceptably cool, means are also provided to substantially seal the drawers from excessive air leakage 5 once they are in their fully closed position. This sealing means is illustrated in Figure 6, which is a top view of the specimen-handling module 12 taken along the line 6--6 in Figure 1. It will be seen that the module includes a bulkhead 78. The bulkhead 78 is fabricated of lo aluminum or another suitable material, and may be lined with an insulating material, such as a rubber pad. Each end of the bulkhead 78 has an adjustment extension 80 which is attached to a corresponding support pillar 82 within the module housing by means of set screws 84.
15 Each set screw 84 passes through an elongated slot (not shown) in the extension 80 and into a threaded receiving aperture (not shown) in the corresponding pillar 82. In this way, the bulkhead 78 may be adjusted at each end to move toward or away from the drawer 16 which slides in and out of the drawer receiving area 86.
By simultaneous reference to Figures 1 and 6, the manner in which the bulkhead 78 functions can be seen.
By adjusting the bulkhead 78 so that it is moved inwardly toward the drawer area 86, a seal is created between the 2s faces of the forward and rear ducts 60, 64 and the base plate 62, on the one hand, and the bulkhead 78, on the other hand, when the drawer 16 is moved inwardly into the drawer receiving area 86. Because the bulkhead 78 travels along slots at each end, it can be adjusted to optimize the seal, even when the drawer 16 does not travel precisely in a perpendicular direction into the drawer receiving area 86, or when the front and rear W094/26874 PCT~S94/05392i ~ 1 3 ~ 2 32 ducts are not precisely aligned with the upper duct, due to mounting tolerances and the like.
It will also be understood that the drawer 18 is likewise equipped with a similar sealing arrangement 5 adjacent the left-most side of the drawer in Fig. 1. The result is that a chamber which is substantially leak-proof is created within the interior of the drawers surrounding the bottle racks. In this way, the heat generated by heating coil 70 can be substantially lo confined to the interior of the drawer in which the bottles are held and does not escape from the bottle-holding drawers. It should be noted, however, that the seal need not be completely airtight, as long as the heated air is substantially confined within the interior of the drawer. In this regard, it has been discovered that once the bottles are heated to the appropriate temperature, much of the heat is held within the liquid media inside the bottles. Thus, once the media is heated to the appropriate temperature, some amount of air leakage can be tolerated. Likewise, the drawers may be opened periodically for addition and removal of bottles without undue heat loss. Indeed, in some instances, a small amount of air leakage can help to more rapidly lower the temperature in the drawers when the temperature 2s rises above the appropriate range.
It will be understood that while a preferred heating system utilizes forced air convection to warm the bottles, as described above, other means for warming the drawer interior (and/or directly warming the specimen bottles) may also be used. For example, the warming means could comprise a heating element which warms the bottle holding racks directly. The heat would then rO94/26874 PCT~S94/05392 21382~4 indirectly warm the specimen-holding bottles and the drawer interior. The heating means could also comprise a radiator-type system, in which heated water is passed through conduits within the drawer, thereby warming the 5 specimen bottles and the interior of the drawer indirectly.
The instrument is also equipped with means for periodically and cyclically rocking or agitating the bottles while they are being held within the racks. It o is known that such agitation assists in more rapidly detecting microorganisms in the bottle by ensuring that Co2 generated by the microorganisms diffuses throughout the media and is thereby rapidly brought into contact with the sensor affixed to the bottom of the bottle.
(Referring to Figure 8, the sensor is identified by reference numeral 100.) Referring first to ~igs. 4 and 5, the agitation system will now be described in detail. Figs. 4 and 5 show three of the bottle holding racks 20, 22, 24 during the agitation cycle. The racks 20, 22, 24 are each pivotally attached to a first pair of rack supports 102a, 102b. Taking rack 20 individually, a pivot pin 106 and bearing (not shown) are used to pivotally mount the first racking support 102a to one side of rack 20 at a position 2s adjacent the back side 109 of the rack 20. A second pivot pin and bearing are used to pivotally mount the second racking support 102b to the opposite side of rack 20 in a similar manner. To prevent the racks from accumulating a buildup of static electricity, which could potentially interfere with the circuitry for the optical units, bearings made of an electrically conductive material, such as sintered metal, are preferred. In this W094/26874 PCT~S94/05392 ~13825~

way, the electronic circuitry for the optical units is provided with a path to electrical ground.
Rack 20 is also attached to a pair of drive supports 112a, 112b at a position adjacent to the bottle-receiving face 116 of rack 20. As with the racking supports 102a, 102b, the pivotal mounting of the drive supports 112a, 112b is accomplished by means of pivot pins and bearings.
Each of the other racks 22, 24 is likewise attached to the racking supports 102a, 102b and the drive supports lo 112a, 112b in a similar manner.
By means of a drive mechanism described in detail below, drive support 112b is alternately and cyclically driven in an upward direction (illustrated by the arrows in Figure 5) and a downward direction (illustrated by the arrows in Figure 4), thereby moving the attached racks 20, 22, 24 between a generally horizontal position (shown in Figure 4) and an upwardly inclined position (shown in Figure 5). This rocking motion agitates the bottles and their contents to facilitate diffusion of C02 generated by bacteria throughout the culture bottles and, in particular, to the sensor affixed to the bottom of the bottles.
Referring now to Fig. 11, the agitation drive mechanism is illustrated in detail. Motor M rotates shaft 170, which is supported on bearings 172a, 172b, 172c. Flexible coupling 174 absorbs any shock caused by misalignment of the shaft 170 relative to the motor M. A
circular cam 176 is mounted at the end of shaft 170. Cam follower 178 is rigidly mounted to the cam at a position adjacent the outer circumference of the cam 176. The cam follower 178, in turn, is slidably received within an oblong slot 180 in arm 182. Arm 182 is rigidly attached ~094/26874 213 8 2 5 ll PCT~S94/05392 - to drive support 112b and conveys power thereto. Upon actuation of the motor M, shaft 170, cam 176, and cam follower 178 are caused to rotate. When cam follower 178 reaches the right side of the oblong slot 180 in arm 182, 5 it imparts a downward motion to arm 182 and, thus, to drive support 112b. (The arm 182 displaced in a downward direction is shown in phantom in Fig. 11.) Likewise, when cam follower 178 reaches the left side of the oblong slot 180 in arm 182, it imparts an upward motion to arm o 182 and, thus, to drive support 112b. Continuous rotation of shaft 170 thereby moves the racks i~ the cyclical rocking motion illustrated in Figs. 4 and 5.
Braking means in the form of a conventional brake assembly (not shown) operatively coupled to the vessel-15 holding means (either directly or by acting on the motorM or the shaft 170) is used to stop the cyclical agitation, when desired.
As shown in Fig. 12, an important feature of the present invention is the type of cyclical rocking motion imparted to the arm 182, drive support 112b, and racks 20, 22, 24. Fig. 12 is a dwell chart showing the distance of a point P located on rack 20 from a fixed reference point. The fixed reference-point is chosen as the position of point P when the rack 20 is in its 25 lowermost position. As the shaft 170 rotates, the drive mechanism of the present invention causes the distance of travel of the point P from the fixed reference point to increase and decrease in a substantially sinusoidal fashion.
It will be seen that at positions substantially near the maximum and minimum travel of point P (indicated by brackets in Fig. 12), the slope of the sinusoidal curve W094/26874 PCT~S94/0~392 ~ 2 ~l~ 36 is relatively small. Since the slope of the curve is proportional to the velocity of point P (and, therefore, the velocity of the bottle holding racks), it can be seen that the velocity of the racks near the maximum and s minimum travel points is relatively low.
This has important consequences for the operation of the instrument. Because optical readings must be taken when the racks are at rest and in an inclined position (to ensure that the sensor is completely covered with liquid during optical readings), it is necessary to periodically stop the bottles while they are in the inclined position. Because the velocity of the racks is lowest when they are in the inclined position (i.e., at the maximum travel point), this provides a convenient point at which to brake the rotating shaft (and, thus, the racks) without imparting undue stress to the braking assembly. Likewise, it is also desirable to stop the racks when they are in their lowermost position (i.e., closest to horizontal) to permit the operator to have ready access to the racks for removal and addition of culture bottles. Once again, because the velocity of the racks is also lowest when they are in their lowermost position (i.e., at substantially the minimum distance of travel point), this is another convenient point at which to stop the rotating shaft. It is also desirable to re-start the shaft rotating from these stopping positions, since this minimizes the stress on the motor.
Such an arrangement also has the significant advantage of reducing the cost of the motor and braking means which can be used in the practice of the invention.
In particular, because the distance the racks travel for a given angular movement of the shaft is small at --~094/26874 ~1~ 8 2 ~ ~ PCT~S94/05392 positions near the maximum and minimum distances of travel of the racks, greater leeway in stopping the rotation of the shaft is allowed at these points.
Because the rotation need not be stopped to move exacting s tolerances, relatively inexpensive motors and braking systems may be used, thus reducing the total cost of the instrument.
Fig. 14 illustrates an alternative mechanical arrangement for imparting a substantially sinusoidal lo pattern of motion to the bottle-holding racks. In this arrangement, pivotal arm 190 is used to convey the rotational motion of the cam 176 to the drive support 112b. A first end of the pivotal arm 190 is pivotally mounted at pivot point 192 to the cam 176 at a location 15 near the circumferential periphery of the cam. A second, opposite end of the pivotal arm 190 is pivotally mounted at a pivot point 194 to drive support 112b. Upon rotation of cam 176 in the direction of the arrow in Fig.
14, a sinusoidal pattern of motion is imparted to the drive support 112b and, ultimately, the bottle-holding racks. The position of the pivotal arm 190 after an approximately 180 rotation of the cam 176 is shown in phantom in Fig. 14.) It will also be understood that various other systems for imparting a substantially 2s sinusoidal pattern of motion, such as gear assemblies and the like, could also be used.
Another important aspect of the present invention is the optical system for mechanically sensing changes in the Co2 sensor. As best seen in Fig. 8, the sensor 100 is affixed to the inside of the bottom wall of the culture bottle 120. In a preferred form, the sensor is made in accordance with the disclosures of copending U.S.

W094/26874 PCT~S94/05392 ~,~3~

patent application S.N. 238,710, filed August 31, 1988 and/or copending U.S. patent application S.N. 609,278, filed November 5, 1990, both of which are entitled "Measurement of Color Reactions by Monitoring a Change of 5 Fluorescence," are assigned to the owner of the present application, and which are incorporated herein by reference and made a part hereof.
As disclosed in U.S. patent application S.N. 609,278, the sensor preferably comprises a chromophore layer 122, o which consists of a pH sensitive chromophore encapsulated within a gas permeable, hydrogen-ion impermeable matrix, such as silicone. Adjacent the chromophore layer 122 is the fluorophore layer 124. The fluorophore layer 124 consists of a fluorescent dye encapsulated within a water 15 and gas impermeable polymer, such as an acrylic polymer.
The fluorophore layer 124 is preferably positioned above the chromophore layer 122 when the bottle 120 is in an upright position. When placed within an aperture in the bottle-handling rack (see Fig. 7), the chromophore layer 20 122 is thereby situated or sandwiched between the optical unit 46 and the fluorophore layer 124. In the form illustrated in Fig. 8, the fluorophore layer 124 has a plurality of radial cut-outs 121, which extend from a position near the center of the fluorophore layer 124 to 25 its periphery. (These cut-outs 121 give the fluorophore layer 124 an appearance similar to that of a "starfish"
when viewed from above.) The cut-outs 121 expose more of the surface area of the chromophore layer 122 to the liquid within the bottle, thereby permitting C02 generated by microorganisms within the bottle to diffuse to the chromophore layer 122 more rapidly.

-rO94/26874 PCT~S94/05392 ~13~2~

Figs. 7 and 8 illustrate the optical unit 46 in detail. The unit includes at least one, and preferably more than one, light emission means in the form-of a light source. A plurality of light sources is preferred, s since this helps to ensure excitation light impinges on the area of the bottle where the sensor is located, even when there are variations in the positioning of the sensor on the culture bottle. In Figs. 7 and 8, four light emitting diodes (LEDs) 126 serve as the light o sources. As best seen in Fig. 8, each LED 126 has a plastic lens 127 which defines the cone of light emitted by the LED 126. It will be understood that it is desirable to have as much light as possible directed to the area of the bottle 120 where the sensor 100 is located; the plastic lenses 127 assist in directing the cone of light emitted by the LED to the vicinity of the sensor and in minimizing stray light. Success has been had with LEDs manufactured by Marktech International of Menands, New York, bearing the designation MT 350 AK-UG.
These LEDs have an ultra-bright GaP green light emission and use a T-l 3/4 water clear lens. According to the manufacturer, these LEDs have the following maximum ratings (Ta = 25 C): forward current, 25 mA; reverse voltage, 5 V, power dissipation, 105 mW; peak pulse 2s current, 150 mA; operative temperature range, -50 to approximately 100 C; storage temperature range, -50 to approximately 100 C. According to the manufacturer, these LEDs also have the following ele~Llo optical characteristics (Ta = 25 C): forward voltage, typical (2.2 V), maximum (2.5 V); reverse current, maximum (10 ~A); luminous intensity, minimum (100/200 mod), maximum (200/300 mod); peak wavelength, typical (565 nm); viewing WOg4/26874 PCT~S94/05392 ~ 1 3 8 2 5 4 angle, typical (30); spectral line half-width, typical (30 nm)-The LEDs 126 are positioned around a centrally-located photodetector module 128, which is described in greater detail below. The LEDs 126 are positioned so that they fully illuminate the sensor 100 affixed to the inside bottom of a culture bottle 120 placed in an aperture 38. Preferably, the LEDs are also held within a housing 130, which can be molded of a suitable plastic or lo made by other conventional means.
The operation of the optical system is best understood by reference to Fig. 8. LEDs 126 are selected so that they emit light falling within an emission wavelength range and, preferably, a generally monochromatic light falling within a wavelength range which will excite the fluorophore in the fluorophore layer 124. For example, the commercially available LEDs identified above emit a generally monochromatic light having a peak wavelength of 565 nm and a spectral line half width of about 30 nm. Light having these characteristics is well-suited to excite the fluorophores oxazine 1,7,0-perchlorate and oxazine 4-perchlorate, which are preferred fluorophores in the practice of the present invention.
Light from the LEDs impinges on the specimen bottle (and, after passing through the bottle, on the sensor) and excites the fluorophore encapsulated within the fluorophore layer 124, causing it to fluoresce, i.e., emit radiation as it passes from a higher to a lower electronic state. Light to be detected emanates from the fluorophore within the specimen bottle. This sensor emission light emanating from the sensor has different ~094/26874 PCT~S94/05392 82~

spectral characteristics from the excitation light, i.e., it has a different peak wavelength. Preferred fluorophores emit light at peak wavelengths of approximately 580-650 nm.
Any microorganisms cultured in the media 132 within the bottle 120 produce C02, which diffuses into the gas permeable chromophore layer 122, thereby causing a change in pH within the chromophore layer 122. This pH change, in turn, causes a change in the absorption spectrum of lo the chromophore. Significant growth of microorganisms results in additional production of CO2, which causes a further change in the absorption of the chromophore. As disclosed in copending U.S. patent application S.N.
609,278, the chromophore is preferably selected so that 15 its absorption spectrum overlaps with the excitation and the emission spectrum of the fluorophore in the fluorophore layer 124. In this way, changes in the absorption spectrum of the chromophore -- which are triggered by microbial growth -- will modulate (in a preferred form, attenuate) the excitation light reaching the fluorophore as well as the sensor light emitted from the fluorophore. This attenuation in both the excitation light reaching the fluorophore and the emission light emanating from the fluorophore is measurable and can be 25 monitored by the optical module 128. The result is that the growth of microorganisms within the bottle 120 can be correlated to a measurable attenuation of fluorophore excitation and emission.
A significant feature contributing to the success of the optical detection system of the present invention is the unique construction of the optical detection unit 128. The detection unit 128 includes light detection W094/26874 PCT~S94/05392 ~ 25 ~ 42 means for converting light energy emanating from the sensor within the specimen bottle into a detectable signal. In a preferred form, the light detection means takes the form of a photodetector (not shown), which 5 converts light energy into an electric current. Success has been had with a photodiode made by United Detector Technology of Hawthorn, California, bearing the designation HDT 455. The current generated by the photodetector is transformed into a voltage by means of a conventional transimpedance amplifier. The voltage, which can be correlated to the amount of bacterial growth in the bottle, is then measured by well-known means.
Significantly, the detection unit 128 is also equipped with filter means optically interposed between 15 the LED light sources and the photodetector for preventing substantially all light falling within the wavelength range emitted by the LEDs from reaching the photodetector. The filter means is carefully chosen in order to achieve substantial isolation between the 20 spectrum of the excitation light and the emission spectrum of the fluorophore. This spectral isolation is best understood by reference to Fig. 13, which is a graph showing schematically both the spectrum of the light emitted by the LEDs and the emission spectrum of the 25 fluorophore. It will be seen that the spectrum of the light emitted by the LEDs has a lower peak wavelength than the sensor light emitted by the fluorophore wavelength. However, because both the excitation light and the emission light have a bandwidth, there is some overlap of the spectra. This area of overlap, greatly exaggerated, is represented by the single-hatched area in Fig. 13. The filter means is chosen so that the ~094n6874 PCT~S94/05392 -- ~1382~'1 - photodetector receives a sufficiently strong fluorescent signal, but the amount of overlap between the spectrum of the excitation light and the spectrum of the fluorescence emission light is minimized and, preferably, eliminated 5 altogether. In Fig. 13, only light having a wavelength falling within the cross-hatched region is permitted to reach the photodetector; the filter means prevents all other light from reaching the photodetector. In this way, an area of fluorophore emission is chosen in which o the overlap of excitation light and emission light (represented by the fully shaded region "a" in Fig. 13) is minimal. It is preferred that the amount of such overlap be less than about 20% of the total signal, more preferably, less than about 5%, and still more 15 preferably, between 1 and 2% or less. In general, to achieve substantial spectral isolation, the difference in peak wavelength between the excitation light and the fluorophore emission should be at least about 10-15 nm and, preferably, 25-80 nm or more. It is also preferred 20 that any small amount of overlap be electronically "subtracted" from the optical signal so that only fluorescence emission is measured.
It will be seen that the filter means is selected in order to substantially prevent light having a wavelength 25 other than that of the light emitted by the f luorophore -- including substantially all of the excitation light emitted by the LEDs 126 -- from entering the photodetector. In this way, the detection system is, to as great a degree as possible, substantially optically "blind" to light having a wavelength other than the light emitted by the fluorescing f luorophore, including the excitation light emitted by LEDs 126.

W094/26874 PCT~S94/05392 ~1382~

In a preferred embodiment, the light filter means consists of a longpass filter which prevents light having a wavelength smaller than a particular selected value from entering the photodetector. When the fluorophore 5 chosen for the fluorophore layer 124 is oxazine 1,7,0-perchlorate or oxazine 4-perchlorate, the longpass filter is selected to prevent light having a wavelength of less than about 645 nm from entering the photodetector. In this way, light emitted by the fluorophore is detected by o the photodetector, but light having a wavelength of less than 645 nm (including substantially all of the excitation light emitted by the LEDs 126, which has a peak wavelength of approximately 565 nm) is not. Success has been had with a glass longpass filter manufactured by 15 Schott Glass of Duryea, Pennsylvania, which bears the designation RG 645. This filter can be attached to the commercially available photodiode described above to form an integrated unit having the optical characteristics for use in practicing the present invention.
Such an optical arrangement has significant advantages for use in a detection system for microorganisms. This optical arrangement permits substantially complete optical isolation between the excitation light and the light emitted by the 2s fluorophore, thus significantly reducing background noise. Comparable systems which rely on directly monitoring monochromatic light transmitted by the sensor have significantly more noise because light from the light source can reflect off of other optical surfaces in the instrument (including the bottom of the bottle) and reach the optical system directly. In direct contrast, because the detection system of the present invention is '~094/26874 2 13 ~ 2 ~ 4 PCT~S94/05392 substantially optically "blind" to the excitation light, the fluorophore can be inundated with excitation light, thereby producing an exceptionally strong fluorescence signal, without substantially increasing the noise 5 affecting the detection system. This helps to improve the sensitivity of the system.
It should be pointed out that because an optical unit is provided for each bottle-receiving opening, problems encountered in calibrating a single detection unit are o greatly reduced. This is because each unit is effectively "self-calibrating" in that variables affecting the signal generated can be read before readings are taken and then "subtracted" from the signal as successive readings are taken.
Although a particular optical arrangement has been disclosed herein, it will be understood that other arrangements may be employed, so long as the detector is rendered substantially "blind" to light other than that emitted by the fluorophore. For example, the location and geometry of the exciting light source relative to the photodetector could be changed to prevent substantially all excitation light from reaching the photodetector.
Similarly, other types of optical devices and filters, including interference filters and filters made from materials other than glass, could also be used.
In particular, in adapting the optical system described above to use with commercial grade specimen culture bottles, it was found to be necessary to improve the overall sensitivity of the system even further. This was due to the fact that the bottom wall of a commercial grade bottle is generally convex, so that a sensor placed on the bottom wall is located a greater distance from the W094/26874 PCT~S94105392 C~i38æ5~

optical system than in more conventional bottles, in which the bottom wall is relatively flat. Because the fluorescence signal decreases as the sensor is placed farther away from the detection system, previously 5 acceptable levels of optical "noise" in the system became unacceptable when the preferred commercial grade bottles were used. In addition, when hemolytic organisms were cultured within the bottle, a "blood blip", or sudden decrease in the fluorescence signal, created additional lo noise, thereby further reducing sensitivity.
As best seen in Figs. 15A and l5B, it was unexpectedly discovered that the level of optical noise in the system could be significantly reduced by more completely isolating the detection system and sensor from 15 external sources of light, such as light from the ambient environment and light from the patient sample and culture medium. This reduction in noise permitted the use of sturdier, but less optically consistent and desirable, commercial glass culture bottles. It is believed that such a system may also permit the use of polymeric culture bottles, which are even sturdier and less costly than commercial glass bottles.
Referring now to Fig. 15A, a preferred form of the improved optical system of the present invention is 2s illustrated. It will be seen that the optical unit ~6 is identical to that described above, except that a specially designed spatial filter 200 is interposed between the optical unit 46 and the culture bottle 202.
Note that the bottle 202 illustrated in Fig. 15A has a convex bottom wall 203 and that the sensor 100, being attached to this bottom wall, is therefore positioned '~0 94/26874 ~13 ~ 2 5 4 PCT/US94/05392 somewhat further away from the optical unit 46 than when a conventional culture bottle is used.
The spatial filter 200 has an aperture 204 formed in the center thereof and is preferably made of a light-5 absorbent material, such as a molded, black polymericmaterial. However, it will be understood that other light blocking materials may be used, as long as the spatial filter substantially blocks the passage of light into the optical unit except through the aperture 204.
lo It is preferred that the filter 200 be made of a material which absorbs as much light as possible so that it performs the function of preventing light from external sources from reaching the optical unit 46 and, in particular the photodetector 128. In this way, 15 excitation light emanating from the LEDs 126 is preferably directed only onto the sensor and, still more preferably, on a selected portion of the sensor. As shown in Fig. 15A, the wall 206 which defines the aperture 204 is arcuate or tapered to help concentrate as 20 much of the excitation light as possible onto the sensor.
As described in greater detail below, in addition to focusing the excitation light onto the sensor, the spatial filter 200 also helps to substantially prevent light other than light from the sensor 100 -- such as 25 ambient light and light from the bottle media and sample -- from reaching the optical detection system and, in particular, the photodetector 128.
Referring now to Fig. 15B, the spatial filter 200 is illustrated in greater detail. As noted above, the 30 spatial filter 200 is preferably molded from a light-absorbent polymeric material, such as black Delrin0. In addition, the upper surface of the spatial filter 200 is W094/26874 PCT~S94/05392 ~1~825~

preferably tapered and contoured to generally conform to the shape of the outside surface of the bottom wall of a specimen culture bottle. However, it will be understood that the filter may be made of any number of materials 5 and may be formed in many conventional ways, as long as it has the effect of creating an optical aperture - directed solely at the bottle sensor or, preferably, a selected portion thereof. For example, the spatial filter could be formed or extruded in many different o shapes with any number of different aperture shapes and configurations. The filter could also be made of a material which selectively absorbs certain wavelengths of light most associated with noise in the system or which otherwise prevents selected light from impinging on the 15 optical detection system.
In a preferred form of the invention, the spatial filter 200 is equipped with a plurality of downwardly extending tabs 208a, 208b, 208c spaced around its periphery. In assembling the spatial filter 200 to the optical unit 46, these tabs 208a, 208b, 208c are inserted into corresponding recesses 210a, 210b, 210c in the housing of the optical unit 46. (A fourth tab and corresponding recess are not visible i-n Fig. 15B.) The spatial filter 200 is then welded to the polymeric 2s housing of the optical module 46 by melting together the polymeric tabs and the polymeric material surrounding the recesses. In this way, the spatial filter 200 is welded to, and becomes integral with, the optical module. It will be understood, however, that the spatial filter may be molded or formed integrally with the polymeric housing of the optical module or may be attached to the module by ~o 94,26874 ~ 1 3 8 2 5 ~ PCT~S94/05392 other means, such as by using adhesives or mechanical locking arrangements.
In addition to the spatial filter, the improved optical system of the present invention includes a 5 further aspect. Referring again to Fig. 15A, an important additional feature is the addition of a light-blocking third layer to the sensor 100. (This third layer is illustrated by the reference numeral 208 in Fig.
15A.) The purpose of the third layer 208 is to lo substantially optically isolate the fluorophore layer 124 and the chromophore layer 122 of the sensor 100 from external sources of light other than excitation light from the LEDs 126 which passes through the aperture 204 of the spatial filter 200. These external sources of light include, for example, light from the ambient environment and, importantly, light emanating or reflected from the sample and media in the bottle.
In a preferred form of the invention, the third layer 208 is made of a light-absorbent material which is gas-permeable so that carbon dioxide generated bymicroorganisms within the bottle can diffuse through the third layer 208 and, eventually, to the chromophore layer 122. Success has been had with a third layer made of silicone into which a fine powder of activated carbon (carbon black) has been uniformly dispersed. The activated carbon makes the third layer black in color and light-absorbent, in order to give it the desired optical properties needed to prevent external light from entering the other layers of the sensor. It will be understood, however, that a variety of materials could be used in the manufacture of the third layer as long as the layer substantially prevents external light from impinging upon W094/26874 PCT~S94/05392 ~138`~4 the other layers of the sensor, while still permitting metabolic products produced by microorganisms in the specimen, such as carbon dioxide, to diffuse through the third layer and, ultimately, into the chromophore layer.
5 For example, a wide variety of light-absorbent materials could also be dispersed in silicone, including charcoal substitutes, powdered obsidian, or other inert, dark-colored materials, so long as the material does not interfere to a great extent with the diffusion of carbon o dioxide to the chromophore layer. Similarly, other gas permeable, proton impermeable materials could also be used to encapsulate the light-absorbent material.
As illustrated in Fig. 15A, the third layer 208 substantially envelopes or covers the outer exposed 15 surfaces of the sensor 100, that is, all surfaces other than the portion affixed to the inside surface of the bottom wall 203 of the bottle 202 through which the sensor is optically interrogated. In this way, a light-absorbent optical barrier substantially surrounds all 20 surfaces of the sensor except the bottom surface through which excitation light passes.
It will be readily understood that the third layer 208 of the sensor 100 and the spatial filter 200 cooperate to form a light blocking means or light barrier 25 which helps to prevent a substantial portion of external light, including light from the outside environment and light emanating or reflecting from the interior of the bottle, from reaching the optical unit and, particularly, the photodetector. In this way, it is possible to substantially isolate the detection system from interfering light from sources other than the fluorescent ~094/26874 PCT~S94/05392 ~138~5~

emission of the fluorophore layer 124, as modulated by the chromophore layer 122.
Of course, it will be understood that the third layer 208 could also be expanded so that it covered the entire inside bottom surface of the bottle, thereby also performing the function of the spatial filter 200.
However, it is generally preferable to use a mechanical filtering means like the spatial filter, since it is relatively easy to include a mechanical structure within the apparatus and to mold the third layer as part of the sensor prior to insertion in the bottle. On the other hand, adding material to the inside surfaces of the bottle often becomes difficult and costly.
In making the three-layer sensor of the present invention, it will be understood that in general the methods set forth in prior applications S.N. 07/638,481 (particularly those set forth in Examples 2 and 3 thereof) and 07/609,278 (now U.S. Patent No. 5,173,434) may be used, with the addition of the third light-absorbent coating layer described above. The third layeris made by uniformly dispersing activated carbon into silicone elastomer and catalyst, degassing the resultant mixture by exposing it to vacuum, and then coating the appropriate surfaces of the two sensor layers with the mixture. The three-layer sensor is then inserted into the bottle and affixed to the bottom wall thereof. (It will be understood that the sensor may be formed with a protrusion or knob on its top surface so that automated or semi-automated insertion apparatus can "grip" the knob to facilitate insertion into the bottle.) W094/26874 PCT~S94/05392 213g~5g The following example further illustrates the manner in which the three layer sensor of the present invention can be made and inserted into the specimen bottle:

E~AMP~E -- THREE-LAYER BEN80R MANUFACTURE
The sensor is preferably comprised of three layers;
the fluorophore layer, the chromophore layer, and the light blocking, "black" third layer. The fluorophore layer is made using an opthalmic grade of clear lo polycarbonate plastic (GE OQ21), which is combined with a laser dye (Eastman Kodak, Oxazine 4 Perchlorate). In the combination process, the dye is dissolved in an organic solvent and the feedstock plastic pellets are uniformly coated with the dye solution. Following the coating of 15 the pellets, the plastic is melted, mixed, and reextruded to form feedstock. The resultant material is molded by melting it and then injecting it at high pressure into an eight-cavity mold. Since the fluorescent dye has been found to be highly sensitive to heat, extremely close control of time/temperature profile of the material must be maintained. The mold is shaped to form the material into the "starfish"-shaped layers described above. In addition, as described in additional detail below, the mold may be designed to form a "knob," which protrudes 25 from the center of the fluorophore layer.
The chromophore layer is a gas permeable silicone which has a pH sensitive dye mixture incorporated therein. The dye mixture is designed to change its absorbance characteristics with respect to passage of light in the 567 nm to 650 nm ranges. The feedstock materials for the chromophore layer are silicone (Wacker SilGel 601), bromothymol blue salt, sodium hydroxide, and -~094/26874 21~ ~ ~ 5 ~ PCT~S94/05392 ,~ , ,.

ethylene glycol. The pH sensitive dye mixture is mixed with the silicone base material and degassed using a vacuum chamber. The material is then injection molded using a Kuntz liquid injection molding machine. In the 5 injection molding process, the mold holds the fluorophore layer while the absorbance layer is injected and cured, thereby encapsulating the fluorophore layer. (It will be understood that if the fluorophore layer is formed with a protruding knob, as described above, this knob extends lo down into the chromophore layer and, when the sensor is affixed to the inside wall of the culture bottle, protrudes downward so that it is closer to the optical detection system. Such an arrangement can be useful, since the protruding knob containing fluorescent dye can 15 be more readily detected by the optical detection system described herein. This, in turn, can make it easier to detect when a bottle is inserted into a bottle-receiving opening.) In the process, the thickness and uniformity of the absorbance layer on the fluorophore layer is of 20 the utmost importance, as small variations in thickness will impact both initial optical values and sensitivity of the system. Current goals are for the chromophore layer to be .015 inch ~/- .001 inch.
The third layer is molded to the back of the 25 previously described subassembly. This layer is made of the same silicone used for the absorbance layer doped with 3~ by weight carbon black. (The resultant material is also degassed, as described above.) The method of manufacture follows that of the chromophore layer, except that a different mold, which accepts the two-layer subassembly described above, allows the molding of a .030 inch black layer on the surfaces which are not to be W094/26874 PCT~S94/05392 ~13825g affixed to the inside wall of the culture bottle. In addition, as noted above, a knob or protrusion may be formed in this black layer to facilitate insertion of the sensor into the culture bottle. The sensor may be affixed to the inside bottom wall of the bottle by conventional means, such as by using silicone as an adhesive.
Although the improved optical system and sensor described above are adapted to substantially reduce noise in the system and thereby improve sensitivity, further improvements in the processing of the resulting signal are also possible. Accordingly, Figs. 16 and 17 in conjunction illustrate another feature of the optical detection system which is designed to further reduce noise and thereby improve the sensitivity of detection.
Viewing Fig. 16, it is seen that the instrument 10 includes a control circuit for the optical units 46, which control circuit is generally referenced with the numeral 400. This control circuit 400 includes a power supply 402, which may receive power from a common 110 volt alternating current source, for example. The power supply 402 provides direct current (DC) voltage and current via a power line 404 at appropriate levels for the operation of the LED's 126, as will be explained further. The line 404 supplies the DC power to a modulator 406 which provides chopped square-wave DC power via a branched power line 408, the voltage wave form for which is depioted as line 410 on the voltage-time graph of Fig. 17. One branch of the power line 408 ~upplies the chopped DC power to the LED's 126 of the optical units 46, so that these LED's produce a light output signal (indicated with arrow 412 leaving the LED 126 on ~094/26874 213 ~ ~ 5 ~ PCT~S94/05392 "_ ~

Fig. 16) substantially replicating the wave form indicated by line 410 of Fig. 17.
As will be well understood in view of the explanation above, the light 412 illuminates the sensors 100, so that these sensors produce a fluorophoric response to the incident excitation light 412. This light produced by the fluorophoric response of the sensors 100 is indicated on Fig. 16 with the arrow 414. The light represented by arrow 414 is incident on the photo diodes 128 of the o optical units 46, so that these photo diodes produce a voltage response to this incident light. Unfortunately, the light 414 is not the only light incident on the photo diodes 128. When the drawers 16, 18 are open, as they must be for the insertion of additional culture bottles 120, the ambient room light also affects the photo diodes 128. This effect from ambient room lighting may include natural sun light, but generally will have the wave form of a sixty-cycle flicker. Also, electronic noise from various sources in the environment of the instrument 10 may also be present in the output signal from the photo diodes 128.
The resulting combination output signal from a photo diode 128 of one of the optical units 46 is indicated on the graph of Fig. 17 with the voltage-time line 416.
This output signal appears on an output line 418 from the photo diode 128. Each of the photo diodes 128 has a separate output line 418 connecting with the microcomputer 14, as will be further explained. As can be seen from a comparison of the lines 410 and 416 of Fig. 17, the output signal 416 from the photo diodes has a significant component 420 which is attributable to the WOg4/26874 PCT~S94/05392 ~13~2~

excitation light 412 from the LED's 126, and has a frequency like the voltage wave form 410.
Respective output lines 418 from each photo diode 128 connect to a band pass filter 422, which has a passage 5 frequency generally matching the frequency of the signal 410, and the component 420 of signal 416. This band pass filter removes any direct current component of the signal 416, and provides rough discrimination of the signal component 420 from other noise components. The filtered o output from band pass filter 422 is provided via a line 424 to an amplifier 426. This amplifier 426 increases the level of the signal to a more easily measurable level, which is provided on a line 428. The voltage wave form for the signal on line 428 is depicted on Fig. 17 with the line 428'. As can be seen, at this point the signal has a generally sinusoidal wave form with unequal positive and negative values, and some rounding of the wave form by capacitances in the circuits. While not depicted on Fig. 17, those ordinarily skilled in the pertinent arts will recognize that the wave form 428' includes noise components which may be of various forms.
Next, the signal on line 428 is subjected to the operation of a clocked demodulator 430. The demodulator 430 is clocked in synchronization with the output 410 of the modulator 406 by a branch connection of the power line 408. This demodulator 430 has an amplification function depicted as line 432 of Fig. 17. The amplification function of demodulator 430 has a negative one (-1) value while the voltage level of signal 410 is zero. That is, a negative one for the amplification function is meant to indicate that the signal is inverted. When the voltage level of signal 410 raises --~094/26874 213 ~ 2 ~ ~ PCT~S94/05392 above zero to produce a light output signal from the LED's 126, the demodulator 430 has an amplification value of positive one (+1). In this case, with a positive one amplification factor, the signal is passed through s substantially without change.
Consequently, the signal 428' is rectified so that all of the signal becomes positive. Noise signals, similarly, pass through the demodulator 430 full wave rectified. That is, the half of the noise signal which is in phase with the signal portion 420 will continue to have a positive value, while the other half of the noise signal will have been inverted by the -1 amplification of the demodulator 430. Moreover, signals of interest are rectified such that they make a positive contribution to an integral. Signals which are not of interest are rectified such that they cancel upon integration. Thus, noise signals cancel one another.
Consideration of Fig. 17 will quickly show that the signal 410 and the amplification value of demodulator 430, as represented by line 432 on Fig. 17, are synchronized and in phase with one another. That is, the driving signal to the light emitting diodes 126, and the amplification level applied to the response signal from the light responsive photo diodes increase and decrease in phase with one another. The output of the demodulator 430 is provided by a line 434 to an integrator 436. On Fig. 17, this demodulator output is represented with line 434'. As can be easily understood, the positive and negative portions of the noise signal cancel one another when they are integrated. On the other hand, the signal - portion 420 when integrated, provides an output voltage (Vout), indicated with arrow 438 on Fig. 16. This output W094/26874 PCT~S94/0~392 ~13825~
signal is provided to the microcomputer 14. Also, the output "Vout", from each of the photo diodes 128 is provided by a similar signal processing channel to the microcomputer 14 so that this computer can receive the s fluorophoric response from the sensor 100 in any opening 38 of the racks 20-30.
Having observed the structure of the control circuit 400 depicted in Fig. 16, attention may now be given to two particularly advantageous methods of operation with this circuit. As can be easily understood, when the drawers 16, 18 are closed, and the presence of microorganisms in media 132 is to be detected, the LED's 126 are illuminated and the responses of the photo diodes 128 is received and analyzed by the microcomputer 14.
S For this operation, a very high level of discrimination between various levels of response of the fluorophore 124, as well as discrimination of changes in response levels of the fluorophore 124 as moderated by the chromophore 122, can be detected using a comparatively long integration time for each specimen bottle 120. That is, a three second integration time conducted at the integrator 436 for each of the specimen bottles 120 in the racks 20-30 will allow the computer 14 to make very fine distinctions between levels of response at the 2s sensors 100. Thus, the presence or absence of microorganism growth in the media 132 is easily detectable.
On the other hand, with the drawers 16 or 18 open for the insertion of additional specimen bottles 120 to the racks 20-30, another mode of operation of the control circuit 400 has particular advantage. That is, when a technician is to insert additional specimen bottles 120, ~-'094/26874 PCT~S94/05392 -- 21382~1 the optical units 46 of each of the vacant cylindrical openings 38 in the racks 20-30 can be rapidly scanned in sequence by the microcomputer 14 in order to identify the openings which receive new specimen bottles, and those 5 openings 38 which remain vacant. Thus, the technician may scan a specimen bottle 120 along channel 162 past the bar code reader 164 so that the computer 14 is informed not only of the bar-coded information concerning patient identification, but is also informed that a new specimen o bottle is about to be loaded into one of the vacant openings 38. Under these circumstances, each of the optical units 46 for the vacant openings 38 is scanned with an integration time of about ten milliseconds each.
This scan is looking simply for some level of characteristic response like that represented by portion 420 of line 416 in Fig. 17. Of course, because the vacant openings 38 do not contain a specimen bottle with its sensor 100, the vacant openings can be identified by the absence of the characteristic response from the associated photo diodes.
When the microcomputer 14 detects such a response at a previously vacant opening, two items of information are established for the inventory control portion of the computer program. First, the computer is informed that the specimen bottle just scanned by the technician has been placed in an identified opening 38, and the computer thereafter identifies the particular patient with any future results from that specimen. Secondly, the computer now knows that the previously vacant opening 38 into which the new specimen bottle has been placed is no longer on the list of vacant openings which need to be W094/26874 2~ S 4 PCT~S94/05392 scanned to identify where subsequent specimen bottles are placed by the attending technician.
The result of this second mode of operation for the control circuit 400 is that a technician attending the 5 instrument 10 need not identify from the keyboard and screen of the microcomputer where specimen bottles are to be inserted into the racks 20-30. The technician can simply scan the specimen bottles along channel 162 past the bar code reader 164, wait briefly for an o acknowledgment signal, which may be visual or audible, and then insert the specimen bottle in any vacant opening 38.
The computer 14 by interface with control circuit 400 will identify the opening into which the new specimen 15 bottle has been placed. With a mere 10 millisecond integration time being sufficient to discriminate vacant from newly occupied openings 38, this identification process can be completed by the computer-so quickly that even if the racks 20-30 are empty, or nearly so, the 20 technician can simply scan and insert specimen bottles at a rate of one bottle about every two seconds, or faster if desired. Consequently, loading the instrument 10 with specimen bottles is both considerably speeded up by use of the control circuit in its second mode of operation, 25 and chances of error because of placing specimen bottles in the wrong openings 38 is virtually eliminated. This second mode of operation also has a corollary advantage when specimen bottles are to be removed from the racks 20-30. The newly vacated openings 38 are quickly identified by the computer and added to the list of vacant openings to be scanned for newly-inserted specimen bottles.

~094126874 ~1 3 8 2 ~ ~ PCT~S94/05392 The following is a sample protocol which further illustrates the manner in which the instrument of the present invention can be used in detecting the presence of bacteria in human blood. A detailed description of a 5 software program which may be used to preprogram the microcomputer to monitor and control the functions performed by the instrument in this protocol is found in the Appendix hereto.
~AMPLE INSTRUMENT PROTOCOL
Blood drawn from a patient exhibiting symptoms of bacteremia is drawn and brought to the hospital microbiology laboratory, where it is inoculated into a culture bottle containing media conducive to bacterial growth and labelled with a bar code containing 15 information linking that sample to the patient. By means of the user interface on the front of one of the drawers of the module, the instrument operator initiates a command to the minicomputer to open the drawer. If the bottle holding racks are being agitated at that time, a command is sent to stop agitation when the bottle holding racks are near their lowermost agitation position.
Alternatively, if optical readings are being-taken at that time, the readings are completed before the drawer is opened. The system is preferably preprogrammed so 25 that the agitation, heating, and optical reading functions are disabled (and cannot be restarted) while the drawer is open.
The microcomputer then signals activation of the drawer-opening motor in order to open the drawer. Once the drawer is opened, the operator draws the bar-code on - the culture bottle across the V-shaped channel and bar-W094126874 PCT~S94/05392 21`3&2~

code reader located inside the drawer, and the bar code information is scanned into the system. This information is transmitted to the microcomputer, which sends a signal to the inside information panel prompting the operator to 5 place the bottle in an available bottle-receiving opening. The operator inserts the bottle into the proper opening until it "snap-fits" into engagement with the bottle-retaining means. The control circuit described above rapidly identifies the opening into which the new lo specimen bottle has been placed. Thereafter, optical readings for that bottle are associated with the patient information which has been scanned into the system.
By means of the temperature control subsystem illustrated in Fig. 3, the temperature inside the drawers 15 and, thus, the temperature of the bottles, is kept at the preferred temperature for microbial growth. The microcomputer signals activation of the fan and heating elements, as required, in order to maintain that temperature within specified limits. Periodically, at regular intervals, the microcomputer signals the agitation motor to agitate the bottles using the system illustrated in Figs. 4, 5, and 11. Also at regular intervals, agitation of the bottle holding racks is stopped when the bottles are in their uppermost agitation 25 position. While the racks are in this position, optical readings are taken. The system is capable of distinguishing between empty openings and openings which contain bottles by the nature of the optical signal. The optical readings are transmitted to the microcomputer where they are associated with the appropriate patient information and stored for later retrieval and use.

~13 8 2 ~ ~ PCT~S94/05392 If the optical reading for a particular ~pecimen exceeds a predetermined threshold, the microcomputer treats that sample as a "positive" and transmits that information to the instrument. An audible alarm is 5 activated to signal this information to those present in the laboratory. The microcomputer also sends a command to illuminate the appropriate LED adjacent that bottle to identify the positive culture for the operator. That bottle can then be removed and subcultured so that the o infecting bacterium can be identified, and an appropriate treatment regimen (including appropriate anti-microbial agents) can be prescribed for that patient.
Since the microcomputer is also programmed to store and manipulate the data pertaining to the specimens, it 15 iS also possible to generate print-outs of the data in various formats, including tables, graphs, and the like.
While the invention has been described in connection with certain presently preferred components and arrangements, those skilled in the art will recognize many modifications to structure, arrangement, portions, elements, materials, steps and components which can be used in the practice of the invention without departing from the principles thereof.

213~2S4 APPENDlX
Terms Used The following terms are used throughout this document. They are presented below for reference.
Boolean Having two possible states - binary.
Comm~nd A message, sent from the host PC to the instrument, which commands the instrument to perform some action, return some data, set some parameter, etc.
Comm~nd Processor A software module which accepts commands (from the host or from other modules) and either acts on those c-omm~nds, or relays them to other module(s) for action.
Context A frame of reference. In multi-tasking systems, the context is the memory (code, data, stack) and processor state (i.e. register contents) which "belong" to a given task.
Context-switch Task-switch.
Event The name of an edge in a state diagram. Events cause states changes to occur.
Message A block of information passed between tasks. In this case, messages are forwarded between tasks by ~X. Commands from the host and responses to the host are a special class of messages.

213~2S4 '~ro 94/26874 65 PCT/US94/05392 MMX
An operating system software component which relays messages between tasks.
Module A logically grouped portion of software. Generally, a module will be contained within a single compilation unit, and will contain functions and data which implenet a particular portion of the requirements for the software system.
Pseudocode An informal, structured F,ngli.~h representation of program coding.
Response A message sent from the instrument to the host which relays the results of a previous command.
Task An independent thread of execution. The operating system provides facilities to make multiple tasks, or threads, appear to execute simultaneously.
Variable A piece of data.

WO 94/26874 ~ 13 ~ 66 PCT/US94/05392 Messa~e Passin~ Fundamentals The Blood Culture Operating System, and MMX in particular, provide me~h~ni.~mc for transporting messages between independent tasks. MMX provides what can be described a sa many-to-many message system. This means that many tasks may send a particular message, and many tasks may receive a particular message.
Passing messages involves (at least) three steps in MMX: First, tasks must declare which message they are "interested" in receiving.
To send a message, a task "Posts" the message to MMX, which, in turn, delivers it to all other tasks which have declared an intent to receive that message. To receive a message, a task "Pends" for one. The execution of the task is suspended until a message is available for the task.
Variations on the basic case outlined above include a "pend with time-out," which limits the amount of time a task will remain suspended when waiting. Message may be "held" - reception deferred until later, while allowing other messages to be passed. Messages which have been hold must eventually be "released" and received.

Z13~4 '''O 94/26874 67 PCT/US94/05392 S~stem Overview The Reller Operating System will be composed of the software components rles~rihed at the Blood Culture System Design Review held previously. Though the operating system plays a key role in system operation, it will not be discussed extensively in this document.
Instead, this document will focus on the software component generally called "the application." VVhile every software component contributes to the overall functionality of the instrument, it is the application that p~rform.~ those functions that are most important to the host computer, and eventually, the user. In short, the application is the component that makes the Blood Culture instrument be a Blood Culture instrument.
The application will be composed of seven modules, and ten tasks:
A Coordinator task, responsible for application start-up and time m~rking; a host communication task, responqih~e for providing a standard command processor interface and response path for tasks; an access task which handles the actions necessary for letting users into drawers; an analog reading task, which allmini~ters the hardware for analog reading; two bottle reading tasks, responsible for handling the ~iming of and storage of bottle reads; two temperature control tasks, which control the temperature into drawers; and lastly, two agitation tasks, which are responsible for the timing and initiation of bottle agitation within d~awels. The bottle reading, temperature control, and agitation tasks will be written so the main code body will be reentrant, with independent data segments.

WO 94/26874 ~ 68 PCT/US94/05392 Global Requirements * For each bottle, the m~chine must read the sensor in bottle and store the inform~tion periodically contingent upon the drawer being open and agitation in progress.
* The m~chine must allow user access to either drawer (but only one drawer) at any time. The access times and duration must be stored.
* The m~hine must maintain and record temperature on some periodic basis.
* M~rhine must report stored data to host computer on request.
* Time of user accesses, and duration of opern drawer will be recorded.
* Termperature in each drawer will be recorded.
* All bottle readings will be recorded.
Global Assumptions * The photoboards sent to ICAAC will comprise the photosystem, with the addition of the lock-in detector.
* We will use the Garrand CPU. 1/0 architecture not .~ignific~ntly changed from the version as of this date.
* Heaters will be installed in each drawer, and the software will be expected to control them.
* New motors will be installed to control the agitation and drawer movement. There will only be crude control of these motors (i.e.
Motor on and direction).
* Optos will be relocated and will privde feedback on: drawer closed, drawer open. Optionally a third opto might be provided to indicate that a drawer is parked (closed all the way).
* The functionality of the agitation home optos will be unchanged.
* Communication will be serial RS-232 with a yet-to-be-determined PC.

~'0 94/26874 ~13 ~ 2 ~ 4 69 PCT/US94/05392 Conventions used throu~hout the document Most modules are described using the format below:
¦ ---A function name (TaskName)--- ¦
START
Overview of TaskName.
requirements---Design requirements of TaskName.
assumptions---Implicit, or practical desig assumptions used during task design.
cornmands supported---Comm ~n d function name (parameter).ideal flow---"Structured~ engli.~hevents---EventName:
[

Pseudocode. -- Comment ]
<Non-MMX generated event>
[

Pseudocode.
]

~Non-event based code block~:
[

WO 94/26874 ~ 3 2 ~ q ~ 70 PCT/US94/05392 Pseudocode.
]

END
---A function name (TaskName)---In the above example task, comma7lds supported--- indicates which functions will be provided by the module's command processor.
(The command processor pseudocode is not described in this document.) The ideal flow--- section of a module description will describe in "structured english," the ideal sequence of operations for major functional requirements of the module.
Lastly, the events--- section describes the functions that each task will perform when a particular event occurs in the system.
Special code blocks, that are neither command processors, nor directly related to supporting a system event are indicated by braces.
Please note that where an asterisk ("*") appears in any identifier, the asterisk may be substituted with either an "R" or an "L". The asterisk is used for tasks that will run to a specific drawer.

-'~O 94/26874 ?~ 2 .j 4 PCT/US94/0~392 ¦ ---Agitation Control (AgCtrl*)--- ¦
START
The agitation control task attempts to agitate the bottles in "its"
drawer as close as possible to the set agitation period.
requirements---Agitation must * occur periodically.
* occur for a fixed duration.
* not interrupt a read in progress.
* disallow reading to occur while agitating.
* be of higher initiation priority than bottle reading.
assumptions---* Agitation period or duration may change.
* ~rking time in five second increments is sufficient temporal resolution to begin an agitation cycle.
commands supported---Set agitation period: time (increments of 5 seconds).
Get agitation period.
Set agitation duration: time (increments of 5 seconds).
Get agitation time.
Enable agitation.
Disable agitation.
Force agitation start.
Force agitation stop.

wo 94126874 72 PcT/uss4/05392 ~i3~2~4 ideal flow---Initialization.
For forever do:
After Agitation Period 5-second time intervals pass, then stop bottle reads in this drawer (ReadInhibit*).
After bottle reads have stopped (ReadInhibited*), start the agitation motor.
If, while agitating, ~gTnhihit* is received, stop agitation;
otherwise continue agitation for AgDuration.
Stop Agitation.
Reset the AgPeriod counter.
End for.
variables---AgPeriod : Number of FiveSecTicks between agitation starts.
AgDuration : Number of FiveSecTicks to agitate bottles.
AgitatingFlag : Boolean indicating that agitation isunderway.
~gTnhihit : Integer where non-zero indicates that agitation should be stopped, and no agitation should commence.
TimeCounter : Number of Time_tick periods to go until commencing next agitation phase (on or off).

- O 94/26874 21~ 8 2 5 4 73 PCT/US94/05392 events---~gTi`,n~hle*:
Reenable agitation.
[
if ~gTnhihited flag <> O then [

decrement ~gTnhihited flag.
EVENT: Agitation Enabled (DEBUG, time, drawer);
]
]

~gTnhibit*:
Something in the system is going to happen that should preclude agitation. If we're agitating, we'll stop. We will inhibit any further agitation.
[

If AgitatingFlag set then [

Stop agitating, and home agitator.
Clear AgitatingFlag.
Send ReadEnable*.
Reset PeriodCounter to AgPeriod.
]

EVENT: Agitation Inhibited a~EBUG, time, drawer).
Increment ~FTnhihited flag.
Send ,AETnhibited*~
Pend with no timeout.
]

WO 94/26874 74 PCT/US94/0~392-;~13~2~4 FiveSecTick:
A standard system time interval has expired. We need to see if it's time to start an agitation cycle.
[

if TimeCounter c~ O then decrement TimeCounter.
if TimeCounter = O then if AgitatingFlag set then [

Stop Agitation, and home agitator.
Send ReadEnable*.
Reload TimeCounter with (AgPeriod-AgDuration).
]

else [

Set AgitatingFlag.
Send ReadInhibit*.
]
]

ReadInhibited*:
If ReadInhibited* was received, we sent a ReadInhibit* message to Bottle*. That means that we intended to commence agitation, and now upon receiving this message, have gotten the go-ahead to do so.
[

If AgitatingFlag --Did an .AgTnhihit* sneak in?
then --Nope. It's cool to go ahead.
[

EVENT: Agitation Started (EVENT, time, drawer).
Start Agitation.
Reload TimeCounter with AgDuration.
]
]

END
¦ ---Agitation Control (AgCtrl*)--- ¦

' 'O 94/26874 ~ ~ 8 2 ~ ~ PCT/US94/05392 ¦ ---Temperature Control (TempCtrl*)--- ¦
START
Maintain the temperature in the drawer.
requirernents---* Temperature must be controlled in drawer with .1 degree C
accuracy. (This is not addressed in this document.) * Heater duty cycle must be adjusted periodically.
* Time/Drawer stamped temperature readings must be stored periodically.
* Temperature control will be disabled from time to time.
Assumptions---* The control algorithm will be able to time-normalize both readings, and control information.
* The time needed to obtain a temperature reading is dependent upon the duration needed for a slow lock-in.
commands supported---Set temperature target: target Get temperature target: target Get current temperature. (Both drawers reported.) Enable heating.
Disable heating.
Fetch next temperature readings: number Fetch temperature reading count.
ideal flow---At every one second interval, attempt to request a temperature reading from this drawer.
Wait for the analog reader task to respond.
When the analog reader task responds, compute the new heater duty cycle, and communicate it to the heater ISR.
If we have taken no readings, store the temperature in a buffer.

uariables---SkipCounter : number of temperature readings to skip before placing reading into circular buffer HeatPeriod : Total control period of drawer heater DutyCycle : Current intended duty cycle of heater TickCounter : Number of main clock ticks to remain in present heater state HeatDisable : non-zero means that the heater will not be activated -'1 94/26874 ~? 1 3 ~ 2 5 ~ 77 PCT/US94/05392 events---OneSecTick:
We will try to read the temperature every second.

If TempInProgress not set then send ReadAnalog (temperature*).

*DrawerChannelRead:
A temperature read has completed.

Decrement SkipCounter.
If SkipCounter=0 then store temperature reading, time, drawer in bufEer.
reset SkipCounter.

Compute new heater duty cycle.
Update DutyCycle.

DrawerOpen*:

Set HeatDisable ~ag.
Turn offheater.

DrawerClose*:

Clear HeatDisable flag.

WO 94/26874 ~ 1 3 ~ 2 5 4 78 PCT/US94/05392 SR, tied into main VRTX clock ISR}:

If HeatDisable flag not set then Decrement TickCounter.
If TickCounter = O then heater is on then Turn of ~ heater.
Reset TickCounter with (HeatPeriod-DutyCycle).

else Turn on heater.
Reset TickCounter with DutyCycle.

]

END
¦ ---Temperature Control (TempCtrl*)--- ¦

94/26874 ~ 82~i PCT/US94/05392 ¦ ---Bottle Reader (Bottle*)--- ¦
START
Read bottles in drawer.
requirements---* For each bottle reads must occur periodically.
* Bottle readings will be disabled from time to time.
* Time/Cell stamped readings will be stored.
? The read will be stored in a mystery format that m~ximi7~esthe amount of time the system can operate without offloading data to a host computer.
assumptions---* calibration (cell standardization) will be a manual process.
* The bottle reader task will be told which bottles to read via a host comm~nd.
* Reading norm~li7.~tion will occur on the host.
operating assumption---* Uncalibrated cells will not be assigned.
commands supported---Enable a cell (Cell number).
Disable a cell (Cell number).
Get number of readings.
Get next readings (number).ideal flow---At each five second interval, a table of active bottles is checked.
If an active bottle is encounted, it is checked to determine if the read period has expired for it.
If a read is required a read is requested from the analog reader task.
Wait for the analog reader to respond.
When the analog reader task responds with the reading, the reading is stored in a circular buffer.

WO 94/26874 80 PCT/US94/0~392 ~38~
variables---ReadInProgress : Flag that indicates that a bottle read is underway.
NoReads : Flag that indicates that no readings should be started.
Bottle : Array of (number of bottles in drawer) of records.
Active : Flag indicating that this cell should be sampled regularly.
PeriodCount : Number of time periods remaining until next read.
events---ReadIn_ibit*:
[

Set NoReads flag.
If ReadInProgress flag not set then Send Rea-lTnhihited*.
]

ReadEnable*:
[

Clear NoReads flag.
]

BottleRead*:
[
Store time, cell, bottle reading, in circular buffer.
Reset Bottle[cell] PeriodCount to ReadPeriod.
If NoReads flag set then send Rear1Tnhihited*.
]

~13~2~
'~0 94/26874 81 PCT/US94/05392 FiveSecTick:
[

index = lowest bottle number (this drawer).
repeat with Bottle[index] do if (Active flag set) and PeriodCount non-zero then decrement PeriodCount.
if (BottlePeriod = O) and (NoReads ~lag not set) then [

Set ReadInProgress flag.
Send ReadBottle*(index).
]
]

increment index.
] until (index = (highest bottle number (this drawer)+1) or (ReadInProgress flag set).
]

END
¦ ---Bottle Reader (Bottle*)--- ¦

wo 94126874 82 PCT/US94/05392 5 ~ -Analog Reader (AnaRead)--- ¦
START
Perform all the operations necessary to perform analog readings.
requirements---* The availability of the analog read circuitry must be m~ximi7.ed.
* No operations concerning the any analog measurement must be allowed to interfere with one another.
assumptions---* There is one VCO. VCO measurement may be initiated atany time.
* There are two drawers. Only one analog measurement may occur in a particular drawer at a time.
* There is only one slow lock-in amp. Performing an analog measurement with the lock-in amp takes a long time.
* Analog readings from a drawer will use the lock-in detect or not.
cornmarlds supported---read a cell (Cell number, drawer number). --uses slow lock-in amp read a drawer channel (cell number, drawer).--measures DC only.
read a drawer channel with gain (cell num, drawer, gain) --DC*gain read a MUX channel. --read a Mux channel set X switch (direction).
set gain (gain).
set mux (mux).
read VCO (time).
read full VCO. --returns time to fill VCO counter.

--'O 94/26874 ~ 1 ~ 8 ~ ~ ~ 83 PCT/US94/05392 ideal flow---For a VCO read:
MUX is selected.
Wait for DC settle time.
Set up VCO timer counter.
Integrate.
After integration, read VCO counter.
Provide VCO reading with 2.5 and 0.0 volt references.
For a drawer channel read:
Drawer channel is selected.
MUX is switched to appropriate drawer.
Wait for DC settle time.
Set up VCO timer counter.
Integrate.
After integration, read VCO counter.
Provide VCO reading with 2.5 and 0.0 volt references.
For a bottle read:
Drawer channel is selected.
Gain is set.
X-Switch is set appropriately (for slow lock-in detect).
Wait for slow lock-in.
MUX is switched to slow lock-in.
Wait for DC settle time.
Set up VCO timer counter.
Integrate.
After integration, read VCO counter.
Provide VCO reading with 2.5 and 0.0 volt references.

2 5 ~

variables---Delay : Number of VRTXticks to delay.
DelayInProgress : A delay is in progress. A better name would be 'Lo~kTnTnProgress'.
Lasttime : The last time we started a pend (in VRTXtime) ~Pend routine~
In this task, there is a single pend point which might pend with a time-out, depending on whether a lock-in is in progress. If a lock-in has been started, we want to be able to service non-competing requests, so we pend for them here. If a request is received, we'll service it, then return here, determine the rem~ining time to lock-in, and pend with a timeout with that value.
[

If DelayInProgress flag set then [

Set Delay to ( (current VRTX ticktime) - Lasttime ) If Delay < O then [

Reset DelayInProgress flag.
Reset Delay to 0.
go execute <time-ouP.
]

else if Delay <> O
[

Set DelayInProgress flag.
]

-- ~ 94/26874 ~ 1 85 PCT/US94/05392 If Delay <> O then [
Save current VRTX ticktime as LastTime.
Pend with timeout Delay.
]

else Pend with no timeout.
- - Pend takes place.
If pend timed-out then [

Reset DelayInProgress flag.
Reset Delay to 0.
go execute ~time-out>.
]
else go execute appropriate event.
]

euents---<Pend Time-out>:
[

Set MUX to slow-lock-in channel.
Delay for minimum 5ms.
Set up VCO counters.
Take VCO reading.
send [ResponseTypel (vco reading, cal values).

-~13 8 2 ~ 4 8G PCT/US94/05392 If ResponseType is BottleReadL then [

Release LeftDrawer message class.
Release BottleReadL.
]

else [

Release RightDrawer message class.
Release BottleReadR.
]
]

ReadBottleL(bottle):
[

Holdoff ReadLDrawerCh.
Holdoff ReadBottleR.
Select bottle within left drawer.
Set X-switch for slow lock-in on left drawer.
Select gain.
Set Delay to SlowLockTime.
Set ResponseType to BottleReadL.
]

ReadBottleR(bottle):

-Holdoff ReadRDrawerCh.Holdoff ReadBottleL.
Select bottle within right drawer.
Set X-switch for slow lock-in on right drawer.
Select gain.
Set Delay to SlowLockTime.
Set ResponseType to BottleReadR.

]

--~ 94/26874 87 PCT/US94/05392 _ ~1382~4 ReadRDrawerCh(channel):
[

Select channel within right drawer.
Set MUX to right drawer channel.
Delay for minimum 5ms.
Set up VCO counters.
Take VCO reading.
send RDrawerChRead(vco reading).
]

ReadLDrawerCh(channel):
[

Select channel within left drawer.
Set MUX to left drawer channel.
Delay for minimum 5ms.
Set up VCO counters.
Take VCO reading.
send LDrawerChRead(vco reading).
]

ReadAnalog(channel):
[
Set MUX to channel.
Delay for minimum 5ms.
Set up VCO counters.
Take VCO reading.
send AnalogRead(vco reading, cal values).
]

END
¦ ---Analog Reader (AnaRead)~

WO 94/26874 88 PCT/US94/05392 `-~1382~

¦ ---Access Control (Access)--- ¦
START
Design yet to be recorded.
The access task is responsible for prim~ly two major operations:
(1) Notifying the bottle reader tasks, and agitation tasks that a particular drawer is going to be opened, and (2) handling all appropriate drawer parking and movement.
END
¦ ---Access Control (Access)--- ¦

Claims (19)

WHAT IS CLAIMED IS:

1. An instrument for detecting the presence of microorganisms in human tissue in a specimen-containing vessel comprising:
means for holding one or more specimen-containing vessels;
light emission means for emitting light, said light emission means being configured to permit emitted light to impinge upon a sensor positioned on an inside wall of a specimen-containing vessel held in the vessel holding means;
light detection means for converting light energy from the sensor into a detectable signal; and light blocking means substantially covering all but a selected portion of the sensor for substantially preventing light other than light from the sensor from reaching the light detection means.

2. The instrument of Claim 1 wherein the light blocking means comprises (a) a spatial filter interposed between the light detection means and the vessel, said spatial filter defining an aperture through which a selected portion of the sensor may be optically interrogated through the vessel, and (b) a light-blocking layer substantially covering all outer surfaces of the sensor other than the surface in contact with the wall of the vessel.

3. The instrument of Claim 1 wherein the light emission means emits excitation light capable of exciting a fluorophore in the sensor and the light blocking means is adapted to prevent substantially all light other than the fluorescent emission from the fluorophore from reaching the light detection means.

4. An instrument for detecting the presence of microorganisms in human tissue comprising:
means for holding one or more specimen-containing vessels;
a plurality of light sources capable of emitting excitation light falling within a light source emission wavelength range, said light sources being configured to permit excitation light from each of the light sources to impinge upon a sensor affixed to an inside wall of a specimen-containing vessel held in the vessel holding means and to thereby cause the sensor to emit sensor emission light;
light detection means configured to convert the sensor emission light into a detectable signal; and light blocking means substantially covering all but a selected portion of the sensor for substantially preventing light other than sensor emission light from reaching the light detection means.

5. The instrument of Claim 4 wherein the light blocking means comprises (a) a spatial filter interposed between the light detection means and the vessel, said spatial filter defining an aperture through which a selected portion of the sensor may be optically interrogated through the vessel, and (b) a light-blocking layer substantially covering all of the outer surfaces of the sensor other than the surface in contact with the wall of the vessel.

6. A sensor for affixing to an inside wall of a vessel and for detecting the growth of microorganisms within the vessel comprising:

a sensor matrix including a material adapted to detect the growth of microorganisms within the vessel;
and a coating layer comprised of a material which substantially prevents the passage of light therethrough, said coating layer substantially covering all of the outer surfaces of the sensor matrix which are not to be in contact with the inner wall of the vessel when the sensor is positioned on an inner wall of the vessel.

7. The sensor of Claim 6 wherein the coating layer comprises a light-absorbent material dispersed in a gas permeable, proton impermeable matrix.

8. The sensor of Claim 6 wherein the sensor matrix comprises a first layer including a pH sensitive absorbance based dye encapsulated in light transmissive, gas permeable, proton impermeable matrix and a second layer positioned adjacent the first layer and including a pH insensitive fluorescence dye in an inert, light transparent matrix.

9. The sensor of Claim 8 wherein the coating layer comprises a light-absorbent material dispersed in a gas permeable, proton impermeable matrix.

10. In an instrument for detecting the presence of microorganisms in tissue, a control circuit comprising:
power supply means;
light emitting means for receiving power from said power supply means and producing a light emission in response thereto;
modulator means for providing a time-variant signal to said light emitting means causing the latter to replicate said time-variant signal;

light responsive means responsive to a fluorophoric response produced by said light emission and producing an electrical response signal;
demodulator means clocked to said time-variant signal to selectively apply a first level and a different second level of amplification to said electrical response signal dependent on the value of said time-variant signal to provide a demodulated response signal;
integrator means receiving said demodulated response signal and time-averaging this signal to provide an output voltage signal;
whereby said demodulator applies an amplification to said response signal which is synchronized with and in phase with said time-variant signal to selectively pass a portion of said electrical response signal to said integrator, which passed signal portion is characteristic of said time-variant signal.

11. The instrument of Claim 10 wherein said time-variant signal has a frequency, and said control circuit further includes a band pass filter tuned to the frequency of said time-variant signal.

12. The instrument of Claim 11 wherein said control circuit further includes an amplifier receiving a signal from said band pass filter and providing an amplified signal to said demodulator in response thereto.

13. The instrument of Claim 10 wherein said light emitting means includes a light emitting diode.

14. The instrument of Claim 10 wherein said light responsive means includes a photo diode.

15. The instrument of Claim 10 wherein said time-variant signal provided by said modulator means includes a chopped square wave direct current signal of substantially equal on and off time intervals.

16. The instrument of Claim 10 wherein said first level of amplification applied to said response signal by said demodulator is a signal inversion level of amplification.

17. The instrument of Claim 10 wherein said second level of amplification applied to said response signal by said demodulator is a zero level of amplification so that said response signal is passed without substantial change thereto.

18. In an instrument for detecting the presence of microorganisms in tissue; the instrument including a rack with plural receptacles each capable of receiving a respective tissue sample vessel therein; each tissue sample vessel including a respective tissue sample, culture medium, and a fluorophoric element; and plural optical units each individually associated with a respective one of said receptacles for detecting metabolism of said microorganisms in said tissue sample vessels by a fluorophoric response of said element to a metabolism product of said microorganisms, each of said optical units including a light emitting device for stimulating said fluorophoric response, and a device responsive to said fluorophoric response to produce a response signal, a method of detecting the location among said plural receptacles of a tissue sample vessel which is newly-inserted into said rack at one of several vacant receptacles thereof, said method including the steps of:
driving said light emitting devices with a time-variant signal having a characteristic frequency;

causing said fluorophoric response to have a time-variation at said characteristic frequency;
producing said response signal having said characteristic time-varying frequency;
identifying vacant receptacles by an absence of said time-variant response signal at each of said vacant receptacles; and identifying the location of said newly-inserted tissue sample vessel by identifying the one of said vacant receptacles from which a response signal at said characteristic frequency is received.

19. The method of Claim 18 further including the steps of:
providing an identifying indicia on each of said tissue sample vessels, scanning said identifying indicia into a listing;
utilizing a new entry into said indicia listing as an indication that a new tissue sample vessel is about to be inserted into a vacant receptacle of said rack, starting said time-variant driving of said light emitting devices in response to said indication, and scanning the vacant receptacles of said rack sequentially awaiting insertion of said new tissue sample vessel and receipt of said time-variant signal from said fluorophoric element of said vessel to identify the one of said vacant receptacles where said vessel is inserted.