CA2113550A1 - Apparatus for culturing and detecting bacteria in human tissue - Google Patents

Abstract

An instrument for culturing and detecting the presence of microorganisms in human tissue specimens is disclosed. The instrument includes one or more drawers slidably received within the instrument housing. The drawers include racks for holding and agitating a plurality of specimen containing bottles. The instrument may include a mechanical drive apparatus designed to move the racks in a substantially sinusoidal pattern of motion. The racks are preferably provided with gripping means for removably and repeatably positioning the bottles within the drawer. An optical detection system is also disclosed, in which an optical filter is used to render a photodetector substantially blind to all light other than light emitted by a fluorescent sensor located within the specimen vessel, including excitation light impinging on the sensor. The instrument preferably includes a forced air convection system for warming the interior of the drawers and the specimen vessels held therein.

Description

~ 93/24~34 2 1 ~ 3 ~ S; O PC~r/U~93/~5233 ~PP~ FOR C~T~ING 3~D
DET~C~I~G BAC~3R~A I~ ~I TI~3 ~EI D OF T~ N'rION
This invention relates ganerally to analytie:al apparatus f or detectlng the pre~;enc:e of bac:teria in hlaman ti~sue, and i particularîy directeà to automated apparatu~ ~or culturing ~nd ~etecting viab~e bacteria in h~:man blos:~d ~pec~men~O
~0 ~c~L5 Bacteremia - the p~olnnged presence of one or mor2 viable-bact~ri~ in the blood ~ a eerious and life-, thr~atening in~ection. The mo~'c cor~morl ~tom of baetere~aia i 5 ~ ~ever of unkno~m origin. Accordingly, hospita~ routinely per~or~ ~ larg~ ~umber oP te~s; to determin~a wh~ther patie~ts exhibit~ng this ~;ymptQ~a have , ba~t~remia. Pr~sently, th~ only way ~ dg~finitiv~
di~gnosis can be~ade is: by i~ol~ting bacteri~ in the bls:llod~ by~ans ~o~ ~a ~;o-¢alled ~Iblood cultur2." Because o : bacteremia is lif~threatening, positive specimens must be: detect~d as quickly as possible ~ that the patient :~ oan be tr~2~ted: with the corr~ct antibioti~ ~O
~: Current}y, lthere ;~re~:~everal methods o~E detecting positive~ blood ~ultur~ he c:onventional manual 25: ~melthod in~tolYes~ inoculating bottles c:ontaining a growth m~di~ with~lood~:~p~ imen~. ~he growth ~edium is : ~:for~ul~ted t~pr~vide nutrient~ for bacterial g~owth.
The bDttles:are~;inspected~daily fo~ obvi~us:~ign~ o~
:b~cterial ~ro~th~ ~mpl~ fr~m b~tles ~u~pected to b~
30~ ip~sitiv~:are~then fur~he~ cultured-to obtain is~la~d bact~ria:l colonies~~which~can;then be ide~ti~led. This : ~ethod~i~ v~ry labor-intensi~e~and ~stly, ~ince daily inspec~ons and~ub~ulturing of:suspect bottlss are ~:: required~

WO 93/24234 - PCr/lJS93/05233 !

Yarious ~ttemptE; have been made to improve the t:on~entic~nal ~nanu~l method~ For example, cultu:re bottles hav~ b~en made with added ~tta ::hment~
containing E;olid media. The u~er imrert~ the ~ttle 5 each day, ther~by inoculating the ~olid medi~ and enabling growth of isolated b~cterial colonies, whic:h can then b~ ~denti~i~d. ~other improved proce~s uses a 'grc>wth indic~tor" which detects the buildup o~ gases in the head~pac:e of the bottle~, ~ third method is to lD c:once~ntr~te org~ni~mæ in the ;pecimen by centrifugat~on and then culture the cg: ncentrat~d bacter~ a on ~:olid media. Despite su~h imp~ovement, these methods still ~u~fer from the drawba::k of being highly labor~
intensive .
Atten~pts to automate the prc~c~ss o~ cul~ur~ng blood ~speci~en~; h~e ~l~o been m~de,, Most auto~ated prc~ce~s rely on the f act that ~ac~eria c:ultured ir a ~edi~ inGluding a carbon ~;ourc~, such a~ glucose, break down this carbon source to form C0~ ~s p~rt of 20 normal growth and metabolism. Early ~c~rts at automation u ed culture bottles cont~ning radioisote>pe-l~bell~d media, ~lood specimen~ are inoculat~d into `th~ bottle. Bactexia, i~ present in the ~pee:imen, ~etabolize the carbon-oontaining 25 co~n~pound in tl~e medi~ a~nd sli~e of radioact~ve-lal3~11e~
t 2 as a ~waste product.~ Gas: in the headspace of ~:he bo:ttle i~ ampled by punc~uring: the ~eal at the top o~
~he bottle wikb ~a needle and xemovin~ ~ portion o~ the gas. ~he r~dioactive 02 can then ~ Zlet~c:ted by :; 3~: conventi~nal r~diometry.
P~ number o:E~ dr~wback~ have been r~poxted with ~;uch ~y~t~ms~ ~ For ~xample,~;EPO P~tent Application No.
85302261~.4/ publIshed October 16, 1985, ~;tates:
"R~dioisot~p~ labeled material~ are experlsl:Y2 ~nd 35 require ~pecial handllng during 6torage, use and :

W0 93/24234 2 1 1 3 ~ 5 0 Pcr/uss3/os233 diFpo~al. Moreover, although the level~ of radic~activity enc:ountered in using euch ~y~te~ are very low, prospecti~re u~ers may be deterred by per onal f ear5 Of radioact~vity, n Mor20v~r, 80m~ rese~rch ha~
5 6ugge~ted that radiom~tric detection Ey~;t~ms are less accur~te th~n oth~r ~ethods and reeult in ~re ~al~e positive re~ding~.
Secc~nd, ~uch ~y~tems are "irlv~si~e, " that is, th~y require the use of a needle to puncture the bottle E;eal 10 tc~ o~tain gas for testing. Be~ause ~ample g~s mu:t actually be removed ~rom the bc~ttle, ~ irly complex pne~matic ~sy~tems ~re needed to handle the gZ15 ~nd return it to the bottle~. Further, if the ne~dl~ ~re not properly ~;~erilized, ~he spe~i~@ns c~n be 15 contaminat~d with bac:teria on the n~edlel xaising ~he potential for "fal~e positiYei' rea~ling~. In addition, ~: becau~e the ~o~tle~ ~re ~;ampled and read inv2~sively, aut~ated instruments~are genex~lly ~ore somplex mechanlcally, ~inc~ the botl;les ~ust b~ tran~port~d 20 mechani~ally frc~m an "incubL~tion" tstion, wher~ the o~t1~ are maintained at the appropriate conditions fclr bacterial~growth~ to a "rsad~ng" ~tation9 where the ~: ~ headspaae gas is fiamp1ed ~nd read. Most signi~ antly, t~ need to ~andle needl~s~ ~or perio~lic t~sting ~a 2s 1abor-intensive and,;; ~ec~use the culture bottles contain blc~od,: increases the~: ri~;;k o~ di~ea~e ransmi~sion du~ to needle ~ticks and the like~ i 13Po ~pplication No. 83108468.6~ ~published Au~ust ~: 27 ~, 1983) ~ummari~:~s the relative; ~ene:tit o . i~ 30 I nol~in~asive ~amp1ing o~er invasive method~
"there is :no possibility of ~contaminatlon c~used by n~ed1e or probe pene~ration of the vial ~;eptu~n;
:~ the design ~of ~rl automated ~ppara~us ~ si~nplified, in that there is no need to proYide provisions for a ::

::

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211~50 WO 93/2423~ . PC~/US93/0~233 nPedle-car:rying head assembly or other imta~ive ~ampling ~pparatu~;
the nee:es~ity t~f repl~cing f lushed head sp~ce gas with ~;terile cultur6~ gaE; i~ eliminated;
S the u~;e oî ~peci~l culture ga~eB i8 not required;
~a~3ter vial ~;~mpling iE po~sible, ~;ince ~nly vi~l pc) i~ioninS~ i~ invol~red;
no ~ertical head motic~n i~ nec~ssary;
the t:GSt of c:ulture media raw mat~rials is reduced âue to the elimin~ion of any radiolabeled ~ubstrat~;
and all radiois~topes ~r~ eliminated, Which eli~mina~s the probl~ms of ~3hipping, handlinsl ~nd storing low level radioisotopes. n (5¢e EP0 Patent Applic~tion Nv. 83108468.5, pp. 3~9. 3 E~rly atte~pts to i~prov~ autoDIated ~ n~trument~
f ocu~ed oa~ impro~ing the detection system . Thus, EPO
Applicakion No. 85302261.;4 dcscri~es ~ ~;ystem in whic:h radioisotope labelling has been replaced with direct ~: ~ 20 d2tection of non-radioactiYe C02 in the headspace gas : by ~ans of infrared ~pectr~scopy. ~hile this : . alle~iated ~he~pro~lems a~soeiated with radiometric de~ection, the ~hortcomings of invasive ~amplin~
re~in. In~addition, the u~e of infrared ~pectroscopy : 25 r~quires that ~ulture~bottles be made o~ ~pecial ateri~
: ~ EP0 ~pplication No~:~:83I08468.8 di~cl~s a ~y~te~
w~ich~dateot~ ~O2;~1~v~16 in the headspace ~as ~y taXing ~: infra~ed r~adings;~d~irectly t~rQugh the culture bottl~, li.e~; n~ninvasivelyO~-H~wever, ~he in~t~ument disclbsed is:eg~ipped with ~nly~a~ngle light ~ource and det2~0r. This, in turn, requir~s that the cultur2 s be periodically cycled paet ~h~ detector f~r readings, thu~ increasi~g the m~chanical ~mplexity of : 3s ~he in rument and limiting the ~umber of samples the ~ .

:~: :

W~ 93/24234 2 1 1 3 ~i ~ O PCr/lJS93/05233 instr~ment can rapidly process. Finally, problems can occur in calibrating the infra-red spectro~eter to the many bottles which must be read, M~re rl3cently, i~proved instru~ents with nor~-5 inva~i~e ~ampliing ~y6tems have been developed. In these systems, the cultur~ bottle i?~ incubated ~nd r~ad in the same loc~t~ on within the in~trument. Each bottle i h~ld oa~ a r~ck inside the incubation chamber.
The bo~tles are periodically agitated (to incre~se the lo diffusion of CO2 and thex~by ~horten detection ti~e) while being in~:ul~ated at approximatel3~ 35 C. :
- -EP0 Paten'c Application Nc~o 1~920055~.7, published ~;eptember 20, 1989, de~cribes the detec:tion syste~ used in ~;uch instrumentæ. A colorimetric ~ensor (pH
15 indicato~ adh~red tc~ the b~ttom inside sur~ace o~
~ach bl~ttle. The ~;~nsor turns from gre~n to yellow as the l~ve? e~f ~2: within the media incr~a~es.
Individual optical unit~ are pxovided for each bo~tle.
These optiaal u~its include LEDæ to illuminate the , 20 sensor, photodet~ctors I and associated electronics and ~ignal corlditioniJlg equipment. The instrtlment periodica~lly: '9reads" ~ach ~engor using r~flect~d ~ight : ~ to ~onit~r change6 in the :transmi~;sion of the ~ensor at a spe:cifi~ wavelength.~ When a lgvel of CO2 G~nsi~tent 5: wit~ microbial: grc~wth is rea~bed, the instr~ment al~rts the user of 8 ~positive blood ulture.
~ hile the~e improYed ~ystems hæv~ all~viated ~me of the problem~ of cc~nventional blocad culture instrwllent~, ~;eYeral~ drawbacks ~till remain. First, 30 I the~ instru~ent~ h~re ~een ~quipped ~i~h ~nclosed, ven-li3ce'~ incuba~ion chambers. ~his, in tur~a, : requixes that: lthe~ instrumellt be fairly l~r~ .
partic:ularly in h~ight) to ac ::ommodate the number of culture ~ottles~ typically proce~sed in a h~spital 35 laboratory . Th~is is a ignif icant disadvant~ge in many '-.
~: :

2 1 ~ 355 WO 93/24234 Pcr/uss3/ns laboratories, I;ince f lo~r and bench E;pac:e i5 typically ~t a premiw~. This arr3ngement i6 ~ 80 unde~irable from the :tandpoint o~ the user, since the topmost bottles may be out of reach when the i n~;trument i~
5 placad on a laboratory benc:h,.
Se~ond, beczllu~e the detection ~y t~m is based on ~:hanges ~n the light transmis;sion of th~ sensor, the light illuminating the a;ensor ~5 the E;a~e wavel~ngth a~
the light ref lected ~rom the 6en~r 0 ~his ~akes lt 10 possible for light which is not indicative of change~
i~ the æ~nsor (e~g., llght r~eGted fro~ the ~bc>ttom of the ~lass or plastic: culture bottlq~, ~5 well as other reflective ~urfa~es) t~ reach the detector. Because the detection systera does nc)t di~criminate between 15 light re~flected from the sensor and ~;uc~h unwan~ed "noi~e,~' th~ dynamic range of d~ection is gen~rally : ~ ~ more limit¢d~ In~ddition, it ~ecomes rritical to :: phy~ically i~olat~ the illumina~ing light ~our~e ~rom the d~t~ctor, pl~cing further de~ign constraints ~n the ~: 20 configuration of the optical ~yst~m.
:Accoxdingly, ~:~need~xi ts *or an automated blood culture:inskrument ~hich is capable of `incubati~g b}ood pecimens under~th~:appropriate~c~ndit~ons, but whi~h : : ha~ a:compact des~n,: thereby reducing th~ laboratory 2s floor:~pace it:occupies ~nd making it more convenien~
: : for u~e by lab~ratory medical ~e~h~icians. Furkher~ a need~exists~or~an ing~rument which uEes non-inv~i am~ling ~nd~non-radio~etr~o detection~ but which has highly accuratè and ~nsi~ive detection system~ which :301 do~-not rely upon~mea~uring c~anges in light transmi sicn of~mon~chromatio~light.

Accordin~ly, ~:it i~ ~n~obi~ct o~ khe pre~;ent vention to p~ovide an autom~ted ~pp~ratus for ~: : 35 c:ulturing and d~etecting bacteria in h~man tissue (in :

2 Ll 3S~ O
W093/242~ PCT/US93/~5~-33 particular, blood~, which ~as a compact d~sign, thereby minimizi~g mechanical complexity ~s well ~ the ~mount of laboratory floor ~pace it occupie~.
It iB a ~urther ~ject Df thi~ invention to provide a blood cultu~e apparatus in which the blo~d ~peci~en bot~les are kept within easy rsach of laboratory technicians for ~impl~fi~d h~ndlingD
It i~ a further object of ~hi~ invention tD provide a blood culkure apparatus with means for maintaining lo specimens at the appropriate temperature c~nditio~s for culturing b~cteria, ~ut with a compact design and a - reduced 'fo~tprint."
It i~ ~ furthe~ ob~ect o~ thi~ inYention t~ provid~
a blood cultur~ ~pparatu~ with a high~y ~ccur~t~ but lS non-invaasive d~tection y~tem, which do~ not re~y on Eadio~etry. ~;
It i~ a further obj~ct of thi~ inventiGn ~ provide an improved opt~cal det~ction ~ystem in which th~
deteetor is ~'spectrally isolated~' ~rom the light : 20 illuminating-the ~ensoF, th~reby improYing reliability ; and s~sitivity:of optical det~ct~on.
t is a further o~j~c~Q~ this inventi~n t~ pro~ide an improved optical det~G~ion system wh'ch is ~imple :and r~latively inexp~nsive, but ~hic~ pxo~id~s the s Bccuracy and~ènsitivi~y;needed for~u~e in d~tecting the~pxe~en~: o~bacteria in human ti su~O
Th~se~and oth~r o~eot~ are~accomplished by .
providi~g:a~:~instsument for detecting the pr~sence of m;iGroorg~ni8ms~in hu~an ti~sue i~aoludi~rlg ~ hou~ing ~nd 301 ~one~or mor~e drawers ~1~dab~y r~ceived~in th~ h~us~ing~ ~
~; The drawer~include ~eans~for ~o~ding a plurality of peci~en-containing v~ssels. The drawer i~ moY~ble be~ween a fir8t,~clo9ed pssition, in which the v~ssel h~ldinq mea~s:is substantia1ly encl~sed wlthin the

3~ housin~ and a :second, open position, in which the :: : :

W~93/242~ 2 1 1 ~ ~ S ~ PCT/US93/05233 vessel holding means i~ located ~ubstantially outside of the housing. In ~hi~ way, a large number of ~peci~en-containing vessels can be ~tored insi~e the in~trument for incubation ~including warming, s agitation, and m~a~ureme~ o~ bacterial growth), while ~till being readily acces~ible to the operator of the instrument upon opening o~ the drawer. Sueh ~n arrangemenk permits a large number of vesselc to be ~tored whii~ ~reatly reducing the overall ~ize and 10 "fc~otprint" of the instrument. A unique warming ~ystem, wh~ch pr~f~rably utilizec forced air conv~ction w~thin the draw~r, i8 used to warm the interior of the drawer to an elevat~d temperature suitable ~or encouraginy growth of microorganisms while ~ e drawer is cl~sed.~
Another ~peot of the present invention i~ an instrument having a unique optical detection ~ystem ~or detecting the presence of bactexial gro~ h with~n the pe~imen. Thi~ system includes ~ight emission means :~ 20 for emitting excit~ti~n light falling withi~ ~n emission wavel~ngth r~nge. The ~ystem i8 co~figured ~o ~hat the excitation light impinge~ upon a ~pecimen-containing ~ssel h~ld~within the instrument and, m~re particularly, upon~a ~ensor located:inside the v~el~ :
; ~ 25 Light ~anating ~rom the sensor (which, preferably, ; includes a light emitting ~luoropho~e) i~ dete~t~d by a light detection means/~;which conve~t~ the light ~nergy emitted by the ~nsor ~nto a d~tectable ~ignal. Of :~
particular i~por~nc~ i5 the use of a filter means 30~ptically i~terpos~d~between the li~ht ~ourc~ and t~e d~tector. The *ilter is desi~ned to achie~e ~ubst~nti~l ~pectra1 iæolation be~ween the exGitatiQn l ight and the light emanating from the ~ensor. In ~his way~ substantially al} light falling within the emission wavelength range i~ prevented from reaching 2113~0

4 PCr/US93/05233 the de~ector, thus rendering the detection means ~ubstantially "blind" to light falling within 'che emission wavelength range. It has been di~co~r~red tllat ~;uc:h an arrangement impro~res the ov~rall s~n~itivity of the ins'crument. :;
~et z~nother aspect o~ the present in~ tion i6 ~n in trument ha~ring ~ uniqlae aS~itati on system ~Eor agitatisls~ the sp~cimen containing vessel~ whi ~e they are being held within the instrument. The ayitatiQn ~;ystem utllize~ echani~:al arx~nSIement designed to ag~ltate the ve~;sel holding means ~n a~ mann~r ~n whis:h it~; di~tance of tr2vel fro~n a fixed referenc~ point ir~sreases ~nd decreases in a E;ubstantially ~E;inusoidal ~anner. ThiC sinusc~ida~ pattern of motic~n makes it possibl~ to start and top th~ gitation more easily, 1 thus helping to si~plify ~nd reduce the cost o~ the components used to manufacture the instru~ent. ;:
Still a further aspect o~ the present in~ention ~8 : an instrument having a unique ~eans ~or gripping the 20~ ~pecimen-containing vessels within the instrument.
This gripping ~ans i5 d*signed ~o remoYably and ~epeata~bly hold the vessel~a~a pr~def~ned, ~ubstantially~fixed~dep~h~within a vessal recei~ing aperture. ~hi5~arrange~en~ helps t~ en~ure tha~ the : 25 ~ ~eæsel is correctly and c~nsistently p~sitioned relative to the:~ptical detection unit. The gxipping ~: means is als~ ~dapt~d:to proYide audi~le or t~ctile ~ eedback to ~n operakor wben the vessel i8 :properly : ~ inser~ed int~the~perture. Such ~edback helps to : 30 ~ ensure~ that the operator inserts t~e Yessel into the ~ aperture correctly. ~
: ~ The foreqoing~feàtures and advan~ages o~ the present ~nvention will be ~ore readily under tood upon consideration of the~following detailed description, :

, WO 93/~4234 PCI/VS93/05~33 1~ , taken in conj~nction with the accompanying dr~wings, in which:
BR~E:F D~CRIE'~ION OF ~R~WINÇ;8 FIG. 1 is a per~pective ~riew of an sutoma~ed bloc~d s c:ulture apparatus made in accordance with the present invention;
FIG. 2 i~ a side view of the apparatus, ~;howing one of the E:pecim~n~holding drawers in i1;s open positisn;
~ IG. 3 is a ~riew simllar to that of FIG. ~ in 10 ~;om~what schematic orm, with portiorls of the ~pecimen-holding assembly removed to show t~ ~;yst~m for heatir~g and-circulatirlg air within the ~pecimen-holdirlg drawers; : ~
F~ G o 4 is a ~ide view o~ the sp~cimerl~agitating l5 - a~se~l~ u~d in c~ne embodimer~t of the pres~nt : ~ : inver~`tion, ~h~wing the gpecimerlc:ontaini~g racks in their low~r~os~ agita~ion position;~
FI~. 5 i~ a view ~imilar tc~ that: o~ FTG . 4, ~;he: wing the ~peci~nen-containing rac}~s in their up3permost 0 agitation p~sition;~
IG. 6 i~ a ~top view of one of the ~pecimen~ ~:
Gsntaining d~awars taken a}ong the;line S--6 in ~IG. ~;
:FIG. 7 is~a~front~iew of one o~ an individual ; ~ : specimen:~older~
: : 2s ~ ~FIG.~8~is~a~ cros~-~e~tion~l~view taken along the lin 7 -7 in~FIG~ 7i ~
FIG~ 9 i~ a ~:ide~:vi~w o~ an a:lternative bottle gripping ~rrang~ment for retaining culture b~ttle within the bot~le holding r~cks;
30i ~ FIG. 14 i~a:per~pective view~f an a~sembly for ~oving:tbe peci~en-holding drawer~s~between their sed and ~pen po~itions; ~ : :
FIG;. ll~is ~a per~pectiYe~view~of ~n assembly for gitat~ng the~peclmen-containi~g~r~cks;

, ::
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: : :

i~0 93/~4234 2 1 1 3 ~ S O Pc-r/US93/05233 FIG. 12 is a dwell chart ~howing the relative position of the ~pecimen-containing ~k~ during ~everal ~git~tion cycles in graphical ~onm;
~ IG. 13 i~ a graph o~ inten~ity ns a function of wavelengrth, ~howin~ ~chemat~cally the optical propertie~ ~f the ~xcitati~n light ~s well as the light :~
emitted by the fluore~cent sensor; and FIG. 14 i~ a ~ide view of an ~lternativ~ as~eD~bly which may b~ u~ed to ~gitate the ~pecimen-containing 1~ r~ck~.
.. ~I=ZI ~', - Figs. ~ ~nd 2 sh~w th~ general arrangement of an instru~nent 10 made ~n accordanc~ with the present inv~ntion. This Specification de~cribes a pr~erred 15 ~O~lm ~f t~he inv~ntion, in which the instrl~ment is ~sed to aulture and d~tect b~cteria in huuman ti~sue ~nd~ in partir-ular, in huuDan blo~d. ~owever, although th~ ;
ins~ruunent is described as being us~a for det2ction of micr~rganisms or b~cte~ia in blood, it will be .
understood that the instrument may be u~ed to detect micro~i~l gpro rth in any nuunber of tissue~, including : ~ :urin~/ cerebral- spinal fluid, ~ynovial ~luid, and : others.
; : Fig. 1 i}lustrate~ the~ instruu~ent of ~he p~esent : : : 2~ invention generally. ~ Instrlum~nt 10 in~lude~ a pecimen~handling~ du1~12 und~r th~ con~rol of micr~comput~ whidh i~ pr~progra~med to ~ollow : : cextain:sp~cimen-ha:ndling protocol~ in accordanc~ wi~h ; input;rrom the Y~er~ A detail~d des~ription ~f ~e g~neral ~y~es of ~oftware comman~s ~nd pr~ce~sing ~teps : : ~ which could b~ u~ed to pro~ram the ~icrocomput~r to perfo nm ~uch protocols i~ ~t~c~ed a~ ~n ~ppendix hereto.
: In ~he e~bodiment shownn, each ~peci~en handling ~:
: 3s ~ module ~2 includes a housing 32 and two ~lide-ou~

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WO 93/24~34 2 1 1 3 S ~ O PCr/US93/0523~

drawer~; 16, 18, each of which includes a plurality c~f ~2~ck~; 20, 22, 24, 26, 28" 3~, which hold the ~pecimen-c:ontaining vessels c: r bottles f or pro;:es~;ing . In Fig .
1, drawer 16 is fihown in it~ open position, whil¢

5 drawer 18 i6 shc~wn ir~ its clo~ed pe~sition~
As de~cribed in gre~ter detail below, each o~ the J!;lide-ou~ drawers ï6, 1~ ~6 equipped with a heating ~;y~;tem (see Fig. 3) designed to warm the drawers to the apprc~pri2te temp~rature f or bacterial ~rowth and ~0 nu~int~in them ~;u~stantially ~t that t~mperzlture. Each of t~e dr~wer li;, 1~ i& ~ l;CS equipp~d wi~h a mec~nic~l ~git~tion 8y8tem (~ee Fig~. 4 and 53 iEor p~riodically agitating the bottle~;. Such ag~t~tion i~
known to ~;ht~rten the time lto detection by cauE;ins~ C02 generat~d by bacterîa wi~hin the bottle to di~fus~ more r~pidly t~ the ~luorescen~ ~ensor, which i6 pre~rably : : affixed to the bottom insid2 o~ the bottle~ Finally, the drawer~ 16, 18 ~re ~16~ eguipped with an optical detection ~ystem, in~luding a plurality of optic~l : 20 units ~s~e Fi~s~ 7 and 8~ which monitQr CO2 productîon by ~ptically int~rrogati~g the ~luore~c~nt sensor~ on ~ : :each of the culture bottles. Optic~l readin~s for each : bottle ~re tra~sferrsd:via a data linX (not ~hown) to the ~icro~o~puter 14,~where~it i~ $tored for later : 2s~ retrie~al a~d:use.
s best s2e~ in:Fi~s. 1 and 2, in a pre~erred form bloo~ cultur~in5trum~nt module includes at lea~t on~, and pref~r~bly:tw~ or ~or~' ~lide-out drawers 16, lidably`r2cei~ed:in~h~using 32 for holding ~he : : 30' blood~pecimen-oontaining~vesselg or bottles during p~ocessing.~:By~config~rin~ the~instrument in thi~
manner in accorda~ce with the pre~ent invention, t~e : : in~t~ument ha~s:~u~ficient bottle-holding cap~city for : hospital laboratory ~e, while ~aintainin~ a compact ~ize and a small "footprint" desirable for mos users.
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WO ~3/24234 - 2 1 1 ~ ~i 5 0 ~/US~3/05233 ~

This is because the bottles can be held within the instrument for ~ost proces~iing steps, while ~ ill k~epi2lg them readily available ~nd with~Jl ea~;y reach of the l~boratory technician up~n ~pening the dra}wer. The 5 compact . iz~ of ~e instrument ~ade in accsrdance with th~ presen~ invention i~ ~n important advan~age in mo~t E;ettinçls, particularly hospit~ ince laborstor~ ;
~pace is generally limited due to the large number of instrument and pieces of e~uipment housed wi'chir~ a lo typical microbiology ~ ~boratory.
Referring to Fig. 1, the front face 5i~ a~ach drawer inc~udes; arl informati~n panel/user interface for digplaying inf onaation relating ~o the E;pecimen~; ~eld within that drawer and~ ~or ~nablirag th~ user to c~ ntrQl 1~ certain~functions pertain~ng to that draw~r~ ~In ~ig~ -1, the inf ormation E~anel for draw~r 16 i~ de~;ig~l~ted by th~ ref~rence numeral 17.~ Inft~a~ion which may b~
di~pl~yed ~n the inf ormation pan~l by, $ox ex2~mple, LEI) or LCD difipl~ys I include the t~mperakure within th~
drawer, the number of 6pecimen bottl~s which have been read z~s "positive, " and the nu~ber o~ available p~sitions fs~r :additional specimen bottle~;. Functions whic:h ~ay be controlled by the user may include opening :~ and clo5in g the~dr~wer, ~s well as di~;abling an al~r~
designe~l to signal, ~or exa~ple, a po itive read~ ng within the drawer. ~ Howe~er, ~ will be understood that c~ther types of info~ation m~y be di~;played on the panel ~nd othe~ commarld~ may be l`ikewis. be input iEr~m th~ user inter~ace, as desire~.
30i The,sy~tem o~ the present invention i~; preferably ~ designed fiO that multiple ~peeimen ~andliny ~dules ~ay : ~e inter~aced ~with a:~ingle microcomputer. In this way~ the specimen holding capacity vf th~ ~y~em may be ~ubstantially:increas~d, as desired. Th~ mo~ule~ are 3s al~o prefersbly designed so that they may be ~tacked ' :

21 1355 ~
WO 93/24234 P~r/U~93/05~33 t~ne atop anothe~ if desired, to minimize the amount of f 105x ~paee the E;y~tem vccupie8 .
Ref erring ~ga ~ n to Fig . 1, the drawer 16 i~
~lidably r~ceived withirl housing 32., In ~ preferred 5 ~rrangement, a pair of ~nt~gral F:lide extensions 34a, 34b are rigidly ~f~ixed to the drawer 16 by means of l;~rew~, bolt~ or the like at a posi~ion adjacent the top of drawer. The ~i;lide extensions are ~lid~ly received within tracks 36a 36b. Txacks 36a, 36b ~re 10 th~mselves ~lidably received wi~hin receiving guides (not shc~ which are rigldly mounted to the in~ide o~
housin~3 32 . Conventional ball b~aring s~sembli es (not ~hown~ permit the ~lide ~xtens~ons 34a, 34b tG ~lide f r~ely within tracks 3 6a, 3 6b, ~nd the trz~s:k~ 3 ~a, 3 6b 15 tl~ ide~ freely within the raceiving guid~. Th~ ~lide e~n~ion~ 34a, 34b, track~, 36a, 36b, ~nd recei~ving guides are co~nerc:ially available in the form of a three ec~ion ball bearing 51~ ~e which permit~ the drswer 16 to sIide in an~ out of housing 32. Success 20 has been had with a three-section ball bearing ~lide Model Nt~o ESBB manufactured b~r Barnes Engineeris~g Company of ~naheim, Cal~fc~rnia. Pref~rably~ the ~lides are made of hardened~t~el which has be~n elec~rc~-pla~:ed ~uch t hat they ~dequately ~upport the drawers 2s 16, ~ while maintaining their corrosion re~i~tans:e ~: ~ und~r the t~mper~ture conditions pre~ailing within the : draw~rs. : :
ig~ 1~ illustrate~ t~e~m~nner i~ which the bottom of drawer ~6 i~ 1 dably mounted within the ~ousing.
30 ingle~ thre~-part~ball bearin~ de, p6~sitis:~ned t~ l~y f}at (~.e:., rotated clockwi~e 90: degree relative tc~
: ~ : the ~lide ext~ns$3ns 34a,: 34b o$ ~he three part lides il~u6trated in Fig. 1) is~ :used~ to prevent th~ dr~wer from "wobbling"~rom ~ide to~ side~within the housing.
3s The slide extension (not ~hown~ rigidly attached to .

W0 93/24234 2 1 1 ~ ~ ~i 1) P~/lJS93~05233 the und2r6id~ of drawer 16 within ~ longi~udinal recess 150 wh~ch run~ ~ubstantially the length of th~ drawer 16~ ~h~ extension iE; received in a track ~5Z, whicht in turn, iE; re ::ei~ed within receiving guide 1~4 mounted to the inside o~ the drawer housing. AE; ira mounting the top of the drawer, ball bearing aE;~emblil2s ar~ used to ~nable the ext~nsion to ~lid2 fre~ly within th~
tra::k 152, ~nd the track lS2 to slide freely within th~
receiving gu~ de 154 .
0 ~lthough Fig~. 1 and ~0 illustrate one ~ethod of ~idably attac~ing the dr3wer to the housing 3~ u~ing ~hr~e-part ball ~earing ~lide~, it will b~ und~r6~00d that the dxaw~r~ may b~ 61idably mounted to the h~sing using ~ny u~table ~e~ns, ~uch ~5, by way og example, conven~onal ~;lides, tongue and groove configurations, ~nd the lik~ .
fn a pref~rred arrangement als~ illust~ated in ~g.
10, m~ans axe ~ pr~vided t~ mov~ the drawer ~6 under power b~tween~a: rst, closed pos~ion, in which the : xo drawér and its contents are substantially enclosed ~: within th~ bousing 32, and a:~econd, open p~sition, in : which the drawgr~d its contents ~re locat~d subst~ntially outsid~ ~he housing 32~ The drawer is moved in respo~se to ~cc~mand ~rom ~h~ u~er, which can :: :: 25 be inp~t~ ~or exampleO ~rom microcomput@r 14 or ~rom : the infoF~ation~display/user interface 17 in Fig. 1.
: As ohown:in:Fig. l~, ~otor M, under the control of the mi~r~o~puter, powers~n associated b~lt drive 156~
The:be~ drive:1~6~) in turn, rotates a ~crew dri~ 15~ :
which engages thre~ded drawer extension 160. The ~: drawer extension ~60 i~ rigidly ~tached ~djacent a :~ ~ l~wer corner:of t~: d~awer 16. Upon actua~ion of th~
, ; ~otor~, tbe rotating:screw~drive ~oves tha drawer under power ln~or out o~ the housing~ as d~sir~d, in ~he directions of the double-headed arrow. Appropriate ~ t W~ 93/24 34 2 1 1 ~ 5 ~i O P~r/VS93/~)5233 f l~gs are u~eà to ~ignal the micr~cc~mputer t~
de~ ti~rate the motor M once the drawer ~ 6 reac:hes its open or closed positios3.
It will also be under~tood th~t other means for s ~echanically moving the drawer in ~r ou~ of the hou~ing, ~E;uh a~, by way of example, belt ~rives, gear ;821~1b~ ; "!lnd the like, ~ay also be used in practic:ing t~ pre~ent inverltion.
P~e~erriT~g now to Fig. 2, the drawer 16 also 10 includes ~means f or holding a plurality c~ ~;pecimen-containing vessels. Thi~ vessel-holding means ~ay take tlie :~orm of a plurality o~ racks ~0, 22, 24, 26, 2~, 30 wb~:h ar~ adapt~d to hold or retain the sp~imen bottles during processing~ Each rack h a plurality o~ bottle~receivin~ openings 38 which ~re ~iz~d to.
~cco ~ odate specimen bottle~ As will be d~crib~d in ~re~ter d~t~il below, a~ th~ base o~ e~h bottl~
r~ceiving opening 38 i~ ~n optical u~i~ 46 *o~ taking optieal r~adings of a ~ensor a~fix~d to the bottom :20 inside of the bottle. Although in ~ig. Z ~he bottle receiving openin~s are illustrated as being cireular ~o : accom~odate a generally cylindrical 5pecime~ bottle, it will be unde~stood that apertur~s ha~ing ~ variety of ~ : ~hap~5 te.g.~ re~tangular, triangular, or poly~onal~, : 25 could ~l~o be u5ed:in appropriate circufflstances. In addition~ although the drawer 16 is illustrat~d wi~h ~ix ra:cks ccommodating 10 bottles eacht it will be under~tood th~t~other quantit~es may~al~ be held within the rack~.~ IndeedO it is preferr~d t~at each Idrawer ac~ommo~ate a~ ~any b~ttle5 ~s possible in order to maximize th2 ~apaci y of.each module.
: Wben the drawer is in itG closed position, the ~:
vessel holding means ~hould be $ubstanti~11y enclosed within, i.e.~ covered by, the housing. It will be `35 understood that the vessel holding mean~ need not be ,~

:~ .

WO 93/24234 ~ 5 0 P~r/US~3/~5~33 ~7 completely enclo~ed within the housing, I;o long 215 the vessels ~re ~;~bstanti~lly located within the hou~ing, thereby redut:ing the amou~t of t;pace the ~n trument module ~ccupie~ . L~ kewi~e, when the dr~wer i ln its 5 open pc~sition, the vessel-holding me~n~; should be lol::ated ~ubstantially outside th~ hc~u~in~ , i . e ., ira a ~:
position in which khe ve~;sels c:an be readily ~cces~ed or re~e~ved by ~he instrument ~3perator. `~
It will be understood that the racks may l~e 10 f astened together to $orm ~n integra~ed assembly, ~s illus~rated in ~ the drawings, or may be ~abricated as individual unit~; wh;ich can be re~o~rably ~ttached within ~`
the draw~r 1~. It snay 3t~e d~sir~ble in c:ertain c:ircums1:ances f or indi~idual racks to be removed ~5 that ~3pecimen bottle6 can be inserted sf f ~ite, and then the rack~ an~ be r~inser*2d into the instrument at a lat~r t~me. It will be understood that thi~ c~n be accc~mplished in ~ny number of way~, including pro~id~ng a frame within the drawer to which the rack~ ~ay be 20 remc~vably a~ached.
The face~: of each ~ ~ottle holding rack i~ aipped with an I,ED (liqht emitting diode) panel 15, which inc:lud~:s ~an array o~ ~EDs~: ~9, two of which are a~ociated:with ~a~h bo~tle receiving opening 38. Th~ `:
2s: LEDs assooiated with each:op~ing pr~id~ the user with : informatio~ concerning the~t~tus o~ the optical :`readings for~the b~ttl~contained in that opening. For example, a red~LED;might~:indicate:a bo~tle t~ting "positive,~l whi~le:~ green ~ED might indieate a b~ttle : 13~ ~whi d h~s as~yet te~ted a'negative.~' The panel ~5 may e~the:~orm~of~a~ printed circuit ~ard whirh includes : ~ ~ the ~rray of LEDs for all ~f the ~ottl~ receiviny enin~B in that rac~, as:well as a~sociated c~rcuitry : :~or t~an~mit~ing on/of$ infsrmation and p~wer to ~he 35 LEDs unde~ the ;control of the micr~computer. The panel ' W093/242~ 1 1 3 ~ 5 PCT/US93tO5233 1~
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lS may the~ be removably mounted to itB rack by means of Velcr~0 fa tener~ or other similar mean6.
Fig. 7 dépicts a portion of one of th~ bottle-h~lding racks in greater detail. Adjacent each bottle-receiving apertur2 is gripping ~eans ~dapted torem~ably grip the pecimen-containing Yess~l 60 th~t it ~ay be r~peatably held at a predefined, ~ubstantially fixed depth within the apertur~. Thi~
depth i~ pred~ined and ~ubstantially ~ixe~ to allow lo the optical u~it to interrogate the ~nsor ~ffixed to.
the ~peci~en-c~ntaining vessel from a well-defined and . repeatable position, thereby ensuring more accurate optical readings when a vess~l is removed ~nd then reins~rted. The gripping means may comprise o~ or ~ore ~lexible arms positioned adjac~nt the periphery o th~ ~pertureO ~he gripping mean~ ~ay ~ke ~he form of one ~r m~re a ~ s. In Fig. 7, the gripping m~ans includes khree outwardly extending fingers 40a, ~Ob, 40c position~d arQund:the periphery of each cylindrical op ning 38 in ~rder to repeatably position and ~upport ~ the bottle within the rack. The fin~ers may be : fastened ~ the base of the ~ck (shown in ~ig~ 9) or : ~ formed integrally therewith ~o that ~hey protrude upwardly adjacent~the op nin~. In one form of the invention, the~fingers 40a, 40b, 40c are molded ~ntegrally with the base of each rack ~rom a ~uitabl thermoplastic resin, 6uch as an acrylonitrile-: ~ ~ butadiene-~tyrene~ BS) resin or ~n;acetal resin (e.g.
Delrin0~ a re~i~tered trademark of E. l . Du ~ont de N~mou~s &:Co.~. Preferably, the fing~rs 40a, 40b~ 40c ~re uni~ormly spaced:~S approximately 120 interYals : around the periphery~of the opening. Each o the fin~ers 40a, ~Ob, 40c includes a reces~ed porti~n 41a, : 41c (the r~cessed porticn of ~inyer 40b is not vi~ible 3s in Fig. 7)~ which i shaped to engage an engagement area :

W0 93/24234 2 1 1 3 ~ ~ O Pcr~u~3/0~233 :

19 , ,',.':

c;n the outside ~urface of a ~pecimen bottle. A flanged end 42a, 42b, 42c on each finger i~ designed to engage the ~hc~ulder of ~. culture bottle insert~d int~ the aperture 38 .
Pre~erab~y, the ~ing~r~ 40a, 40b, ~oc ~re ~rranged to form an opening which i 6mall~r than the diameter o~ the culture bo'ctle. In that ca~e, the ~ g~rE; 40a, ~;' 4 0~ 0c s~ould al2sso b~ ~apable o~ f lexing or de~orming outwardly to admit the ~ottle and, in coop~ration with ~:~
o the ~langed ends 42a, 42b, 42c, to engage the shoulder o~ the culture bottle in a ^'6nap-~ittable" ~echanic:al - arrangemerlt once the bottle has b~en insert~d to the pr~-defined dep~h with~n the aperl:ure. Such ~n arrang~m~nt h~s ~everal advantagé~. Fir:t, it helps to properly position the bottom of the bottle tand, ag a result, the E;en~or affixed to the ~ottle) ~ecurely and :i~
repea~ably against the optic~l unit~6 to` ~nsure accurat~ and con~i~tent o~ptica} readings. S~cond, ~;uch a~n ~rxangem~nt pref erably giYes the instrument oper? tor ::
t~ctile and/or audib~e ~eedba~k when tbe bo~tl~
properly ~at~d within the opening, -helping tv reduce erro~t~ in loading ~nd p~iti~ing the bottl2~. In the :~ absence o~ ~uch~ tactile feedback, the op~r~tor could in~ert the bottle~ to the:c7pening ~o varying degre~s, 2s~ causl~g inaccuraay and inconsiskency in the optical r~adings.
ernative ~fflean6 of gripping the bottl~ within the bottle r~ceiving opening is illustrated in ~ig. 9, which ehow~ ~a: portion o~ c~ne~ of the bottle holding ~:
rac~s. I In thi~ embodi~nt, the bottle gripping m~ans :~:
includ~s 73prings :53: fQrmed of a resili~t ~etal, ;uch ;~
prinsl ~;tainless; steel.~ Again; ~it: ;`is ~ preferred tha~ :
at least three, ;~nd preerably four:,; ~prings 53 be ~:
: pro~rided for ~ach l~ottle and that they be e~ually ~;paced around e~e :opening. HoweYer, it will be ;.

~: : :

21 l 3~S ~
WO 93~2~234 ~cr/VS~3/05233 underE~tood that ~wo or even one,E;pring c:ould be used.
Tbe ~prings 53 ~re attached to base pl~te 57 (which, in thi~ embodiment iF: ~ade Irom ;~l~inum or another ~uitable metal ~ by rivet`~g, welding, or other 5 conventional means. Base plate 57 has a plur~lity of apertures formed therein ~;o th~t the ~;en or ~not ~how~) affixed to the insid~ o~ th~ bottle 120 can be opticall~ ~ nterrogated by th~ op~ical un~ t~ 46 . Each spriny 53 has a cximp 55 formed in one end for gripping 10 the bottle lX0.: q~he crimp~; 55 are shaped to en~age a corresponding engagement area taking the f orm of zn - i.n~nta~'cion or de~ent J~7 in the bot~le 120. ~e ~prings are ~lexible and resiliently deformable ~o that wh~n the bottle 120 i~; insert~d into the b~ttle ~s r~cei~ g opening~ ~e prin~ 53 are resiliently deI ormed in an outward direction ~o admit the ~3Qttle ~: 120. Once th~ bottle i~ fully s~ated at the :~ appropriate depth within it~ ap~tur~, the springs 52 : return substantially to their o~iginal position ~nd 20 ~ngage the detent 47 in the ~ottle 120. This is evident to the operator by the taGtils and audible eedback pro~id~d~whe~ the bo~tle " napfits" into ~ , : tight, mechanicaI engag~ment with the ~prings 53.
It will be un~er~t~od~by those ~killed in the ~rt that other simil~r way~ of rem~vably holding the ottles::within~the racks may ~ls~ be used, ~uch as, by :~ :way of example~ ball-spring plu~g~r6 designed to ~ngaqe a detent in khe bo~le,~ a plurali~y o~ spring~ arranged ~; : within the bottle~r~ce~ing opening ~o a~ to grip the ~i 30i bottle,la deP~rm~ble pl~st~c or rubber O;;ring, or a cam : and leYer ~ripping arranqem~nt~ ~ikewi e, the engagement area ~on: the bottle may take any number of hapes, ~uch a~::a cQntinuous~detent around the entire circu~ference o~:~the bottle (as illustrated in Fig. 8 : 35 or a mor~ l~ca~lized~area. In t~is regard, as noted W0 93/2~34 2 1 1 3 ~ S O PCI/US93/05233 ~`

nbove, it i~; important to k~ep in mind that the lpurpose of such arrangementE; i~; Sl) to hold the botltom of the culture bottle ~;ecur~ly in a pre-defirled poE;ition adjacerlk to, zandl 6ubstarltially centered ~ith respet:t 5 to, lthe opt~cal un~t to help a~;ure greater ~ccuracy and predit:tability in the clptiral re~dings, (2) to pro~ride the ~perator with so~ form o~ t~ctile and/or ~udible f eedback once the bottîe is properly se2t~d within the rzl ck ~ and ( 3 ) to assi~t the op~rator ~n 1~ positioning the b~ttle within the rack irl a repr~ducible and repsatable ~a~hi~n.
~ Fig. g also ;llustrates the manner in which the optical unit~ aTId related c:ircuitry are attach~d tc~ the base pl~te 57 o~ ~:he bo*le holding racks. ~ plurality of PEM ~a~tener~ 59 ~re rigidly ~f f ixed to ~he ba~
pl~t 57 at ~pao~d inter~ral~ along it~3 length. ~5ash P~ ~astener has an ~r~ul~r base 54 ~nd plur~ y of prongs 56 ad~acent i t:8 oppo~ e end. A plurality of optical uni~: 46 -- olle for :each bottle receiving 2c opening -- ~are at~aehed along the length of a printed cirt:uit board ~PC ~ 41. The PCB 4i is etauippad with the ~ne¢~:ssary :circuitry for pro~riding p~wer ~o the : opti ::a:L units and~: ~ox tran~mitting the optical xeadins~s .
- (wh~ich, :as ~ ined in~: greater detail below~ ~re 25 c:omert~d ~n~o:: a ~o~t~ge ~y the optical unilt3 to ~he ::
micro~ompu~er~ ~fDr ~torage~and la~er use. The PCB 41 also ;haæ ~plurality of ho~es formed al~ng it~ lengthO
To~:a~ach~ t~e PCB:`~41~ ~o :it~ bottle~ holding rack, the , pron~æ~ 56 on:the~ PE~ ~steners 59 ~re in~;erted into the . ,:30 i hole~ th~ PCB 41 until the PCB enga~es; the ~nnular -ba~es 54~ The pronq~ 56 d~form inwardly ~;c) that th~3y ean pa~s through the aperture~ in the PC~ 41 ~nd thez pring back ~to~ their original posi~ion s;o tha~ they xetain ~he PCB 41 în en~agement with the annular bases :; 3s54. In thi~ way,~: the PCBs 41 are easily assembled to :
:
~ ~ ' ~135~0 WO 93/24234 Pcr/us93/05233 tlle bottle holding racks, and can easily be r~moved f or repair or replas::ement.
A~ be~t ~;een in Figs . ~ and 2, the ins~ de o~ e~ch drawer i6 pref erably e~uipped with a b,ar-code r~der 5 162 ~:entrally positioned within ~ V-shaped channel 16~, which extends longitudinally ~ros~ the drawer 1~. The c:h~nnel 16~ ized to accommodate 2~pecimen bottl~
whic:h are to l~e inserted into one of the bo~tle receiving openings 38. Preferably, a bar-c~de lab~l i5 10 placed or~ the side o~ each ~;pecimen !bot1:1e lto identify the patient ~rom whom the specimen was t~ken. It will be underg~ood th~t many hospitals now emplc~y systQms in which detailed infon~at1on about a pat:ient i5 as~;ociated with a uniquP bar-c:vde ~or that pa~ient.
15 L~bel~; containing that bar-code are then u~;~d to t:rack Bnd identiSy t~atments and proredure~ pertaining to :~
t~at patient. It is:intended that the i~;trument o~ ~
~he pre~ent invention ~hould be capabl~ o~ interfacing with the hosp~tal` bar-code ~y~t~m, if a~aila~
Al~ernativ~ly, bar-code labels ~ould be generated ol~ly for u~e with:the in~trument of t~e pre~ent inYention to track ~pecimens ~nd identify th~m ~s having come from a~particul r patient.
When the user wishes to in~ert a;~pecimen bot~le into ~he drawe~:, he ~r ~he p}aces the:area of the specimen bottle bearing the ~ar-code~label in the V-~` shape~d~ oh:annel~164~and draws~the~:~bottl~:acros~ th~ bar-: : code;:reader 1~2 ~o scan the patient~inonmation int~
:~: t~e~cr~co~puter.~ :$he sy~te~Aukomatically dete~s :~ 30i where t~e bot~le is placed within:the drawer eo that he patient information can~:be~assQc~ated with the opti~ai readings~ for tha~:bot~le. ~ The op~ical readings : ~ a~d associated patient information are ~ored for later ~: retrieval and~use.

WO 93/~4234 21 1 3 S ~ O pcr/lJs93/o5233 As al~o 6een in Figs. 1 ~nd 2, the interior face of khe drawer i~; e~ipped with a };econd u~er interf acef in$ormation panel 166~, ThiE; u~;er interf~ce enables the u~er tc~ perform certain ~d~litit~nal operation~, ~nd 5 provide~; cert~in ~ddit~onal inf or~ation, ~uch a instructions f or ill~erting ~ new bottle ~nto ~n available bottle-receivin~ aperture.
Another ~iynif icant featurç of the present invention is a ~sy~te:m for controlling and maintaining 10 the t~mperAture c~f the ~pecimen bvttles while they ~re ~einS~ held wi~hin th~ ~lide-out drawers of the - instnament. Because the optimal temperature ~or encouraging gro~erth~ s~f many bac~eria is approximately 35-37 C z~nd, ~ore pr~f~rab~y, close to 35 C, f or ~any 15 blood cu}ture applicatic~ns it i8 import~nt t,G ~aintaia~
the bottles near or at ~thi t~nper~ture 80 that any ~: bacteri~ in the ~pecimen will multiply as r~pidly as pos~ibl~, thereby dec~ea~ing the tim~ i~ tak~ to detect a posi~iv~cultur~. Accordingly, the pre~ent 20 inv ntion includes mea~s operably associa~ed with ~he slide-out drawers for:~l):`warming the interior of the : drawer:to ~n~elevated temperature ui~able for ~: en~ouraging gro~th o~ mi~ro~rganisms, and t2~
:maintaining~the~1nte~ior~:of the~drawer~ ~ubstantially at 2s ~or~near ~h~t~elevated~te~perature, when the drawer i8 ; in~ closed p~sition.~ In~a preferxed form, ~uch means co~p~i~es~a~;~orc~d air convecti:on ~ystem which : will~now be:~d~s~ribed~in det~
Fig. 3 :illustrstes ~h~ int~rior of one of the ~:::. ~ 30l ~lide-o~t ~raw~rs 16~with the b~ttle-hold~ng rack6 : rem~ved~: Adjac~nt~the interior:front end:of th~ drawer 16~ :a forward~;~duc~ 60~:pos~itioned~ vertical~y within the:drawer 16.~ Th~ ~ ard~duct~60~ ubstan~ially h~llow ~nd open at:side 61, ~hi~h~faces the interior of 3s:~ the dx~wer 16. ~ Fo~ward::~duct 60~is attaohed at it~ base : ~ :

21135~0 W~3/24234 P~r/vs93/0523~
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to base plate 62, which i pc7sitioned transvergely to the forward duct 60 adjacent the interiQr bottom o~ the~
drawer 16. Adjacent lthe interior rear end o~ the draw~r 16 iE; a vertically positioned rear duc:t 64, 5 whic:h is cspen at ~;ide 63 ~scing the int~rior of the dr~wer 16 and which i~ ~lfio atta ::hed to ba~e plate 62 .
Pref erahly, the du;::ts are ~ormed of punched ~heet metal, which i~ then bent a~nd welded, or by other 3 c:onverltional methods of m~tal ~orming. It will be lO under~;toc3d, ho~ev~r, that the ducts may be formed o$ .
other materi~l~, æuch as molded plastic:, and may b~ :
f ormed in a variety o~ ~;hapes and conf igurationg .
When the drawer 16 i~ in it~ closed position within the ~peci~en-h~ndling module, the upper opening~; 63, 65 15 of th~ v6!rtirally ~ext~nding ~orward and rear du::ts 62, 64 ~r~ bro~aght into aligmaerlt w~Lth corresponding opening~ in upper duGt 66, located witlain the ~o~ule in the ~ol~owing:: manner. Upper duct 66 fe~rms a passas~eway wl~ h ~ g~nerally in the hape of an invert~d tJ. When , : : ; 20 the drawer lS is closed, the vertîcal ~eg~ents of thiC
:~ : in terted U-. haped pa~sa~eway ~re brought into alignmen~
with the upper~ openings 63, 65 of the Iorward and rear , ducts loca~ed :wit~in th~ drawer 16, ~c that air may circul~te ~rom~this upper passageway into the rorward 2~ ~nd rear du~t~: 60, 62.
Lo~ated wit:hi~: the upper duct 6Ç are a blower fan :: ~ : : . .
68 ~nd ~ h:ea~ing coi~ 7û. In response to direc:tion frc~m the ~icrocomputer, the fan 68 is energi2ed and ~orce air ln :the :dixection of the ~rr~ws in ~igure 3.
3~1 The air passes:~over the l~eating coil 70, where it; i~ :
w~rmedO ~he ~heated ~;a~r then pas~es downwardly in the direction of the ~arrows into the interior of the ~r~wer 16 lthrough ~ e upper openin~ 65 in the re~r duct 64 loc~ated within the drawer 16. The rear duct 64 ~s ~guipped wieh a plurallty of louvres 72 r which ara~

:

~0 ~3/24234 ~ ) Pcr/uss3/o5233 ~loped in order to direct and channel the heated air over, around, and ~cross the cul~ure bottles held within the racks . The openings between the lou ~ s 72 coincide generally with the position of the ~ottle-5 holding rac:k~. ta~ representative ~ot~le, ~llustratedwith~ut it~ hol~ing rack, is id~ntified by reference numeral 76 in Fi~re 3. ) A ~h~wn in. Fis~. 3, the louuxe~ æl~o increa~e in ~ize (an~, in particular, width) from the top to the 10 bottom o~ the rear duct 64 . Because the air f low decrease~: 3't ~reater distances f rom the f an 68, thi~
configuration assi~ts in distributin~. th~ h0ated air in a ~;ubstantially ~qual manner to each of the bottle hGlding rack~ in th~ drawer.
Af ter ~the heated air circulates within the closed drawer~ passing o~er ~he bottle~ and ther~by warming the specimens ~nd media cont~ined inside, it p~ss~s : under the for~e of ~an 68 into the forward duct 60.
; T~e air then pa~ses upwardly (in the direction of the ~ 20 leftmos~ arrows in ~igure 3) past a temperature probe :
~ 67 which m~nîtor~ th~ air temperature. Temperature : information is:conveyed:to the microcomputer/ which is progra~med ~o energize the fan 68 and heating coil 70 as neede~ in order to ~al~tain th~ temp~ra~ur~ of ~h~
: 25 int~rior of th~ dr~wer at about 35-37 0C and, more preferably, at ~35 +2~ "C, in order t~ encourage ba~terial grow~h~wit~in~ghe ~pecim~n b~ttle. Although : ~ this is~the preferr~d~temperature ~or ~os~
: ~i~r~organi~s, ~it will b~ understood that t~e 3~ nstr~me~t may be designed to maîntain the internal ; :~ tempera~ture in:other~appropriate tempera~ure ran~s.
:: : For ~x~mple, ~he:~preferred temper~ture for cultusing many t~pes of fungi~is~approximately~31 C. In ge~eral~ the înstrum~nt hculd be~ designed to maîntain : 35 a temperature which i~ optîmal for:tbe particular type .

2 1~ 3 ~ S O
WO 93/2~234 Pcr/us93/05233 of microorgani~m to ~e detecte :1. I$ will al~o be under tood th~t ~me f luctuation in the temperature of the drawer interior i~ permis~:ible, ~s long as the temper~ture of the ruitur~ Ye~els i~ kept wilthin 5 ~cc~ptable limi~ f or encouraging growth of microo:eg nisms.
To preYent heated air from escapins~ fro~ the drawer~ in ~ub~tantial quarltitie~;, thereby permitting the bott~es ~o become unaeceptably cool, means nre al~o 10 provided to gubstantially ~;eal ~he drawe~R ~rc~m excessiv~ air leakage onc:e they are in th~ir fully clo~ed position~ This ~ealing ~e~ns is illustrated in Figur~ 6, whic:h is a tvp view o~ the specimenohandling module 12 1:a~en alc~ng th~ line 6--6 in Fi~e 1. It will be~seen that the module. includes a bulkhe~d 78. ~:
The bulkheadl 78 i ~bris::at~d o~ alumir~um or another suitable materi~ nd ~ay be lined wi~h ~n insulating aterial, E;uch as a rubber pad" :E5ach end Os~ the ~ulkhead 78 has an adju~Pnt extension B0 which i~ ~
~tached to a correspond~ng ~upport pillar B~ within ..
~he m~dule hou~ing by means o~ set crews 84 . :i :ach &et ~crQw 84 p~sses through an elongat~d slot (not ~hown) in the extension 80 and in~o a thr~aded receiving aperture (not ~h~m~ in the ~orre~ponding pillar 8~
2s In this way~ the bulkhe~d 78 may b~ adjusted at each Qnd to move toward or a~ay from the drawer 16 which ~: ~ slides in~ ~nd ou~ of the drawer ~ceiYing area 86.
By ~ imultaneous ref ererlce t~ ~igures 1 and 6, tlle manner in whi~h the bulkhead 78 functions c~n be ~enD
3Q By ~djusting the bulkhead 7~ s~ that it i~; mov~d inwardly toward the ~aw~r are~ B6, a ~eal i6 c:reatad between the f aces ~ the ~orward and rear duct~ 6 0, 64 - and the base pl~te~ 62, on the one hand, and the bul3~heaà 78, on the other hand, w~en the drawer 16 i~
3s moved inwardly into the drawer receiving area 8 6, -:
.~

WO 93/24~34 2 1 1 3 5 S O PCr/US93/05233 Bec~u~e the bulkhead 7B travels along ~ilot~; ~t eac~
end, it can be adju~ted t~ optim~ze the ~eal, even when the ~lrawer 16 doe~ not tr.a~el pre ~ ely ~ n per~endicular direction into the draw~r rec:eiYing ~rea 5 86, or when the front a~nd :re~r ducts ~re rsot precisely aligned with the upper duct, t31ue t~ mounting toleranc~;
and the 1~ ke.
It will al~o be under~;tood that the drawer î8 i;
likewi~;e equipped with a similar ~ealing arrangement 10 ~djacent ~h~ le~t-most side of 1:he drawer in Fig. 1.
The result i~i that a c:ha~ber which is sub~tantially leak-proo~ i~ created within the ia~erior of the drawers 23urrounding tne bottle rack~. In th~ w~y, the heat g~nerated by heatirl~ c~il 70 can be ~ubstantially 15 c:onfined to the interiox of the drawer in which the bottles are held~ ~nd :doe~ not esczpe grDm ~e bottle ho~diTlg drawers. ~t ~;hould be n6~ted r ~owever, th~t the ~e~l need not be ~ompletely airtight~ ~5 long a~ the heated ~i~ is sub~tantially confined within th~ ~::: ? interior o~ th~ dr~wer. :In this r~gard, it has be~n discovered that once the bottl~s are h~ed tD the appropriate~temperature, ~uch o~ t~e heat is held : ; ~ within the liquid:media inside the b~ttles. Thus, once :: ~the media is~`he~ted~to the:~ppropriate ~mperature, 2s ~ome ~mount~of a~r:l~aXage can:b~ tolerated. Likewis~
the drawers~may~be opened ~eriodically for ~dditicn and removal of ~ottles~withou~undue heat loss. I~deed, in ome:in~tances:,~a ~mall ~mount of ~ir leakage c n h~lp ~ore r~pidly lower the temperature in the drawers 3l0 ~when;tlhe~ mperature ri~s above the appropriate range~
t will be underst~od~ ~hat while a pr~ferred h~ating Bystem: utilizes forced ~ir cQn~rection to warm , th~ b~ttle~,~as~described ab~ove, other me~ns for warming t~e drawer:~interior (and/or di~ectly warming the ~pecimen bottles) may also be used.~ For ex~mple, ' ~ :

' 21~355~ ;
WO ~3/24234 P~r/~S93/~233 the warming means could compris~ a heating elem~nt which warms the bottle holding rack~ direc:tly,, Th~
heat would then indirectl~ wa~ the g;pecim~n-holding bot~cle~ a~nd the drawer interior. The h~atins~ ~ans 5 could ~lso compri~e a ~eadi~tor type ~;y~tem, irl which heated wat~r i~; lpassed throu~h conduit~; within the draw~r, ther~by warmirlg the ~pecimen bottl~ and the interior of the dxawer indirectly.
The instrument is ~lst) e~uipped wi~h means f or 10 periodically and ~yc~ ally ro::lcing or ~gita~ing the bottles while they are being held within the r~::ks. It i~ kr~own th~t such agitation Zl~;8i6t:5 in mor~ rapidly 9 detecting mi~:roorgani~;ms in the bc~tt~e by ensuring that C~ gener~t~d by th~ microorganis2~s di~fuses throughout 15 t:he media~ ~nd i~; there~y rapidly 3brou5~ht into contac~ :
with the ~en~or a~ffixed to ~he bottom of the bottl~4 (Ref errlng to ~igur~ B, the ~ensor i5 ~denti~ied 3by ref~srence numeral ~00.) ~eferring firgit to Figs. 4 and 5, the a~gitation 20 ;ystem will now be described is~ detail. Figs. 4 and 5 ~;h~w thr~@ of the bottle holding raclcs 20, 22, 24 : ~ during the a~itation cyele. The ~a~ks 20, ~2, 24 ~re each pivotall:y attached to a fir~t pair o~ raclc ~:upports 102a, 1û2b. T~king r~c:k 20 in~ividually, a 25 ~ivot pin 106 a~sd~ bearing (not hown) ~re u~ed to pi~otally mount the first racking support ~02~ to one ~ide of rack 20 at ;a position adj~cen~ the ~ack ~ide ~09 o the rack 20. A ~;econd pivot pin ~nd bearing are used t~ pi~otally ~aount th~ #~cond racking suppc~rt 132b 3~ 1 t~ the opposit~ ~;ide c~f rack 2 0 in a ~imilar ~manner .
To prevent the rack~ ~ro~ arcumula~:ing a buildup o~
;tat~:c-ele5tricity, which c:ould p~tenti~lly irlterfere with the circuil:ry for the optical uni~, bearings made of an electrically c~nductive material, ~uc:h as 35 ~intered metal, are preferred. In this way, the .

.

WO 93/24234 P~r/US93/05~33 211~550 electronic: circuitry for the optical unit~ i6 provided with a path to electrical ground.
Rack 2Q i~ also att~ched to a pair of drive s~upport~ 112a, 112b ~t a position adjac:ent to the s bottle-rec:eiving ~ce 116 of rack 20. ~s with the racking supports 102a t 102b, the pi~c~t2l1 ~nountîng of tg~e dr~ve &upport~ 112a, 112b i zlccomplished by m~ans of pivot l?ins and be~rin~s~ Each of the other r~ck~
2~, 24 i~ likewige att~ched to tbe racking ~upport~
102a, lO~b and the drive ~upports 112a, 112~ in a nilar ~anner~
By means of a dri~re mechanism desc:ribed in detai~
D belc~w, drive support ll~b is aIternately z~nd e:y ::lically driven in an upward direction ~illustrated by the arrows ^in Figure 5 ) and a downward ~lirection : ~illustrated by the arrow~ in ~igure 4~, th~reby moringthe attached racks 20, 22, 24 b~tween a generally horizontal po6ition ~h~m in Figure ~) and an upwardly inelined position ~hown in Pigure 5). Thi~ rorking motion agitates~the bottles and their ~ontents ~o facilitat~diffusion of C02 generated by bacteria : ~hr~ughQut the~culture ~ottle~ ~nd, i~ particular, t~
the ensor ~f ixed t~ the b~ttom of:the b~ttles.
Re~erring n~w t~ Fig. ~1, the ag~tation drive : 2s~ mechani~m is illu~trated in ~e~ail. ~ot~r M ~otates ~haft 170~ which~ upported on bearings 172a, 172b, 17~c. Flexible;~ooupl~ng 174:a~sorbs any ~hock caused y m~s~lignm~nt of :the ~haf~ 170 r~la~i~e tD ~he motvr .~ A~ oiroular cam;176 ~5 ~unted at the end o~ ~haft 170, C~m ~ollower~ 178 i~ ~igidly m~unted.to the cam at ~ : a position adj~cent ths outer circumference of the cam : ~: : 17~6.: The c~m~.ollow~r 178, in turn, is ~lidably :~
recei~ed within::~n o~long slot~180 in ~rm 182. ~rm 182 5 rigid~y attached to drive~;6upp~rt 112b and con~eys power thereto~ Up~n a~tuation~of the motor M, shaft .

211~ 0 WO 93/24234 Pcr/u~93/05233 170, cam 176, ~nd c:~m follower 178 ~re caused to rot~te. When csm follower 178 reaches the right side of the oblong ~lot 180 in ~r:m 182, it i~part~ a :~
downward motion to ~rm 182 uld, thu~, to dri~.re E;upport s 112b. ~The A~ 182 di~placed in a downward direction hc~ ir phantc~m in Fig. 11. ) Likewise, when cam follower 178 reas:lle~ the le~ ide o~ tl e oblc~ng ~;lot 180 ~n arm 182, it impart~ an upward motion ts arm 182 and, thus, ~o drive s3~pport 112b. Continuous rotati~n 10 o~ shaf~ 1~0 ~hereby :moves the racks in the cyclical rock~ng motion illustrated in Figs. ~ and 5. Braking .
means in 'the f ~rm of a Gon~rentional brake assembly ~not howrl) operatively coupl~d t~ the ves~el-holding means (ei~her directly or by ac~ing on the ~oto~ M or th~!
1~ I;haft 170~ is used to stop the ~:yclical agi'cation, when desir~d~. -As ~hown in Fig. 12, ~n i~port~nt featur~ of the pr~sent invention ig the t ~ e of cyclical rooking ~:~
motion imparted to:the ar~ lB2, drive ~upport 112b; and ~acks: 20, 22, 24. ~ig. 12 is a dwell chart ~h~wing the distance o a point P }ocated on rack 20 from a ~ixed reference poin~. Th~ ~ixed reference point i~ chosen as the position of point:P when ~he rack 20 is in its lowermos~ posi~ion.~ A8 ~h2 ~haft 170 Eotat~ the 2s dri~e~echani~m of the present invention cau~es th~
: distance of tr~el o~ the point P from the ~ixed ~:~ ref~rence point ~o incre~se ~nd decr2~se in a subst~ntially ~inusoidal fashion.
~t will be saen that at po~itio~s sub~t~nti~lly near the maximum ~nd ~ini~um travel o~ point P
indicated by brackets l~:Flg. 12), t~e ~lope o~ the inu~oidal curve i~ relatively ~mall. 5ince t~e 810pe of the ~urve is pr~portiona~ to the velocity o point P
(and, ther~ore,:the~veloci~y of the bottle~holdi~g 3s rccks), it can be ~een that th- velocity ~f the racks ':

~V0 93/24234 2 1 1 ~ ~ ~ O P~r/US93//~5~33 near the maximum and ~inimum travel point~ i r~l~tively low.
Thi s has i~npo~t2lnt c:onseguent::es for the operation o f the instr~ment. Bç!c~use optical readings ~aust be s taken when the rack~; are ~t res~ and ~n an inclixled position ~te~ ensure that the ~ensor is completely covered with liquid durirlg Dptical re~dings) r it is nec:e~ary t~ periodically E;top th~ bottles while they are in the inclined position. E~cause the velocity of the racks i~ lowest when they are in the inclilled position (i . e ., at the maximum tra~rel point~, thi~
pro~rides a ::onvenient point at which to brake the rotating ;haft (and, thus, the racks) without imparting undue ~tre~s to the braking a~sembly. ~ikewi~e, it i~
al~o desir~ble ~ts E;top the rac~c~ when ~y 2Ire in their ~owermoct po ition ~ , clo~est t~ hc~rizc~ntal3 to permit the opexator to ha~e ready ~ces~ to the ra::ks f or removal and add ition of culture bo~tle~ . Onc~
as~ain, b~cause the velocity of the racks is al~;o lowest :: ~ 20 when they are in theîr lowermvst position ( i . ~3 ., ak ub~tantial~y the minimum di~tance o~ tr~Yel p~int) ~.
: ~ ~ this is another cor~vsnient point ~t which to ~;top the rot~ti~g;~;ha~t~ is also Zlesirable tc:~ re start the shaft rotatin9 fr~a the~e ~topping positions, ince :; 2s this minimizes the~ ~t~e~s on the ~oto~.
Such a~n~arr nge~ent ~lso h~s the sigrliIicank advan~ g~ oiE ~ducing the co~t of the motor and br~king m~ns which can~b~ used in:the practic~ o~ the inventionO I~ particular, because the di~tance th~
- 3~ racks ~ravel for ~ given ~nguI~r movement of ~he ~ha~t mall at position~ near the maximum and minimum :: :
; ~ di~tanc~s o~ travel of the racXs, greater leeway in topping the rotation of the:sha~ allowed at these ~ : poin~s.- BeGause~the rotation need not be stopped to :~ ~ 35 mo~e exarting toleranc~s, relatively inexpen~iYe mQtors :
: :

2113~S~
W093/2~23~ PCT~US93/05233 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 pattern of ~otion to the bottle-holding racks. In this arrangement, pivotal arm lgO is used to convey the rotational motion of the cam 176 to the dri~e sUpport 112b. A ~irst end of the piv~tal arm l90 i~ pi~otally mount d at pivot point 192 to the cam 176 at a location near the circumf~rential periphery o~ the cam.
second, opposite end of the pi~otal arm 190 iS ..
pivotally mounted at a: pi~ot point 194 to drive support 112b. Upon rotation o~ cam 176 in the dir~ction of the arrow in FigO 14 ~ a sinusoidal pattern of motion is imparte~ t:o the dri~re support 112b and, ultimate~y, the bottle~holding racks. The posltlon of the pivotal arm 190 after an ~pproximately 180 r~ta~ion of th~ cam 176 ~ hown in phantom in ~ig. 14.) It will also be : und~r tood that various other systems for imparting a substan~ia}ly sinusoidal pattern of motion, such as gear assemblies and the like, could a~s~ b~ used.
~ nother i~portant:aspect o~ the pr~sent in~ention i5 the~optieal~sy9tem for mechanically sensing changes :~ in~the C02 sensor. As best seen in Fig. ~, the sensor 100 is affixed~to the inside of ~he bottom wall of the culture bottl~e 120. ~ In a preferred: :form1 the sensor is :: made in ~accordanc2 with the disclosure~ of copending U.S. patent:`applica~ion S.N. 2:38,710, filed August 31, l9X8~and/o~ copending U.S. pat~nt application S.N.
30l 6Q9~27~ iled~November 5, lg90~, both of which are entit~ed "Measurement of Color Reaction5~by Monitoring a Change~of Fluorescence, 1l are assigned to the owner of the present application, and which are incorp~rated hèrein by~reference and made a part he~enf.

~`:~ : : :

:: :

WO 93/24234 2 11 3 5 5 O Pcr~uss3/os~33 33 ~ :

As di~closed in U . S . patent ~pplication S . N ..
609,278, the ~enscr preferably c~mpri~es a chromophore layer 122, which consists of A pH ~ensitive chro~ophore encap~ulated within a ga~ permeable, hydroge!n-ion 5 impermeable matrix, ~uch as ~ili¢one. At!lj~cerlt the chro~nophGre layer 122 i~; the f luorophor~ l~yer 124 .
~he f luorc~phore layer 124 cor~ t~; o~ a f luore~c~nt dy~
encapsulat~d within a wa~er and g~s impermeabl~
polymer, E;UC~ ~s an acrylic polymer . The f luorophore 1~ layer 124 i~ preferably positior~ed ~b~e the e~romophore layer 122 when the bottle 1~ 0 i~ in an upright posî~ion. When placed within zln aperl:ure in the bottle-harldling rack t~ee Fi~. 7), the ~:hromophore lz~yer 122 i~ hereby situated or ~ ndwiched b~tween the 15 ~ptiCZIl unit ~6 ~Fid the ~luorophore layer 124. ~n the fo~ illustrzlt~d in Fig. 8, the Iluorophore layer 12 has a plurality o~ r~dial cut-out~ 121, which extend from a position near the c~r~ter of the f luorophore layer 124 to it~ periphery. (~h~se c:ut-outs 121 gi~re 20 the ~luorophore ? ayer 124 an appearance simi}ar to that of a: ~'sl:arfis~'l when ~iewed from above. ) The cut-suts 121 expc~se: m~re~ of the~ ~urface 2rea of the chromophoxe layer 122 tc~ .he liquid wit~ the ~ot~le, thereby permit~ing ~C~2 :~ener~ted ~y microorganisms within the 25 bottle to dif~u~e to: the chrom~phore layer 122 more rapidly. : ~:
Flg~. 7 and ~8 il;lu5trate the optical unit 46 in detail. ~h~ unit in~lude~ at least one, and pre~er~bly more than one, ~ t emi~ion ~eans in the form o~ B
30 light so~rce. A plurality ~f light ~ource~
preferred, ~;ince thi~s~ helps t~ ~ensure excit2tion lis~ht :~ ~ impinges on the zlrea of t~e bottle where the ;~nsor is located~ even :when there~:ar2 vaxia~ions in the positior~ing s~P the~ ~ens~r orl the ::ulture bottle. In 35 Figs. 7 and B,: f5ur light emitting diodes [LEDs) 126 2~ 5~
W093/24~34 PCT/US93/0523~ ` `

3~ :

~erve as the light 6Qurce~. As best ~een in Fig. 8, each LED 126 ha6 a plastic lens 127 which de~ines the cone of light ~mitted ~y th~ LED 126. It will be under~tood that it i~ desirable to ~ave as ~uch light ~æ possible directed to the area of the bottle 120 wh~re the ~ensor 100 i~ locat~d; the plastic lenæes ~27 h~sist in dir~cting ~he ~one of light emitted ~y the - ~ED to the vicinity of the Bensor ~nd in ~inimizing stray light. Success has been had~with ~EDs ~anufactured by ~arktech International o~ ~enands, ~ew ~ork, bearing the designation MT 350 AK-UG. These LEDs havë an ultra bright GaP gr~en }ight,emission and u~e ~
T-l 3/4 water clear lens. According to the :~:
~anufacturer, these LEDs h~ve th~ following maximum ~s r~t~ng~T~ e 25 0C):~ forward curr~nt, 2S mA; reYer~e ~slta~e, 5 V, power dissipation, 105 ~; peaX pul~e ; curr~nt, 150 mA; oper~tive temperature raDge~ 50 to : approxi2ately 100 ~C; torage t~mp~r~ture r~nge, -50 to : approxima~ly 100 ~C. According:to the ~anu~acturer, 20: the~e LE~s~also~have the following electroooptical chara~teri6tics:~Ta - 25~C): forward v~ltage, typical (2.2 V),:~axi~ (2~.5 V3; reverse current, maxi~um (10 A); lumi~ous~ intens:ity, :~ mini~um ~l~0/200 mod), maximum : (2~00/3~0 ~od)~t~:pea~k~waYelen~eh,~typical (5~5 n~);
2s~ Yiewing angle,~t~pical:(30); ~pectral:line half-width, : typi~al (3~ nm)~
T~e LEDs~ 2~ re positioned aroun~ a centrally-located photodetector~m~dule 128, whieh is described in gre~ter detail~bel~w. ~he LEDs l26 ~ po~ition~d 60 3~ that they~fully illuminate the`~ nsor 100 ~ffixed to , he~ side bott~m~of~a~culture bottle 120 pl~ced in an per~ure:38~ ~Pre~er~bly, the~LEDs~re al~o held within : a~h:~using 130,~w~ich can be molded of a suitable pl~stic or made~by other conventional means.

:, :

,:
:

21~3SSQ
WO 93/24234 PCr/US~3/05233 The operation of the optical ~ystem i6 b~t understood by 2 ef erence to Fig ~ 8 . LED~ 12 6 ~re 6elected ~o that they emit light falling within an emission wavelensth range and, preferably, ~ genera~ ly 5 ~c~no::hro~atic li~ht falling within a wav~length range whic:h will excite ~he ~luorophor~ in the fluorophore l~yer 124~ For exa~ple, ~e commercially available LEDs identi~ied above emit ~ generally mon~chromz~tic light h~ving a peaX wavelength of 565 nm and ~ ~pectral ~0 line hali~ wid~h of about 30 nm. Light ha~ring the~e . charact~ristiGs i~ well-guit~d to exci~e the ~luorophores oxazine 1, 7, 0-perchlorat and oxazine 4-perchlorate, which are pref~rr~d ~luorophores in ~he ;`
pr~ctice of the present invention.
Lig~t f rom the I.ED~ imping~s on the specimen bottle (and, ~f~r passing through th~ bottle, on th¢ e~ensor) and ~xcites th~ fluorophore encapsulated within the ~luoxophore layer 124, causing it to ~luoresce, i.e.,, ;;: emi~ radiation~s it p~sses ~rom a higher to a lower electronic gtate. ~ight to be detected emanates fr~mhe~fluo~ophore~:within th~ specimen b~*tle. Thi~
.
~;~nsor emi~s~on l~ght e~anating:from the ~ensor ha~; ;
~: di~rent spectral chsracteristics from the excitation light, iOe. ~ it b~s;a;differe~t p~ak wa~eleng~hO
2s:~ P~èferr~d~fluoro~hores~emit light at peak wav~lensths of ~pproximately~5~0-~50 nm.
; ~ny~microorgani~Ms~culture~ ~n ~he media ~32 wi~hin the~ b~ttle 12`0 produce ~S:2, :whic:h diffu~es inlto the gas perme~ble chromophoxe layer 122, there~y c:au~ g ~
30 change ~n pH;within the chromophore layer 12~. This F~I
hang~, in turn, cau es a change iD the absorption :
p~trum of the ~hro~ophor~.~: Si~nifi~ant growth of : microorganisms resul~6 in additional production of C02, which causes:a~ further change in th~ absorption of the 3s chromophore. :As disclo~ed in copending U.S. patent : : , ':

21135~0 W~ 93/2D~234 PCr/US93/05233 application S.N. 609,278, the chromophore ~ preferal:ly 6elected 80 that its absorption ~;pectrum overlaps with the excitation zlnd the emission ~pectrum of the fluorophore in the fluorophore l~yer 124. In thi~ way, 5 t:har1ges in the absorpticn ;pectr~m of the chromophore -whil:h a~r~ triggered by ~nicrobial growth -- will ~odulate ( in ~ pre~erred f orm, a~t~nuate ) the excita~lon light reaching the ~luorophore a!~5 well as th2 ~;ensor light emitted from the ~luorophore. Thi~
1~ attenu2tion in both the excitation liÇ~t r~ac~ing the fluorophore and the emission light emanating ~rom the ~luorophore i6 m~asurable and can be.~onitored by the optical module 128. T~e result i5 tlh~t the growth of microorganisms within the hottle 120 can be correlated 15 to a ~e~surable attenuation of ~luorophc~re exc:itation and emi~ion.
A sigrli~ieant feature contribut~ng ts:~ th& 6uc:cess of the optical detection sy~;k~m o~ th~ pre~enlt invention ~s~he unique e:onstruction~ og the optical 20 ~detectic)n unit 12 8 . The detection unit 12 8 includes ght d~tection means for ccmv~rting light ~ner~y ~emana~i~g ~rom the ~ensor within ~he ~pecimen bot~le : ~ ~nto a det~ctable~ nal. In a preferred form, ~he ght detection ~eans takes th~ ~orm o~ a ph~todetect~
(no~ ~hown), which conver~s light energy into an electric:current.~ Success h~s been had with a : :photo~:iode ~ade by~United Detector Technology of Hawthorn,: ~alifornia, bearing the designatio~ ~T 45~.
The curxen~ genera~ed by the photodetector ~
`: 30 transformed in~o a voltage ~y mean~ of a ~onventional transimpeda~ce~:~ampli~ier. ::~he voltage, whic~ can be correlat~d to:~the:~amount of b~cter~al ~rowth in ~he : : bottle, iæ then ~ea~ured by:well-kn~wn me~ns.
~Significantly, the detection unit 128 i~ al~o 35 e~uipped with filter means:optically interp~sed between ::

W~ 93/2~2~4 . 2 1 1 3 ~ S O PCI/US93/05233 the LED light sources and the photodetector f or preven'cing substantialïy all light falling within the wavelength range emitted by the L~:Ds from reaching the photodetector. The filter means is carefully c:hosen in 5 order to achieve substantial isolatiorl be~ween the ~;pectrum of the excitation light and the emission ;pectrum of the ~luorop~ore. This spectral i~olation i~; best understood by re~erence to Fig. 13, which is a graph showing ~;chematically both the spectrum of the 13 light emitted by th~ L~Ds and the emission spectrum of the f luorophore . It will be seen that the spectrum of the right emitted by the LEDs has a lower peak waveleng th than the sensor 1 ight emit1~ed by the .;.
f luorophore wavelength . However ~ becaus~s bokh the 15 excitation light and the emission light have a bandwidth, there is ~some overlap o~ the spec:tra. This area o~ overlap, greatly exaggerated, i8 rep~esented by the single-~atched area in Fig. 13 O : The f ilter means is chosen 50 that the photodete~:tor receives a ~: ~20 su~iciently strong f luoresce~t ignal, but the amount of overlap b~tween :the ~spectrum of the excitation light and the spectrum: o~ the fluorescen~:e ~emission light is minimized and, preferably, eliminated altogether. In Fig. 13, only light having a wavelength falling wi~hin 2s the cro s-hatched region is perlaitt~d to reach th2 ~; ~ phot~odetector; the~ filter means pre~rents all other light from rea¢liing ~the ~photodetect:or. In this way, an :.
area of f luorophore emission is ~:hoser~ in whirh the : ~ ;
overlap of excitatlon light and e~i~;sion light 30 ~ epresented by ~he intersecting region 7~a~ in Fig .~ 13 ) is minimal. It is: preferred that the amount of such o~r~rlap b~ ~e55 than about 20% of the total signal, more preferably, less than about 5%, an~ still more pre~erabïy, between 1: and 2% or less. In general, to 35 achie~re substarltial spectral isolation, the dif f erence ;

21135~0 WO 93/24234 . PC~r/VS93/û5233 in pea~c wavelength between t~e excitation light and the f luorophore eml~;sion E;hould be at least ab~ut 10-15 nm and, preferably, 25-80 nm or moreO I'c i~
pref erred that any ~mall ~mount c>f overlap be 5 electronically "~ubtrac~ed7' from the optical sigllal ~o that c~nly f luorescence emi~sion i~ measured .
It will be E;een ~at the ~i lter means i~; gelected in order to E;ub tantially prevent light having a wavelength other than that o~ the light emitted by th~
10 f luor~phore -- - including ~;u~stantially all of the excitatiorl light emi~ted b~r the LEDs 126 frc~m entering the photodetectc~r. In this way, the detee:tion ~ystem is, to ~s gre~t: a degr~e as po;sil~1e, ~;ubstantially optic:ally ~'b~indll t4 light ha~ ing a 15 wavelen~th o~her than the light ~mitted by the f luores~::ing f luorophore, including the exci~tion light emitted by l.E:Ds 12 6 .
~ n a pre~erred embodiment, the lîght filter means consi^~t~ of a lon~ass f îlter which prevents light 20 having a wavelength ~;maller than a partic:ular ~3elected value from Qn~ring the ph~todetector. ~hen the : : fluorophore chosen for:the flu~xophore layer 124 is : oxazine 1,7,0-perchlorate or oxazine 4;perchlorate, the .
longpass ~ilter~is selected ~o pr~vent light having ~
~5 wa~elength o~ l~s~ than about 645:nm from entering the photodetect~r. In ~his way, light emitted by the ~ : fluorophor i~:det~cted ~y the photodetector, but light : ~ havin~ a wavelength of less th~n 645 nm (including ~ubstantially ~ of the excitati~:n light emitted by ~30 ~he ~E~s 126~ which~ha~ a peak wa~elength o~
: approxim~tely 565 ~m) i5 not. Succe~s~ha be~n had ~ ~ with a glass lonqpa5~: filter manu~ac~ured by Schott : G~a s of Durye~ t Pennsylvania, which ~ears the designation RG: 64 5 o Thls filter can be attached to the co~mercially a-ailable photodiode described aboYe to , WO 93/2423~ 2 1 1 3 ~ ~i O PCr/llS~3/05233 ~orm an integrateà unit . haYing the optical charac~erigtics ~or u~e in prac:tic:ing the pre~;ent in~rention.
E;uch ~n optical ~rr~nge~ent has signif icant 5 ~d~ntages for use in a detection E;yE;tem for mic:ro~rgani~ms. Thi~ op~cal ~rr~ngelDeJ~ Qrmit8 E;ubstantially complete c pti~al ~ ~;olat~on between the excitation light ~nd the light smitted by the ~luorophore; thu5 ~ignif ic~ntly reduc:ins~ bas:ks~round 10 n~ . Compa.rable ~y~;~ems whic:h rely on dir~ctly moni~oxing monoc:hrc~matic light tran~3mi~te~1 by the ~:
~;~n~or have Isignificantly ~;ore noise becau~e light from th~ light source can ref lect of ~ c~f other optic:al surfaces in ~he~ instrument (~Lncluding the botto~ of the ~s bottle~ and r~ch the opl:ical ~;ystem directly. In dir~a~t ~:ontr~st, ~ec~use 1:he det~ction ~yfitem of the present învention i~ ~substantia~ly optically ~7blind" to the excitation light, the ~luorophor~ can be inun~ated with excitation light " thereby producing an 20 excepti~nally strong fl~lorescence ~ignal,, without ubst~nti~lly in reasin~ the nol~e a~f~c:ting the detec~:ion system. :This ~lps *o improYe the ~ensitiv~ty of ~ ~he ~;y~tem.
It ~h~uld ~be p~ t~d out that bec~us~ an sp1:ical unit i; pro~rided~;for~ach b~t~le-r~cei~ing opening, probl~ms ~ncountered in calibratins~ a slnçlle d~teGtion uni~ are sreatly reduced. ql~his is becau e each unit i~
eff~ti~rely~ "&elf-calibr~ting" in thak variables fPecting the ~ignal generated ca~ be read before 3~ reading~ are 1:aken and then "~ubtracted" ~m ~he .

~: fiignal as ~uccessive~ readings a~e takenO
Althouqh ~ a~par~icu~r c~ptical ~rrangement has b~en : di~closed her~in, ~:it ~ill be understood th~t other rr ng~ment~ ~may ~e employed, ~ long a!~s the detector 35 is rendered bstantially "blind" to l~ght other than ~113~50 WO 93~242~4 PCr/US93/0~233 that emitted by the f luorophore . For example, 'che location and geometry of the ~xciting light ~urce relati~e t~ the photodetector eould be chanqed to prevent ~;ub~antially ~ xcitation }i~ht ~rom s reaching the phokod~tectorr Similarly, other types of c3ptical devices ~nd f ilter~, including interference ~ilter~; ~nd ~ilters made from material~ other than glas~, could al~;o be uE;ed.
The following i8 a 6ample prc:~tocol which further o illustrate~; ~e manrler in wh~ch the instrumeTIt of the pr~nt invention can be used in det~cting the pre!sence of ~acteria in human blood. A detailed descriptiorl of o a E;oftware program which may be used to preprogram the ~icroco~puter tD monitor and control the ~unction~
S performe~ by the in~trument in thi~ protocol i~; found in the ~ppendix hereto, ~P~2a~T~sl~l! lP~OTO~ ~
Blo~d drawn from a pati~nt ~ibiting symptoms of bact~remia i~ drawn and :brought to the ~o~pit~l 20 microbiology la}: oratory ~ where it is inoculated irlto a :culture bottle~ ~ontaining media corlducive to bacterial growth ~nd lab~lled with a ~ar c~dle cont~inin~
in~o~mation liT~cing that sa~ple to t~e patient. :By means of the Jl~er interfac~ on the ~xont of one o~E the 25 drawers o~ the module, the instru~ent operator initiates a~ ~Qmmand to the minicoallputer to operl the drawer. If the bot~ bolding r~cks are being ;~gitated bat ti~e, ~ a~o~mman~ i5 sent to ~top agitation when th~ bottle holdiny racks are n~ar ~heir lowermost 30 1 agita~ion position. Alternatively, if optical realdings ~r~ bei~g taken at that time, the readins~s ~re co~p~eted bef ore the drawer is opened . The ~;ystem is ~: pr~ferably pr~pr~grammed ~o that the agitation, heaitin~, nd optical reading func~ions ~r disabled 35 (and canno~ be restarted~ while the drawer is open.

: ~ ' WO 93/24234 2 1 1 3 5 5 0 PCrJUS93/0S233 The microcomputer then ignals activatl~n of the drawer--open~ng motor in ~rder to op~n the dr~wer. Once the drawer i~ opened, th~ operator draws the b~r-code on the culture bl~ttle across the V-shaped char1nel and 5 bar code reader located inside the drawe~, and the bar c~d~ inf ormation is scanned into the E;y~t~m. This information is transmitted to the microc:Qmputer, which 6ends ~ ~isJnal to the inside ~nformation panel p:rompting th~ c~perator to place ~he bot~le in ~n 10 ~vailable bottle-r~:eiving opening. The operator . insert~ th~ bottle into the ~proper opening until it "E;nap-fits" ~ntl:3 eng~gement with the bottle~retaining mean~;. Thereafter, ~ optical read~ngs fc)r that ~ttle are associated with the patient info~ation which has 15 be~n scanned into the ~y~tem, :~By ~eans o:f the te~apera~ure control subsy~ e~
~:illustrated in~ig. 3, thQ temperature insid~ the drawer~ and, thus, ~e temperature of the bottles, i~
kept at the;preferred te~per~ure for ~icrobial growth.
o The ~icrocomputer gi~nal~ a~tivatio~ of the fan and heating ~lements,~as reguired, in ~rder t~ maintain t~at ~empera~ure within ~p0ci~ied limit~.
Periodically, ~t~regular ~ntervals, the microco~puter ~ignal~ the agitation motor to ~gitate ~he bottles :using the ~y~tem:;~llustrated~in~Figs. 4, 5, and 11.
1 o at reg~lar: interval6, agitatio~ of the bottle holdlDg:r2cks~ 0pped:wh2n the bot~l~s ar~ in their uppermost a~t~tion position. While the racks ~re in ~hi~ p~sition, optical r~adin~ are ~aXen. The sys~em 30 i8 cap~bl~;o~ distin~uishing bëtween empty openings and openi~ngs whic~ contain~bottles:by~the nature of ~he op~ical ~ignal.: The op~ical readings are t~ansmitted to~he microcomputer where they are a6soci~ted with the :~ appropriate:patient lnfoFma~ion:~nd st~red for l~ter 3s~ r:etrieval and~use. ~ ~

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2113~ 0 W093/24234 PCT/~S93/05~33 ~2 If the optical reading ~or a particul~r ~pec~menexceeds ~ pr~determined threshold, the microcomputer tre~t~ that ~ample as a "positivet' and tran~its that inf or~ation to the in~trument. ~n ~udible ~l~rm i8 ~ctivated to siynal thi~ infDrm~tio~ to th~se present in the laboratory~ The microcomputer al~o se~ds a command to illumi~at~ the appropxiate LED adjacent that bottle t~ ident~y the positive culture ~or ~hQ
operator. That bottle can then be removed and ~ubcultured ~ that th~ infecti~ bacterium can b~
identified, ~nd a~ appr~priate tr~atment regimen (inciuding appropriate anti-m~crobial agen~s) ~n be prescribed for that patient.
Since khe ~icroc~mputer i~ al~o programm~d to store ~nd ~anipulate the data pertaining ~o the sp~cime~s, it is ~lso possible to generate print-out~ of th~ data in Yari~us formats,:including ta~les~ graphs, ~nd th~
like.
~hile the invention has been describ~ in connection with cextain presently pre~rred component~
and ~rrangements, those ~kill~d in ~he art will :~ r~cognize many ~odifications to ~tructure~ ~rrangement, portions, elements,`~terialæ, ~teps and comp~nent~`
which G~n be used in~the practice o~ the inve~t~on without depar~ing~from the pxinciples thereof.
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. ~ W~93/2~23~ 43 PC~/~IS93/0~233 APPEND~

Terms Used The following terms are used throughout this document. They are presented be10w fox reference.
Boolea~
Having two possible states - b~ary.
Co~a~d A messagej se~t ~rom the host PC to the instrument, which commands the instrument to perform some action, retum some data, set some paxameter, etc.
Command Pro~essor A software module which accepts commands (from the host or ~rom other modules) and either acts on those commands, ol~ relays them to other module(s) ~or action.
~ontext ~ f rame of reference. In multi-tasking systems, the context is ti~e memory (code, data, stack) a~d processor state (I.e. register contents) which 'ibe10llg" to a given tas~.
Collte~t-switch Task-switch.
Event The name of an edge in a state diagram. EveIlts cause states changes to occur.
Message ~ !
- ~ A block of information passed be~ween tasks. In t~is case, messages are forwarded between tasks~by MMX. Gommands from the :: host: and responses ~o the host are a special claas of messages~

SWi~ST~T~ EET

:

WO 93/24~ 3 5 5 0 PCr/US93/05233 ~!1~ : '' An operatin~ system software component which relays messages between tasks Module A logically grouped portion of so~tware. Genera~ly, a module will be contained withi~ a single compila~on unit, and wi~l contain ~unctions a~d data whic~l implenet a p.articular portion of the requireménts for the so~tware system.
Pseudocode - -An i~formal, structured English 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 prov~des faeilities to make multiple tasks, or threads, appear to execute simultaneously.
Variable ; ~ :
: : A piece of data.~::

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SlJæSTITl~TE ~EET

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w093/24234 4~ 2113~0 Pcr/US93,~5233 Messa~e Passi~ Fundam~Iltals The Blood Culture Opera~g System, and ~ in particular, provide mechanisms for transpor~ing messages between i~dependent tasks. M~ provides what can be described a sa many-to-many message sys~em. This means that many tasks may send a particular messa~e, and many tasks may receive a particular message.
Passing messages involves (at least) t~ree steps i~ MNIX: :First, tasks must declare which message they are "interested" in recei~ing.
To send a rne~sage, a task "Posts" the messa~e to MMX, which, in tur~, delivers it to all other tasks which have declared an intent to receive t~at message. To receive a message~ a task "Pends" for one. The execution of the task is su~pended until a méssage is a~ailable for the task.
Yariations on the basic case outlined above include a "pe~d with ~e-out," which limits the amount of lime a task will remain suspended when waiting. Mess~ge may be "held" - reception deferred until later, while allowing other messages to be passed. Messages which have been hold must eventually be "released" and rece*ed.

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~ iW B~iTIlF U~E 5~ E~ET
., 2113~S~ :
WO 93/24234 46 P~/US93/~)~233 SYstem Overview The Reller Operating System will be composed of the software components described at the Blood Culture System Design Review held previously. Though the opera~i~g system plays a key role in system operation, it will not be discussed extensively L~ this document.
Instead, this document will focus on the softwalre compoIlerlt generally called "the application." While every software component contributes to the overall unctionality of the in~trument, it is the application that performs those functions th~t are most important to the host computer, and eventually, the user. In short, the application is the component that makcs the Blood Culture instrument be a Blood Culture ..
L~strument.
The application will be composed of seven modules, and ten tasks:
A Coordinator task, responsible for application start-up and 1~me marl~; a host communication task, responsible for providin~ a standard command processor interface and:response path ~or tasks; a access task which haxl:dles the ac~ions necessary for lettiIlg users into drawers; an analog reading task, which administers the hardware for analog reading; two bottle reading tasks, responsible for hand~ing the timing of and storage of bottle reads; two temperature control tasks, which control the temperature ~nto dlawers; and lastly, two agita~on tasks, whi~ are responsible for the timing :and initiation of bottle agitation within~drawers. The bottle reading, temperature control, and agitation tasks wi~l be written so the ma:in code body will be reentrant, with independent data segments.

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5L~ ES;T0TUT E 5~1E~T

21i3550 WV 93/~4234 a~7 PCI/US93/~5;~33 Global Requirements * For each bottle, the machine must read ~e sensor Ln bottle and store the information pe~iodically contin~ent upon the drawer being open and agitation in progress.
* The machine must allow user access tn either drawer ~but o~ly one drawer) at any time. The access times and duration must be stored.
* The machine must maintain and record temperature on some periodic basls.
Machine must report stored data to host computer on request.
* Time of user accesses, and duration of opern drawer will be recorded.
* Te~nperature 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 significantly changed f rom the version as of this d~te.
* Heaters will be installed in each~ ~awer, and the software will be expected to control them.
* New motors will be installed to control the agitati~n and drawer nnovement. There will only be crude control of these motors (i.e.
Motor on and direction).
* Optos will be relocated and will privde ~eed~ack ~on: drawer closed, drawer open. Optionally a third opto might be provided to indicate that a drawer is parked ~closed aLI the way).
* The functionality of the agitation home optos will be unchanged.
* Communication~will be .se~al RS-232 with a ~et-to-be-determined PC.

SUB5T1TUTE ~eEET
:

WO 93/24~1 1 3 ~ 48 PCI /US~3/05233 Co~ventions used throu~hoNt the document Most modules are- described using the format below:
A function name (TaskName)- - ¦
START
O~rerview of Tas}~ame.
requirements~
Design requirements of TaskName~
assumptions-- :
Implicit~ or practical design assumptions used during task desi~.
: '' commands supported---Command funcl;ion name (parameter).
?ow---, ~: "Structured" english.
euents---EventName: ;
~ - .
~ ~: r L
~ ~ Pseudocode. -- Comment ~ , .
Non-~aX generated event~
[~
Pseudocode.

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{Non-eveIlt based code block}:
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S~ 3:gT~T~TE ~HEET
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~ w093/~423~ 49 2113.~SO Pcr/US93,05233 Pseudocode.

:E~ND ;:
---A function name (TaskName)~

In the above example task, commands supported--- indicates which functions will be pro~rided by the module's command processor.
~I'he command processor pseudocode is not descxibed:in this document.) ~ The ideal ~ow--- section of a module description wi~l describe in "structured english," the ideal sequence of operations ~or xnajor unctional requirements of the module.
Last~ly, l;he events--- se~ion describes the ~uxlc~ons tha~ 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 iden~fier, the astensk may be substituted with either an l'R" or an "I~". The asterisk is used for tasks that will run to a specifie:drawer.

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SlJBSll~lTlJTE~ S~ ~T

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211~55~ ~
WO 93/24234 50 PCr/l lS93/05233 Agitation Control (A~Ctrl*) -- ¦
START
The agitation control task attempts to agitate the bottles in "its"
drawer as close as possible to the set agitation pe~iod.
requirements~
Agitatio~ must * occur peFiodically.
* occur ~or a fixed duration.
* -not interrllpt 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.
* Marking time in ~;ve secoIld incremen~s is suf~icient temporal resolution to begin an agitation cycle.
.
commands slbpported---Set agitatlon~ pe~od: time (increments of 5 second~).
Get a~tation period.~
; ~ Set agitation duration: tlme (mcrements of 5 seconds).
Get agitatlon ~ime.
:E:IlabIe agitation.
~Disable agitation.
:E;orce agitation start.
Force agitabon stop.

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W093/24234 5~1135~i~ Pcr~lJss3/o~233 ideal flow~
Initialization .
For fore~er do:
Ater Agitation Period 5-second time intervals pass, then stop bottle reads in this drawer (~eadInhibit*).
After bottle reads have stopped (ReadInhibited*), start t1ne agitation motor.
Lf, while agitating, AgInhibit~ is receive~, stop ~- agitation;
: : ~ otherwise continue agitation for AgDuration.
Stop Agitation.
Reset the AgPe~iod counter.
End ~or.
uariables~
AgPeriod : Number of FiveSeclicks between agit~tion starts. ~:
AgDuration ~ Numberof~iveSe~licks tv agitatebottles.
gita~ing~lag ~ Boolean indicating that a~t~tion is u~derway. ~: ;
~gInhibit: ; ~ Integer:where non-zero iIldiates that agitahon should~be stopped, and no agitation should:commence.
TimeCounter : Numbex of Time_tick periods to go un~l commencing next agitation phase (on or of~).

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WO 93/241234 52 PC~/US93/05233.

events---AgEnable*: , Reenable agitation.
.
if AgInhibited flag <> O then, ' [
decrement AgInhibited 1ag. , EVENT: Agitation Enabled (DEBIJG, time, drawer);
..

]- ~
,, AgIn~ibit*:
Somethi~g in the system is going to happ~n that should pres:lude agit~tion. If we're agitating, we'll stop. We will inhibit a~y ~uxther agitation.

Lf AgitatingFlag ~et~
tbsn Stop, agitating,~ and home agitator.
, , Clear~ AgitatingFlag. ;
Sen~dReadEnable*. , ; Reset Pe~od~ouIlter to~AgPeriod.

EYENT: ~Agitation~Inhibited ~EBUG, time, drawer).
crem~ent AgInhibited flag. , Send ~AgInhiblted*.
Pe~dwith no timeout.~ ~ ~

SUE31STITUTE '~ EET

211~S50 wC~ 93/2q234 53 Pc~r/uss3/o5233 FiveSecTick:
A standard system time interval ha~ expired. We need to see if it's time ~o start an agitation cycle.
, if ~neCounter <> O then decrement TimeCounter.
if l~neCounter = O then if Agitati~g~ag set then [
Stop Agitation, and home agitator.
Send ReadEnable*.
t . ReloaLd IXmeCounter with (~gPeriod-AgDuration).
]
~lse [
* Set AgitatingFlag.
: Send ReadInhibit*.
:

eadInhibited*: ~ :
ReadInhibited* was received9 we sent a ReadInhibit* message :~ : : to Bottle*. That means :that we intended to commence a~tation, and now upon receiving this~me~sage, have gott~n the go-ahead to do 50.
[~
If Agitating~lag ~ Did an AgInhibit* sneak Ln?
then ~ Nope. It'sco~lto~goahead.

E~NT: Agitation Started ~VENT, time, drawer~.
Start~Agitation. ::
Reload TimeCounter wit~ Agl:)uratlon.

END
, ; ~ --A tation Control~(~gCtrl*)-~

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3U B5T~T~ ITE 5~E~:T

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WO 93/Z~234 5a~ PCI /US93/05233 ¦ ---Temperature Control (TempCtrl*~
START
Maintain the temperature in the drawer.
requ~rements---* Temperature must be controlled in drawer with .1 degree C
accuracy. (This is not addressed in this docume~t.) * Heater duty cycle must be adjusted periodically.
* Time/Drawer stamped temperature readings must be stoxed periQdically. ...
* Temperature control will be disabled from time to ~me.Assumptions---* The control algorithm will be able to ~me-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 tar~et: taxget Get temperature target: target ~; Get current temperature. (Both drawers reported.) 13nableheating.
Disable heating.
Fetch next temperature xead~ngs: number FetGh temperature reading count.
:
ideal ~low~
every one second inte~v~lj attempt to request a temperature xeading ~rom t~is ~awer.
Wait iEor the analog reader task to respond.
When the analog reader task respoIlds, compute the new heater duty cycle, an~ oommunicate it to the heater ISR;
.

If we have taken no readings, store the temperature in a buf~er.
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5UE3ST~ 5HEE~

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211~SO
WO\ 93/24234 55 PClr/US93/~5233 varuzbles---SkipCounter : rlumber of temperature readings to skip before placing reading illto cireular buf~er 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 wi~l not be activated ; ~ :

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21~3aSO
WO ~3/2423~ 56 P~r/US~3~5233 events~
OneSecTick:
We will try to read the temperature every second.
..
If TempInProgress not set then send ReadAnalog (temperature*).
' *DrawerChannelRead:
~ temperature read has completed.

Decrement SkipCounter.
If SkipCounter=0 then store temperature reading, time, drawer in bu~er.
rexet SkipCounter.
, ]
Compute new heater duty cycle.
Update DutyCyele.
] ~ ~:
, DrawerOp~en*: ~
, r L
Set~HeatDIsable flag.
Turn off heater. ~ ~
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DrawerClose*~

Clear HeatI)lsable flag.
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2113~5(~
w0 93/2~3~ 57 ~cr/ LlS~3JO5233 {IS~, tied into main VRTX clock ISR}:
'.
If HeatDisable llag not set then [
Decrement TickCounter.
If TickCounter - 0 then [
If heater is on then [ "
Turn of~heater.
Reset TickCountex with~HeatPeriod-DutyCycle).
]
else [
Turn on heater.
Xeset TickCounter u~ith DutyCy~le.
]

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END
---Temperature Control :(Tem~Ctxl*)---~: ~ ~

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wo 93~2423~ 1 1 3 ~ ~ 0 58 Pcr/v~93/~5233 ¦ ---BottleReader (Bottle*)~
START
:Read bottles in drawer.
requirements---* For each bottle reads must occur pe~iodica~ly.
* Bottle readings will be disabled f~om ~me to time.
* Time/Cell stamped readi~gs will be stored.
T~le read will be stored ~ a mystery format that maximizes the amount of time the system can operate without of ~loadi~g data t~a host computer.
assumptions~
* ca~ibration (cell standardizatio~) ~ be a manual process.
* The bottle reader task will be told w~ich bottles to read ~ria a ~ host comma~d * Reading no~malization will QCCUr` on the host.
operating assumption---Unca~rated ceils will not be assigned.
commands supported~
Enablc a cell (Cell number).
Disable a celI (Cell number).
; ~ ~ : Get ~umber of readings.
r : : : Get ~ext readings (number).
ideal ~flow~
At each five second mterval,: a table of acti~7e bottles is checked.
I a~ ac~ve bottle is encou~ted, it is checked to determille if the read period has~ expired for it.
:
~ ~ If a read is ~required a read is reqLuested from the analog reader : ` ~ task.
Wait for the:analog reader to respond.
en the analog reader task respo~ds~with the reading, the :: ~ reading is :stored in a cixeular buf~e~. ~

::

: ~ ~ 5 LJ~STITUT~ IEET
:
: :~::

wo 93/24234 - ~9 2 1 1 3 ~ PC~/US93~05233 variables---:E~eadIllProgress : ~Flag that indicates that a bottle read is underway.
NoReads : Fla~ 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.
PexiodCount : Number of time periods rema~ning un~l ne.xt read.
- even~s---Readlnhibit*:
[
Set NoReads flag.
If ReadInPro~ress ilag not set then ~: Send ReadInhibited*.

ReadEnable*: ~ ;

Clear NoReads flag.

BottleRead*:

Stor~ time, cell, bottle reading, in~circular buf~er.
Reset Bottle[ce~ PeriodCount to ReadPeIiod.
If NvReads 1ag set then sénd ReadInhibited*.

~:: : : :
' - ~
SU~RS7~1TUTE S~E~T
:
::

WO 93~ 60 pcr/uss3/o5233 FiveSecTick:
[

index = lowest bottle number ~this drawer).
repeat [

wi~h Bottle[index~ do if (Active flag set) and PeriodCount non-zexo then decrement Pe~iodCouIlt.
if (:BottlePeriod = 0) and (NoReads 1ag not set) then [
Set ReadInProgress flag.
Send ReadBottle*(index).

increment index.
untill ~index = ~ighest bottle number (this drawer)+1) or ~eadlnProgress ag set).
~: ]
END ;

.
~ ~ L--~Bottle :Reader @ottle*)-- ¦

.
::

~ ' :
s~ r3~rw~ T

:
.

w~ 93~24~ 1 2 1 1 3 ~ ~ 0 Pcr/usg3/os233 ---Analo~ Reader (AnaRead)~
STA:RT
Perorm all $he operations necessary to perforrn analog readings.
requirements---* The avaîlability of the analog read circuitry must be maximized.
* No operations concerning the any analog measurement must b-e a~lowed to interfere with one another.
assumptions---- ~ ~ There is one YCO VCO measurement may be initiated at any ~me.
* There are two drawers. O~ly one analog measurement may oc~r in a particular drawer at a time.
* ~nereis~onlyoneslowloc~ amp. Performi~gananalog measurement with the lLock-in amp t~kes a long time.
* ~alo~ readîngs ~rorn a drawer will use the lock-în de~ect sr not.
commands supported~
read a cell~ ell number, drawer number). --uses slow lock-in amp~
read a drawer ~hannel (cell number, drawer).--measures DC only.
read a ~drawer channel with gain (cell ~um, ~awer, gain~
DG*gain ~
read a ~UX channel. : ~ read a Mux :cha~nel;
set X switch~(direction).
set ga~n (~ain). ::
set mux ~mux) read YGO~(time)~
read full VCO. - returns time to fill :VCO counter `: : : : :: :
SUI~TI i Ur~ .~ ET

` : ~ , . :

W~ 93/2~ 5 o 62 PC~US93/05233 ideal ~low---For a VCO read:
MUX is selected.
Wait for DC settle time.
Set up VCO timer counter.
Xntegrate.
After in$egration, read VCO counter.
Provide VCO reading with 2.S and O.O volt references.
For a drawer channel read:
- ~ Drawer channel is selected.
is switched to appropriate drawer.
Wait ~or DC settle time.
Set up VCO timer counter.
Integrate.
After integration, re~ad VCO counter.
Pronde VCO reading with 2.5 and O.O volt references.
~: For abottleread:
Drawer channèl is selected.
~ai~ is set.
: X-Switch is:set appropriately (for slow lock-in detect~. -Wait for slow lock-in.
, MUX IS switched to slow lock-in.
W~it for D~ settle time.
Set up ~O: timer counter.
Integrate.:
After mtegration, read V(:~O counter.
Pros~ide VCO rea~ing with 2.5 and O.O volt references.

.
S~E3~TOTU~ ~ ~E~T

~o 93/24234 63 2 1 1 3 ~ ~ Q p~VS93/05233 variables---Delay : Number of VRTXticks to delay.
Delay~nProgress : A delay is in progress. A better name would be 'LockInInProgress'.
Last~e : The last tirne we started a pend (in YRTX~e) ~Pend xou~
In this task, there is a single pen~ point wh~ch might pe~d with a tLme-out, depending on whether a lock-i~ is in progress. If a loek-in has been started, we want to be able to sernce non-compe~ng requests, so we pend for them here. If a reques~ is recei~ed, we'll servi~e it, then return here, determine the remaining time to lock-in, aIld pend with a timeout with that value.

[ ~
If DelayInProgress flag set then [
Set Delay to ( (current VRTX ticktime) - L.asttime , If Delay ~ O then [ : ~ :
Reset DelayInProgress flag.
Resét Delay to O.
go execute ~hme-out>.

] : : :

se i~DeIay~> O~

Set~DdayInPlogress flag. ~ ~

~ SU~STITUTE ~gE

:: : ~

WO 93~2423~ 6~ PCT/lJS93/~523~.

If Delay c~ O then Save curreIlt VRTX ticktime as LastTime.
Pend with ~imeout Delay.
] ''"'' else Pend with no timeout.
- - Pend takes place.
- If pend timed-out then I ~
Reset DelayInProgress ~lag.
Reset Delay to 0.
: ; go sxecute ctime-out~.
~ ~]
: else :
go execute appropr~ate event.

~: ~ events~
<Pend Time-out>~
, ~ ~

: :5etM~JXtosl:owlock-inchannel.
Delay~for~minimum 5ms.
~L`~ ` ~ : : Set up VCO counters.
: ::
Take VCO~ reading.
send ~ResponseType] (vco reading, cal values).
:: ::

SU~5T~TUT~- ~;ii~EET
:
: : : :
; ~ ~: : .

Wo 93/2~234 ~5 ~ 1 1 3 S ~ P~/US~3/05233 If ResponseType is BottleReadL then L :
Release LeftDrawer mes.sage class.
Release BottleReadL.
else Release RightDrawer message class.
Release BottleReadR.

D ReadBottleL(bottle):
[
Holdo~ ReadLDrawerCh.
Eoldoff ReadBottleR.
Select ~ottle within left drawer.
:
Set X-swit~ ~or slow lock-in on left drawer. ::
Select gain.
Set Delay :to SlowLock~ime. .
Set ResponseType to Bottie:ReadL.

:~ ReadBottleR(bottle)~

HoldoE RèadR~DrawerCh.;
Holdof~Rea~BottleL..:: ~ ~
; Select: bottle witliin~right drawer.: ~ ~ :
Se~ X-switch:for~slow lock-in an right arawer.
Select gain.
: Set Del:~y to SlowLockTime.
::Set ResponseType to BottleRead~

, 5T~ T ~

:: : `:: : :

2113~0

6~ PCrtUS93/05~33 ReadRDrawerCh(channel):
- .
Select channel within right drawer.
~et MUX to right drawer channel.
Delay for miimum ~ms.
Set up VCO counters.
Take VCO reading.
send RDxawerCh~ead(vco reading).
]
-ReadLDrawerCh(cha~nel):
[
Select channel within left drawer.
Set MUX to left drawer chaImel.
;: Delay or:minimum 5ms.
Set up VGO: counters.
.
T~ke V(:~O:reading.
send LDrawerChRead(vco reading).

Rea~Analog(chan~el)~

Set MUX to channel. ~:
:Del~ay~for minimum 5ms. ~
Set up VGO~ counters. ` ~ :
Take VCO reading.
; ` send Analog~ad(vco reading, cal values~.

_ ~

SU~E~STIT~TE $~EE~T
, :: :
`

wO 93/2423q 67 2 1 1 3 ~ ~ ~ pcr/US93/05~33 Access Control (Access) -- ¦
START
Design yet to be recorded.
The access task is responsible or primalily two major operations:
(1~ No~fying the bottle reader tasks, and agitation tasks that a particular drawer is going to be ope~ed, and (2) handling all appropliate drawer parking and movement.
END
r;--Access r,O~ G

..

:.

:: :
'~
:
1' SU:~35~-~ ~TE 5~EE~

:'~

Claims (17)

WHAT IS CLAIMED IS:

1. An instrument for detecting the presence of microorganisms in human tissue comprising:
a housing;
a drawer slidably received in said housing, said drawer including means for holding a plurality of specimen containing vessels, and being movable between a first, closed positions in which the holding means is substantially enclosed within the housing, and a second, open position, is which the holding means is located substantially outside said housing;
means operably connected to said drawer f or warming the interior of the drawer to an elevated temperature suitable for encouraging growth of microorganisms when the drawer is in its first, closed position.

2. The instrument of claim 1 in which said warming means includes duct means for allowing heated air to circulate within the closed drawer.

3. The instrument of claim 2 in which said duct means includes a first duct and a second duct, said vessel holding means being positioned between said first and second ducts, and said first and second ducts being configured to allow heated air to pass over specimen vessels located in said vessel holding means.

4. An instrument for detecting the presence of microorganisms in human tissue comprising:
means for holding one or more specimen-containing vessels;
light emission means for emitting excitation light falling within an emission wavelength range, said light emission means being configured to permit excitation light to impinge upon a specimen-containing vessel held in the vessel holding means;

light detection means for converting light energy emanating from a specimen-containing vessel held in the vessel holding means into a detectable signal;
filter means optically interposed between the light emission means and the light detection means for preventing substantially all light falling within the emission wavelength range from reaching the light detection means, whereby the filter means renders the detection means substantially blind to light falling within the emission wavelength range.

5. The instrument of claim 4 wherein the light emission means includes one or more light emitting diodes (LEDs) designed to emit substantially monochromatic excitation light.

6. The instrument of claim 5 wherein a plurality of LEDs are positioned to illuminate an area of a specimen-holding vessel held within the vessel holding means.

7. The instrument of claim 4 wherein said filter means comprises an optical filter which absorbs substantially all light falling within the emission wavelength range.

8. The instrument of claim 4 wherein said light emission means emits excitation light capable of exciting a fluorophore and said filter means is capable of permitting at least a portion of a fluorescence emission from said fluorophore to reach the light detection means.

9. An instrument for detecting the presence 9 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 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 permit the sensor emission light into a detectable signal;
an optical filter optically interposed between the light sources and the light detection means for permitting at least some of the sensor emission light to reach said light detection means while preventing substantially all light falling within the light source emission wavelength range from reaching the light detection means, whereby the optical filter renders the detection means substantially blind to light falling within the emission wavelength range.

10. An instrument for detecting the presence of microorganisms in human tissue comprising:
means for holding one or more specimen-containing vessels;
agitation means coupled to said holding means for cyclically agitating said holding means, said agitation means being configured to agitate said holding means in a manner in which the distance of travel of said holding means from a fixed reference point increases and decreases in a substantially sinusoidal manner.

11. The instrument of claim 10 further comprising braking means operatively coupled to said holding means for stopping the cyclical agitation of the holding means at substantially the maximum distance of travel of the holding means from the fixed reference point.

12. The instrument of claim 10 further comprising braking means operatively coupled to said holding means for stopping the cyclical agitation of the holding means at substantially the minimum distance of travel of the holding means from the fixed reference point.

13. The instrument of claim 10 wherein the agitation means comprises arm means rigidly affixed to said holding means for conveying power to said holding means, said arm means having a substantially oblong aperture along its length;
drive means for moving the arm means in a reciprocal manner, said drive means including a drive element adapted to travel within the oblong aperture in the arm means.

14. An instrument for detecting the presence of microorganisms in human tissue comprising:
means or holding a specimen-containing vessel, said means defining an aperture sized to accommodate a specimen-containing vessel;
gripping means adjacent said aperture for removably gripping a specimen-containing vessel and for repeatably holding the vessel at a pre-defined, substantially fixed depth within the aperture, said gripping means being adapted to provide audible or tactile feedback to an operator when the operator inserts the vessel into the aperture to said pre-defined substantially fixed depth.

15. The instrument of claim 14 wherein the gripping means comprises a flexible arm adjacent the periphery of said aperture, said flexible arm being outwardly deformable in order to admit the specimen-containing vessel.

16. The instrument of claim 15 wherein the flexible arm includes a gripping member adapted to engage an engagement area on the specimen-containing vessel.

17. The instrument of claim 16 wherein the flexible arm is made of a flexible metal and the gripping member is a crimp in the flexible arm, said crimp being adapted to engage an indentation in the specimen-containing vessel.