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User Guide - Ecologie Microbienne Lyon

1. Note Filling out a manual worksheet in preparation of the setup helps with workflow See Appendix 2 for a sample worksheet Checking Load and Batch Status In the normal course of operation the Read window will be displayed when you begin the process of loading MicroPlates The Load window shows a picture of the tray stack and indicates the current status of all MicroPlates in the incubator reader The Read window gives details about each MicroPlate currently in the incubator reader Table 6 1 explains the entries you will see on this screen TABLE 6 1 LOAD WINDOW ENTRIES Key Numbers along left and right edges Explanation Correlate to tray numbers starting with number 1 at the bottom through number 25 at the top A and B designations along left and right edges A left column of MicroPlates B right column of MicroPlates White slots with Slot empty of both MicroPlates and tray White slots with Slot contains tray but not MicroPlate Green background with red checkmark icon Yellow background with hand writing icon Slots that contain MicroPlates that have been read and are ready to be removed Slots containing MicroPlates that have been read but are not ready to be removed Data still saving Red background with clock icon Slots containing plates that haven not been read yet 1 Click Load on the top menu bar 2 Click on any row for an explanatory key Omn
2. Pipetting problems Wells inoculated unevenly Dispense first aliquot from pipettor back into reservoir Depress lever smoothly and completely Make sure tips are lined up evenly and tightly seated Avoid pipetting or trapping air bubbles Visually check wells after inoculating Incorrect volumes used Incubating MicroPlates Symptom Cause 150 ul for aerobic bacteria Solution Wrong incubation conditions Poor growth or poor pattern formation in Micro Planes Wrong MicroPlate Organism not in Database OmniLog System User Guide 25 Jun 06 Incubate according to specified temperature and conditions See Section 5 and Appendices Incubate the MicroPlate at the same temperature as the growth plate Make sure incubator humidity is sufficient Section 12 X Page 5 OmniLog Incubator Reader Symptom Cause Troubleshooting Solution Erratic or inaccurate reading Software won t communicate with or initialize incubator reader MicroPlate won t go into incubator reader Software can t contact the incubator reader via the serial port No video signal footer bar error message Video Error Specified error message in footer bar Not at Temperature error message in footer bar and Not at Temp light in front of instrument goes on Moisture scratches or smudges on MicroPlate If using an off line incubator wipe bottom of MicroPlate before putting into i
3. First Log In and Setting up an Administrator OmniLog System User Guide 25 Jun 06 The program is ready to be opened for the first time The program operates in the Restricted Access Mode that is also available in the MicroStation system See Section 4 Program Administration Restricted Access Mode requires that only the Program Administrator oversees and controls who has access to the program The person who is designated as the Original Program Administrator should perform the first Log in This individual then manages who has access to the application and what tasks they can perform If Section2 Page 2 Installation and Registration desired more than one user can be assigned Administrator Privileges on the User List The Administrator will Assign User names and passwords for those who will use the system Assign access privileges to each user The following steps must be implemented by the user who will act as the program Administrator OmniLog System User Guide 25 Jun 06 Click on the OmniLog shortcut icon on your desktop The Welcome screen will appear Click the First Log In key in the lower right hand corner OmniLog ID Welcome Load Read Unload Exit Reader Setup Administration Print Hardware Status Save Hardware Status amp First Log In The Administrator Dialog box will open e Enter a Username that is at least 1 character in length e Enter a Password that is at least 6 characters i
4. First Log In and Setting up an Administrator Please refer to Section 2 Installation and Registration for full instructions on how to set up an Administrator and Log In to the program for the first time Ideally this will be done soon after the program is installed Administrator Functions When a program administrator is logged into the program the Administration selection bar on the Welcome screen will be active When other users are logged in the Administration functions cannot be accessed Options Tab Functions Once you have selected the Administration Options buttons the Administration Window will open By default it will appear with the Options Tab selected Make your selections from the available options and then click the Save and Close button OmniLog System User Guide Section4 Page 2 25 Jun 06 P A Important Ifyou test Password Expiration Period or Time Out Period features using system clock changes the program must be closed when system clock changes are made Ifnot the Administration screen may appear with each Administrator Log in until 100 Log In Log Outs occur Program Administration C Program Files Biolog OLID_13_01 Logins C Program Files E Biolog acrobat 7 briahtloa Fifteen Minutes E v Restricted Access Mode This is the Administrator s opportunity to disable Restricted Access Mode by unchecking the Restricted Access Mode checkBox The Administra
5. B 1 Mix the following in a 2 3 liter container Caution I ouo maine 57 grams BUG Agar VOUI OWI sn 950 ml purified distilled or deionized water OLLOW instructions 2 Gently boil mixture while stirring to dissolve the agar and exactly Take care other components to avoid 3 contamination Cool an aliquot and measure the pH Adjust pH with NaOH or HCI to achieve a final pH of 7 3 0 1 at 25 C 4 Sterilize by autoclaving at 15 pounds of pressure and 121 C for 15 minutes Cool to 45 50 C Add 50 ml sterile fresh defibrinated sheep s blood just prior to dispensing and mix gently Use good quality blood with a hematocrit of at least 40 7 Dispense into sterile petri dishes Making Biolog Universal Growth Agar maltose BUG M 1 Follow steps 1 5 above for BUG B except use 990 ml purified water 2 Add 10 ml sterile solution of 2596 maltose and mix thoroughly 3 Dispense into sterile petri dishes Making Biolog Universal Growth Agar BUG 1 Mix the following in a 2 3 liter flask 57 grams BUG Agar 1 000 ml purified distilled or deionized water 2 Gently boil while stirring to dissolve the agar and other components 3 Cool an aliquot and measure the pH Adjust pH with NaOH or HCI to achieve a final pH of 7 3 0 1 4 Sterilize by autoclaving at 15 pounds of pressure at 121 C for 15 minutes 5 Cool to 45 50 C 6 Dispense into sterile petri dishes OmniLog System User Guid
6. The user name of each person who logged in is listed here Registered If this person was an approved user this entry will say Yes if not this entry will say No Attempt Date This is the exact date and time the user logged in or attempted to do so Log Out Time This is the exact date and time the user logged out The entry here will read Never in the event of a failed log in and when the program administrator is currently using the software User Privileges Yes if access was given during that log in period No if not Yes if access was given during that log in period No if not Yes if access was given during that log in period No if not Yes if access was given during that log in period No if not Yes if access was given during that log in period No if not Log In Set Up View Print Edit Admin Form Color Change To change the screen background from Teal to White or White to Teal click Form Color on the Reader Setup window Caution Admin Options button is only be used on the instruction of Field Service or Technical Service Reader serial number and Frame grabber revision letters are preset before shipment OmniLog System User Guide 25 Jun 06 Section4 Page 6 Program Administration Administration Suggestions Warning It is important for the Administrator to use identical usernames in the OmniLog ID and other Biolog software programs to ensure c
7. What It Means Heading 2 gray Tray The designated tray position Plate The type of MicroPlate used for that sample Strain Strain type Sample Number The sample number you assigned that MicroPlate Name The classification of that microbe Number Strain number Other Other pertinent information you entered Last Read When MicroPlate was read last Inc Hrs How long the MicroPlate has been incubating ID Shows whether result is in progress or final e green box with red checkmark means final ID e red box with clock face means in progress ID or not read yet e in progress results are updated every 30 minutes at each reading Species Gives full identification of microbe If this area is blank no reading has been done yet Prob Confidence probability of a called ID Sim ID Score value Dis Equivalent number of mismatches Note The headings on the Read window worksheets reflect the information you selected during worksheet setup As a result these headings will change depending on your data entered 1 Check the Read window for in progress and final identifications 2 For more detailed results click on any part of any row in the Read window A Plate Data window will appear for that MicroPlate If you get a No Identification result the Prob value will not be displayed When this happens check for black and signs in the on screen MicroPlate OmniLog System User Guide 25 Jun 06 If the
8. 14 gt 1 gt Acinetobacter baumannii genospecies 2 100 0 857 2 13 GN NENT OXI 2 Acinetobacter calcoaceticus genospecies 0 0 000 4 96 GN NENT OXI 3 Acinetobacter caleoaceticus genospecies 0 0 000 5 85 GN NENT OxXi 4 Acinetobacter calcoaceticus genospecies 0 0 000 10 59 GN NENT OXI 5 Acinetubacter genospecies 14 0 0 000 11 86 GN NENT OXI 6 Pseudomonas viridilivida 0 000 12 38 ON NENT OXI 7 Pseudomonas alcaligenes 0 0 000 14 47 GN NENT 8 Burkholdcria pyrrocinia 0 0 000 15 64 GN NENT OXI 9 Pscudomonas fluorcsaccns biotype G 0 0 000 15 85 GN NENT 10 Acinetobacter johnsonii genospecies 7 0 0 000 16 46 GN NENT OXI Read Errore No Errors Plate Errors No Errors 1523 General Errors No Errors Temp Frrors No Errors Print Ti me Mar 14 2002 12 43 PM OmniLog System User Guide 25 Jun 06 Section 15 X Page 19 Appendix 5 Program Printouts Reader and Saved File Modes Printout Key Software version Operator Does user have Unrestricted Access to Software Worksheet file name Time MicroPlate was setup Time MicroPlate was read for ID MicroPlate Position Sample identifiers Name of database searched Number of positive borderline and negative reactions 0 If the printout is from a saved file this entry lists file name position of the entry in the file and edit status 11 Reaction Key 12 Numbers seen in each well is the Color Intensity Values Positive lt gt borderline 1
9. Do not allow cultures to grow for too long Maximum growth is 24 hours for most bacteria Some exceptionally slow growing or fastidious bacteria may require 48 hours growth or the use of multiple growth plates Section5 X Page 1 Preparing an inoculum directly from a mixed growth plate will cause identification problems Use the colony magnifier lamp to closely examine colonies Preparing Samples Checking to see if your culture is pure Colonies on the plate that seem to be isolated may in fact be the result of mixed growth This is especially true with Staphylococcus species Careful visual examination is essential to ensuring that a culture is pure If a colony shows any hint of pleomorphism it is probably not a pure culture and requires additional re streaking and isolation Carefully examine areas of confluent growth If the lawn is not uniform in texture and color this may indicate that the culture is not pure Once again re streak for isolation Note Unless your organism is a very slow grower we don t recommend using lawn growth The opposite problem can also occur sometimes a culture may be pure but gives the appearance of heterogeneity This is due to a rather common phenomenon whereby microorganisms produce more than one colony type To be certain of its identity purify and test each colony type individually Gram Staining OmniLog System User Guide 25 Jun 06 A Gram stain is essential in orde
10. for growth or forming 1 mm colonies on BUG B If control well A1 is positive add salicylate along with thioglycolate to inoculating fluid Agricultural species may be grown on BUG without blood ABBREVIATIONS 4 Air unless organism requires CO for growth Oxi Oxidase TSI Triple Sugar Iron Slant A Acid A Weak Acid K Alkaline OmniLog System User Guide Section 15 X Page 2 25 Jun 06 Appendix 2 Appendix 2 OmniLog Sample Worksheet Plate Tray Type Strain Type D LLL LL LLL Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 x Page 3 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Appendix 3 Characteristics wo 00 10 Uta UG rt2 Database Species Gram Negative Aerobic Bacteria Species Name Achromobacter cholinophagum Achromobacter xylosoxidans ss denitrificans Achromobacter xylosoxydans ss xylosoxidans Acidovorax avenae ss avenae Acidovorax avenae ss cattleyae Acidovorax avenae ss citruli Acidovorax delafieldii Acidovorax facilis Acidovorax konjaci Acidovorax temperans Acinetobacter baumanii genospecies 2 Acinetobacter calcoaceticus bv alc Acinetobacter calcoaceticus genospecies 1 Acinetobacter calcoaceticus genospecies 3 Acinetobacter calcoaceticus genospecies 13 Acinetobacter genospecies 6 Acinetobacter genospecies 10 Acinetobacter genospecies 11 Acineto
11. see Bailey amp Scott s Diagnostic Microbiology Baron E J and Finegold S M C V Mosby Co 1990 pages 102 103 OmniLog System User Guide Section 12 X Page 2 25 Jun 06 Culturing Microorganisms Symptom Cause Troubleshooting Solution Using nonrecommended media Poor overall growth Some environmental organisms take several days to become visible on growth plate at which point culture may be too old for successful ID Isolate takes several days to form a colony Bacterium will not grow on BUG B or forms pinpoint Fastidious gram negative bacteria need special culture conditions Use Biolog recommended media Subculture one or two passages in broth medium Set up two or three agar plates to obtain sufficient growth Use Chocolate agar and incubate with elevated CO at 35 37 C colonies Some environmental bacteria may be oligotrophic or temporarily in an oligotrophic state i e they will only grow on low nutrient media such as R2A Sub optimal growth temperature and or humidity and or atmosphere Slow growth and or weak pattern formation Mixed growth on Sticky bacterial surfaces agar plates OmniLog System User Guide 25 Jun 06 Try to subculture the bacterium from R2A and see if they will gradually adapt to growing on BUG B If not it is a species that is not included in our Biolog database Agricultural bacteria may be grown on BUG without blood Use spe
12. 35 37 237 Rhodococcus erythropolis GP ROD C Y BUG B Air 35 37 238 Rhodococcus fascians GP ROD C Y BUG B Air 35 37 239 Rhodococcus globerulus GP ROD C Y BUG B Air 35 37 240 Rhodococcus rhodnii GP ROD C Y BUG B Air 35 37 241 Rhodococcus rhodochrous GP ROD C Y BUG B Air 35 37 242 Rhodococcus ruber GP ROD C Y BUG B Air 35 37 243 Rothia dentocariosa GP ROD C Y BUG B Air 35 37 244 Rothia mucilaginosa GP COCCUS C W Y BUG B Air 35 37 245 Sanguibacter inulinus GP ROD C Y BUG B 6 5 C02 35 37 246 Sanguibacter keddieii GP ROD C Y BUG B Air 30 247 Sanguibacter suarezii GP ROD C Y BUG B Air 30 248 Staphylococcus arlettae GP COCCUS C Y BUG B Air 35 37 249 Staphylococcus aureus ss aureus GP COCCUS C Y BUG B Air 35 37 250 Staphylococcus aureus ss anaerobius GP COCCUS C Y BUG B Air 35 37 251 Staphylococcus auricularis GP COCCUS C Y BUG B Air 35 37 252 Staphylococcus capitis GP COCCUS C Y BUG B Air 35 37 253 Staphylococcus caprae GP COCCUS C Y BUG B Air 35 37 254 Staphylococcus carnosus GP COCCUS C Y BUG B Air 35 37 255 Staphylococcus chromogenes GP COCCUS C Y BUG B Air 35 37 256 Staphylococcus cohnii GP COCCUS C Y BUG B Air 35 37 257 Staphylococcus delphini GP COCCUS C Y BUG B Air 35 37 258 Staphylococcus epidermidis GP COCCUS C Y BUG B Air 35 37 259 Staphylococcus equorum GP COCCUS C Y BUG B Air 35 37 260 Staphylococcus felis GP COCCUS C Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n th
13. 35 37 98 Corynebacterium mastitidis GP ROD C Y BUG B Air 35 37 99 Corynebacterium matruchotii GP ROD C Y BUG B Air 35 37 100 Corynebacterium minutissimum GP ROD C Y BUG B Air 35 37 101 Corynebacterium mucifaciens GP ROD C Y BUG B Air 35 37 102 Corynebacterium mycetoides GP ROD C Y BUG B Air 35 37 103 Corynebacterium nitrilophilus GP ROD C Y BUG B Air 35 37 104 Corynebacterium pilosum GP ROD C Y BUG B Air 35 37 105 Corynebacterium pseudodiphtheriticum propinquum CDC ANF 3 GP ROD C Y BUG B Air 35 37 106 Corynebacterium pseudotuberculosis GP ROD C Y BUG B Air 35 37 107 Corynebacterium renale GP ROD C Y BUG B Air 35 37 108 Corynebacterium riegelii GP ROD C Y BUG B Air 35 37 109 Corynebacterium seminale GP ROD C Y BUG B Air 35 37 110 Corynebacterium singulare GP ROD C Y BUG B Air 35 37 111 Corynebacterium spp CDC G GP ROD C Y BUG B Air 35 37 112 Corynebacterium striatum CDC I 1 GP ROD C Y BUG B Air 35 37 113 Corynebacterium thomssenii GP ROD C Y BUG B Air 35 37 114 Corynebacterium ulcerans GP ROD C Y BUG B 6 5 CO2 35 37 115 Corynebacterium urealyticum GP ROD C Y BUG B Air 35 37 116 Corynebacterium variabile Caseobacter polymorphus GP ROD C Y BUG B Air 35 37 117 Corynebacterium vitaeruminis GP ROD C Y BUG B Air 35 37 118 Corynebacterium xerosis GPC GP COCCUS C Y BUG B Air 35 37 119 Curtobacterium albidum GP ROD C N BUG Air 30 120 Curtobacterium citreum GP ROD C N BUG Air 30 121 Curtobacterium flaccumfaciens GP ROD C N B
14. 439 Shewanella putrefaciens A GN NENT O N BUG B Air 30 440 Shewanella putrefaciens B GN NENT O N BUG B Air 30 441 Shigella boydii GN ENT O Y BUG B Air 35 37 442 Shigella dysenteriae GN ENT O Y BUG B Air 35 37 443 Shigella flexneri GN ENT O Y BUG B Air 35 37 444 Shigella sonnei GN ENT O Y BUG B Air 35 37 445 Simonsiella crassa GN FAS O Y CHOC 6 5 CO2 35 37 446 Simonsiella muelleri GN FAS O Y CHOC 6 5 CO2 35 37 447 Simonsiella steedae GN FAS O Y CHOC 6 5 CO2 35 37 448 Sinorhizobium meliloti GN NENT O N BUG B Air 30 449 Sphingobacterium multivorum GN NENT O N BUG B Air 30 450 Sphingobacterium multivorum like GN NENT O N BUG B Air 30 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 10 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 451 Sphingobacterium spiritovorum GN NENT O N BUG B Air 30 452 Sphingobacterium thalpophilum GN NENT O N BUG B Air 30 453 Sphingomonas adhaesiva GN NENT O N BUG B Air 30 454 Sphingomonas capsulata GN NENT O N BUG B Air 30 455 Sphingomonas echinoides GN NENT O N BUG By Air 30 456 Sphingomonas macrogoltabidus GN NENT O N BUG B Air 30 457 Sphingomonas parapaucimobilis GN NENT O N BUG B Air 30 458 Sphingomonas paucimobilis A GN NENT O N BUG B Air 30 459 Sphingomonas paucimobilis B GN NENT O N BUG B Air 30
15. 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 Air 35 37 Air 35 37 Air 30 Air 30 Air 35 37 Air 35 37 Air 30 Air 30 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 30 Air 30 Air 35 37 Air 35 37 Air 30 Air 30 Air 35 37 Air 30 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 35 37 Air 30 Section 15 X Page 8 Appendix 3 Database Species Lists and Their Characteristics 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 Species Name Pseudomonas agarici Pseudomonas alcaligenes Pseudomonas asplenii Pseudomonas aurantiaca Pseudomonas bathycetes Pseudomonas boreopolis Stenotrophomonas Pseudomonas caricapapayae syringae Pseudomonas chlororaphis Pseudomonas cichorii syringae Pseudomonas cissicola Xanthomonas like Pseudomonas citronellolis Pseudomonas corrugata Pseudomonas
16. Air 35 37 148 Edwardsiella ictaluri GN ENT O N BUG B Air 30 149 Edwardsiella tarda GN ENT O Y BUG B Air 35 37 150 Eikenella corrodens GN FAS O X CHOC 6 5 CO2 35 37 151 Empedobacter brevis GN NENT O N BUG B Air 30 152 Enterobacter aerogenes Klebsiella mobilis GN ENT O Y BUG B Air 35 37 153 Enterobacter agglomerans bgp 2 GN ENT O Y BUG B Air 35 37 154 Enterobacter agglomerans bgp 3 GN ENT O Y BUG B Air 35 37 155 Enterobacter agglomerans bgp 4 Pantoea GN ENT O Y BUG B Air 35 37 156 Enterobacter agglomerans bgp 5 GN ENT O Y BUG B Air 35 37 157 Enterobacter agglomerans bgp 6 Pectobacterium GN ENT O Y BUG B Air 35 37 158 Enterobacter agglomerans bgp 7 Pantoea GN ENT O Y BUG B Air 35 37 159 Enterobacter amnigenus GN ENT O Y BUG B Air 35 37 160 Enterobacter asburiae GN ENT O Y BUG B Air 35 37 161 Enterobacter cancerogenus GN ENT O Y BUG B Air 35 37 162 Enterobacter cloacae GN ENT O Y BUG B Air 35 37 163 Enterobacter gergoviae GN ENT O Y BUG B Air 35 37 164 Enterobacter hormaechei GN ENT O Y BUG B Air 35 37 165 Enterobacter intermedius GN ENT O Y BUG B Air 35 37 166 Enterobacter nimipressuralis GN ENT O Y BUG B Air 35 37 167 Enterobacter sakazakii GN ENT O Y BUG B Air 35 37 168 Erwinia amylovora GN ENT O N BUG By Air 30 169 Escherichia blattae GN ENT O Y BUG B Air 35 37 170 Escherichia coli GN ENT O Y BUG B Air 35 37 171 Escherichia coli USP5 7085 GN ENT O Y BUG B Air 35 37 172 Escherichia coli inactive GN ENT O
17. BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU G Bt G Bt G Bt G Bt G Bt G Bt G B G Bt G Bt G B G B G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt G Bt Atm Temp Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Section 15 X Page 9 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 385 Pseudomonas syringae pv syringae GN NENT O N BUG By Air 30 386 Pseudomonas syringae pv tabaci A GN NENT O N BUG By Air 30 387 Pseudomonas syringae pv tabaci B GN NENT O N BUG Bt Air 30 388 Pseudomonas syringae pv taget
18. BUG Air 30 74 Clavibacter michiganensis ss tessellarius GP ROD C N BUG Air 30 75 Corynebacterium accolens GP ROD C Y BUG B Air 35 37 76 Corynebacterium afermentans ss afermentans CDC ANF 1 GP ROD C Y BUG B Air 35 37 TI Corynebacterium afermentans ss lipophilum GP ROD C Y BUG B Air 35 37 78 Corynebacterium ammoniagenes Brevibacterium like GP ROD C Y BUG B Air 35 37 79 Corynebacterium amycolatum CDC F 2 GP ROD C Y BUG B Air 35 37 80 Corynebacterium argentoratense GP ROD C Y BUG B Air 35 37 81 Corynebacterium auris GP ROD C Y BUG B Air 35 37 82 Corynebacterium bovis GP ROD C Y BUG B Air 35 37 83 Corynebacterium callunae GP ROD C Y BUG B Air 35 37 84 Corynebacterium camporrealensis GP ROD C Y BUG B Air 35 37 85 Corynebacterium coyleae GP ROD C Y BUG B Air 35 37 86 Corynebacterium cystitidis GP ROD C Y BUG B Air 35 37 87 Corynebacterium diphtheriae GP ROD C Y BUG B Air 35 37 88 Corynebacterium durum GP ROD C Y BUG B Air 35 37 89 Corynebacterium falsenii GP ROD C Y BUG B Air 35 37 90 Corynebacterium flavescens GP ROD C Y BUG B Air 35 37 91 Corynebacterium glucuronolyticum GP ROD C Y BUG B Air 35 37 92 Corynebacterium glutamicum GP ROD C Y BUG B Air 35 37 93 Corynebacterium imitans GP ROD C Y BUG B Air 35 37 94 Corynebacterium jeikeium GP ROD C Y BUG B Air 35 37 95 Corynebacterium kutscheri GP ROD C Y BUG B Air 35 37 96 Corynebacterium lipophiloflavum GP ROD C Y BUG B Air 35 37 97 Corynebacterium macginleyi GP ROD C Y BUG B Air
19. Brevibacterium otitidis GP ROD C Y BUG B Air 35 37 54 Brochothrix campestris GP ROD C Y BUG B 6 5 CO2 35 37 55 Brochothrix thermosphacta GP ROD C Y BUG B Air 30 56 Carnobacterium alterfunditum GP ROD C Y BUG B Air 26 57 Carnobacterium divergens GP ROD C Y BUG B Air 26 58 Carnobacterium gallinarum GP ROD C Y BUG B Air 26 59 Carnobacterium mobile GP ROD C Y BUG B Air 26 60 Carnobacterium piscicola GP ROD C Y BUG B Air 26 61 Cellolosimicrobium cellulans GP ROD C Y BUG B Air 35 37 62 Cellulomonas biazotea GP ROD C Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 13 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 63 Cellulomonas cellasea GP ROD C Y BUG B Air 30 64 Cellulomonas fimi GP ROD C Y BUG B Air 35 37 65 Cellulomonas flavigena GP ROD C Y BUG B Air 35 37 66 Cellulomonas gelida GP ROD C Y BUG B Air 35 37 67 Cellulomonas hominis CDC A 3 GP ROD C Y BUG B Air 35 37 68 Cellulomonas turbata Oerskovia turbata GP ROD C Y BUG B Air 35 37 69 Cellulomonas uda GP ROD C Y BUG B Air 35 37 70 Clavibacter michiganensis ss insidiosus GP ROD C N BUG Air 30 71 Clavibacter michiganensis ss michiganensis GP ROD C N BUG Air 30 72 Clavibacter michiganensis ss nebraskensis GP ROD C N BUG Air 30 73 Clavibacter michiganensis ss sepedonicus GP ROD C N
20. Clear All User Entries Zero Pending Loads Zero Video Status Zero All Rows Start Unload Sequence UNLOAD WINDOW Once you ascertain which MicroPlates have completed the ID process you simply open the incubator reader door remove one tray at a time take the appropriate MicroPlate s out of each tray replace the tray in the same slot of the incubator reader and close the door If you wish you can load a new batch while the door is open The system allows 20 minutes for each load unload cycle OmniLog System User Guide Section 1 X Page 10 25 Jun 06 Introducing the OmniLog ID System Using the Footer Bar No matter which OmniLog ID window you display there will always be a footer bar running across the bottom of the window This offers a handy display of important status indicators such as time incubator reader temperature and the time until the next reading The footer bar consists of ten cells laid out as follows OmniLog ID XJ Welcome Load Read Unload Exit Version mem B Administration Print Hardware Status Save Hardware Status Door status Reader Status Plate Status User Name and Access Minutes to Next Read Error Messages Temperature Status Current System Time Time to Auto Log Out Time of Next Read Table 1 1 explains the possible entries in the footer bar cells TABLE 1 1 FOOTER BAR ENTRIES Cell Message Color Meaning Door Status Door Closed
21. D and negative reactions no brackets Numbers with no brackets and a plus on the right side are mismatches The well read as negative but at least 80 of the strains of that organism tested in our database were positive for that well Numbers with a lt on the left and a minus on the right are also mismatches but the well read as positive while the strains in our database were mostly negative for that well Numbers with a minus to the left of the well value mean that the well s OD was less than the OD of the control well 13 Species Identification 1 identification 14 42 9 choices 15 Error Listing 20200 cT N OmniLog System User Guide Section 15 X Page 20 25 Jun 06 Appendix 5 Dangerous Pathogen Database Appendix 5 Dangerous Pathogen DP Database Biolog makes a supplemental database for species falling into a category called Dangerous Pathogens e g the organisms that generally require BL2 BL3 handling protocols If your laboratory is testing for these pathogens you will know in advance if any samples are suspected of containing these organisms Follow the instructions in the body of this user guide As appropriate also follow the special procedures listed here Safety Considerations To comply with government safety regulations use Biosafety Level 2 BL2 methods containment equipment and facilities Immunization of laboratory personnel may be required if frequent work with clinical specimens or
22. Enter Username l Enter Password Cancel Registering Your Software Before working with the OmniLog it is important to register the software with Biolog technical service department By registering the software you become eligible for software upgrades and you will receive regular correspondence from the company Note There is only 1 ETE i T Yeb isfiation After initial installation the Welcome tab will show Temporary button access Registration Days Left 60 in red The software will count down per session how many days you have left to register You must click the Log Out and Registration button to start the registration process Log In for additional Registration Process access 1 Generate a User Key and send to Biolog 2 Load the Registration Key from Biolog OmniLog System User Guide Section2 Page 4 25 Jun 06 Installation and Registration Follow the steps outlined below to generate a User Key l 2 oe p Each computer requires a separate 6 registration key 7 Your 8 registration key should arrive within 48 business hours 1 providing it is received Monday to Thursday during 2 regular Biolog business hours M F 8 30 A M 3 5 00 P M PST OmniLog System User Guide 25 Jun 06 At the Welcome tab click on the Registration button The Registration Form window appears istration Form i Registration Ke Instructions 1 Enter
23. Green Incubator reader door is closed Door Open OK Green OK to have door open at current menu When loading and unloading plates Close Door Yellow Close the door to maintain temperature and ensure Green future incubator reader movement Door Open Error Red The incubator reader cannot move because the door Yellow is open Error Messages Hardware Abort Red The incubator reader is in mechanical failure Yellow Video Error Red The camera failed during reading Yellow Temperature Error Red The temperature is not at target setting while Yellow MicroPlates are in the incubator reader Plate Error Red A MicroPlate is missing from the read position Yellow OmniLog System User Guide Section 1 X Page 11 25 Jun 06 Introducing the OmniLog ID System Cell Message Color Meaning User Cancel Red User clicked Stop Commands User time out Yellow commands Re trying Contact Red The incubator reader is not responding and the Yellow software is trying to re establish contact Logged Auto Auto Red Loss of computer power during read incubation Restart Yellow period Number of restarts will appear in this box Reader Status Reader OK Idle Green The incubator reader is not moving or reading cycle on reader idle Com Not Open Red Serial port is not initialized Yellow Reader Not Initialized Red Incubator reader is not initialized Yellow Cycle Off Red The software is not in
24. Incubator reader you should not run any non Biolog programs on it If you do need to quit the program for routine re booting or for example to move the OmniLog Incubator Reader to another location the program will save all current MicroPlate information and data to files When you start the OmniLog program back up the software will retrieve all the MicroPlate information in it when you quit the program It will resume all pending reads using a current time as the read time not the plate setup time If you quit the program while readings are pending you will lose all the readings that would have occurred while the system was off 1 Click Exit on the Welcome screen menu bar A pending read status warning will appear in the center of the screen If there are pending reads the warning box will be red if not the box will be green and the message will say OK to exit Welcome EXIT WINDOW 2 Click Exit OmniLog ID will close Section 7 X Page 3 Interpreting Results 8 Interpreting Results During normal operation the Read window will display As OmniLog In this section gt Assessing the ID makes identifications the results will show for all MicroPlates in Accuracy of your all current worksheets The worksheets are shown in the order in ID which they were loaded with the one that s been in the longest on top 2 Pinning Down Scroll down to see all results an Uncertain ID Each worksheet begins with
25. N BUG B Air 30 415 Roseomonas gilardii GN NENT O N BUG B Air 30 416 Salmonella gp 1 choleraesuis GN ENT O Y BUG B Air 35 37 417 Salmonella gp 1 choleraesuis st choleraesuis GN ENT O Y BUG B Air 35 37 418 Salmonella gp 1 choleraesuis st gallinarum GN ENT O Y BUG B Air 35 37 419 Salmonella gp 1 choleraesuis st paratyphi A GN ENT O Y BUG B Air 35 37 420 Salmonella gp 1 choleraesuis st pullorum GN ENT O Y BUG B Air 35 37 421 Salmonella gp 1 choleraesuis st typhi GN ENT O Y BUG B Air 35 37 422 Salmonella gp 1 choleraesuis st typhimurium GN ENT O Y BUG B Air 35 37 423 Salmonella gp 3a arizonae GN ENT O Y BUG B Air 35 37 424 Salmonella gp 3b diarizonae GN ENT O Y BUG B Air 35 37 425 Salmonella gp 4 houtenae GN ENT O Y BUG B Air 35 37 426 Salmonella gp 5 bongori GN ENT O Y BUG B Air 35 37 427 Salmonella gp 6 indica GN ENT O Y BUG B Air 35 37 428 Serpens flexibilis GN NENT O N BUG B Air 30 429 Serratia entomophila GN ENT O Y BUG B Air 35 37 430 Serratia ficaria GN ENT O v Y BUG B Air 35 37 431 Serratia fonticola GN ENT O Y BUG B Air 35 37 432 Serratia liquefaciens grimesii GN ENT O Y BUG B Air 35 37 433 Serratia marcescens GN ENT O Y BUG B Air 35 37 434 Serratia odorifera GN ENT O Y BUG B Air 35 37 435 Serratia plymuthica GN ENT O Y BUG B Air 35 37 436 Serratia proteamaculans ss proteamaculans GN ENT O Y BUG B Air 35 37 437 Serratia rubidaea GN ENT O Y BUG B Air 35 37 438 Shewanella algae GN NENT O N BUG B Air 30
26. N BUG M Air 30 27 Bacillus anthracis subgroup C GP RODSB C W N BUG M Air 30 28 Bacillus anthracis subgroup D GP RODSB C W N BUG M Air 30 29 Bacillus badius GP RODSB C W N BUG M Air 30 30 Bacillus cereus thuringiensis GP RODSB C W N BUG M Air 30 31 Bacillus circulans GP RODSB C W N BUG M Air 30 32 Bacillus coagulans GP RODSB C W N BUG M Air 30 33 Bacillus fastidiosus GP RODSB C W N BUG M Air 30 34 Bacillus firmus GP RODSB C W N BUG M Air 30 35 Bacillus halodurans GP RODSB C W N BUG M Air 30 36 Bacillus laevolacticus GP RODSB C W N BUG M Air 30 37 Bacillus licheniformis GP RODSB C W N BUG M Air 30 38 Bacillus maroccanus GP RODSB C W N BUG M Air 30 39 Bacillus megaterium GP RODSB C W N BUG M Air 30 40 Bacillus mycoides GP RODSB C W N BUG M Air 30 41 Bacillus psychrosaccharolyticus GP RODSB C W N BUG M Air 30 42 Bacillus pumilus GP RODSB C W N BUG M Air 30 43 Bacillus racemilacticus GP RODSB C W N BUG M Air 30 44 Bacillus sphaericus GP RODSB C W N BUG M Air 30 45 Bacillus subtilis GP RODSB C W N BUG M Air 30 46 Bacillus subtilis ATCC 6633 GP RODSB C W N BUG M Air 30 47 Brevibacillus brevis GP RODSB C W N BUG M Air 30 48 Brevibacterium casei GP ROD C Y BUG B Air 35 37 49 Brevibacterium epidermidis GP ROD C Y BUG B Air 35 37 50 Brevibacterium linens GP ROD C Y BUG B Air 35 37 51 Brevibacterium liquifaciens GP ROD C Y BUG B Air 35 37 52 Brevibacterium mcbrellneri GP ROD C Y BUG B Air 35 37 53
27. NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT Lists Test O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O Thio ZZZAAAZAZAZA ANANANAAAAKRKKKKKKKKKKKKKAZZAZAZAZAZAZAZAZAAZAZZAAAZAZAAAAAZAYA NAYNZ and Their Medium BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU G B G B G B G Bt G Bt G Bt G Bt G Bt G Bt G Bt G B G B G B G B G B G B G B G B G B G B G B G B G B G B G B CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU G B G B G B G B G B G B G B G B G B G B G B G B G B G B G B Atm Temp Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5
28. User datafiles to designate the reaction patterns of organism group clusters for specialized identification purposes Use RetroSpect Trending and Tracking Software OmniLog System User Guide Section 14 X Page 2 25 Jun 06 Appendices 15 Appendices In this section gt Setup Flowchart gt OmniLog Sample Worksheet gt Database Species Lists and Their Characteristics gt Program ID Printout gt Using the Dangerous Pathogen Database OmniLog System User Guide Section 15 X Page 1 25 Jun 06 Appendices Appendix 1 Release 1 1 Setup Flowchart Determine Gram Stain Morphology and Optimal Incubation Temperature and Atmosphere Aerobic Bacteria GN ENT GN FAS GP COCCUS GP ROD Culture Media BUG B or CHOC BUG B BUG M T TSA B PLUS streaking Atmosphere AIR 6 5 CO AIR 6 5 96 CO AIR Temperature Typically Typically Typically 35 37 C Typically Typically 35 37 C 30 C 30 C 35 37 C reactions GN GP IF T Inoculating Fluid GN GP IF GN GP IF T GN GP IF GN GP IF T 20 T Inoculum T 52 T 61 T 20 T 28 T GN2 150 ul MicroPlate ul per well GN2 150 pl GN2 150 ul GP2 150 ul GP2 150 ul Incubation Time hours 4 6 16 22 4 6 16 22 4 6 16 22 4 6 16 22 4 6 16 22 With the exception of thermophiles all species are either 26 C 30 or 35 37 C Tf control well A1 is positive add thioglycolate to inoculating fluid Requiring CHOC or CO
29. Wherever it parks that tray locks into place you will not be able to remove it for loading If for example if the incubator reader is empty and you are loading a batch of 50 MicroPlates you will not be able to remove tray 25 until you move the camera out of the way Occasionally the camera will move behind a slot while you have that tray out to load MicroPlates In both cases you must move the camera out of the way If you encounter any difficulty inserting a tray all the way or closing the door because one tray is sticking out it is most likely because the camera has locked that slot DO NOT FORCE TRAYS INTO SLOT Simply remove the tray and move the camera out of the way using OmniLog ID software To move the camera 1 Remove the tray causing the problem 2 Close the door 3 Click Move Camera on the Load Plates window Note If you click Move Camera before closing the door you will get an on screen prompt to close the door 4 The camera will move to another slot An on screen message will appear telling you when it s ok to open the door and resume loading that row 5 Open the door and load the tray OmniLog System User Guide Section6 X Page 12 25 Jun 06 Special Functions 7 Special Functions In this section gt Using the Snooze Bar gt Using an Offline Incubator gt Quitting the Program OmniLog ID has several special functions that allow you to do the following e Geta little extra time
30. a two row header the top one is yellow the one beneath it gray OmniLog ID fOrnitog TO x Welcome Load Read Unload Exit EE ro j s 050630 M4Pletes Jun 30 2006 5 40 Am gt Jui 01 2006 12 11 PM 22rs Short Data Logger Plate Strain Sampe Name Inc Hr Number Other amp ow2 owewr 1 Unknown af vit re ow2 owewr 2 unknowns vii2 alona onen s ummwnc vius 25 jew2 owewr a ummowno viis so50630 P 4Pites Jun 29 2006 2 45 PM gt Jun 30 2006 12 Piate strain other 1 ms 1 name Number ssce cemooca owos _ ss ce2 o coccus rez CAC fear2 __ _ LECA CAE C READ WINDOW WITH RESULTS Table 8 1 explains the column headings on the Read window TABLE 8 1 READ WINDOW COLUMNS Column Heading What It Means Heading 1 yellow 001029A W4C File name yy mm dd worksheet code 7 plates Number of plates in a batch Oct 27 2000 Setup date 1 48 PM gt Time run began Oct 30 2000 Current date 1 31 PM Current time 24 hrs Inc Time set for incubation OmniLog System User Guide Section 8 X Page 1 25 Jun 06 Possible IDCall Results Species ID Genus ID NO ID Too Few Positives e Too Few Matching Positives e Too Many Borderlines Interpreting Results Column Heading
31. case Occasionally a user might simply forget or misplace their password sensitive The user may have attempted entry 5 times with the incorrect password If the user is NOT the only Administrator this situation is easily remedied Any Program Administrator can easily go to the User List under Administrator Options and assign the person a new password Make sure to re assign the user s privileges as well or the new password will not work OmniLog System User Guide Section4 X Page 4 25 Jun 06 Program Administration Log In Privileges Privilege What It Allows In OmniLog ID Log In Set Up View Print Edit User will be able to log onto the OmniLog ID software This privilege is in tandem with all other privileges It should be revoked when a user no longer Uses the system User will be able to perform general ID functions Reader Setup worksheet Load Unload and change screen background to white User will be able to view or print data from Read Menu and view error logs User will be able to mark Plates as done Restore plate clear all runs in progress Snooze Function and change temp or quit program with pending reads clear error logs User will have complete access to all aspects of the software including all Administration functions Interpreting the Log In Log Only the program administrator has access to the Log In Log This feature of the software keeps meticulous track of program use
32. changed Section 4 X Page 3 Program Administration 1 Click the User List tab A numbered list will appear showing all users registered to that point starting with the program administrator in row 1 2 To add a new user click in the next blank white field in the User Name column Enter the new user name Ce CL 1 Jun 28 2006 13 28 Jun 28 2006 13 59 vgomez Original Administrator NLE 2 un 28 2006 10 35 Jun 28 2006 1224 edituser edituser0 Yes Yes Yes Yes No s resa Jun 28 2006 10 34 viewuser viewuser Yes Yes Yes No No No No No No No Click here to add next new user Privilege columns USER LIST 3 Click in the blank assigned Password field next to that new user name Enter a password for that new user 4 Click in each Privilege box to the right toggling between Yes and No to assign or deny specific access levels to that user 5 Click the Save and Close button when you are finished Remember 6 Give the User Name and Password to the person you have A username registered and refer them to Logging In and Out starting on must be at least 1 Pg 5 if they need help using the program Remember that the character in password you have chosen is only temporary the user will be length prompted to enter a new password the first time they Log In to e The password net must be at least 6 characters in length ost or Revoked Password contain at least one number and is
33. diagnostic cultures is performed It is recommended that Biosafety Level 3 BL3 practices containment equipment and facilities are used for work involving production volumes or concentration of cultures and for activities that have a high potential for aerosol production In these facilities immunization is recommended for all persons working with the agent all persons working in the same laboratory room where the cultures are handled and all persons working with infected animals Special Procedures for Dangerous Pathogens For the most part you will prepare read and interpret these samples exactly as described throughout this manual There are however a few exceptions Table 16 1 lists the special procedures required for dangerous pathogens Biosafety in Microbiological and Biomedical Laboratories U S Department of Health and Human Services Centers for Disease Control and Prevention and National Institutes of Health Fourth Edition May 1999 OmniLog System User Guide Section 15 X Page 21 25 Jun 06 Appendix 5 Dangerous Pathogen Database TABLE 13 1 PROCEDURE EXCEPTIONS FOR DANGEROUS PATHOGENS Organism Special Procedures Follow special precautions and the procedure outline on page Bacillus anthracis Bacillus species Grow on BUG Maltose agar media Do not add Thioglycolate to GN GP IF Brucella melitensis Use this procedure for all species of Brucella that have been reclassified as Brucella
34. difficult to set up Am a beginner at preparing samples and inoculating MicroPlates If the answer to these questions is yes break batch up into several batches approximately 10 MicroPlates per batch 2 Assess Stack Status Before opening the door check the Load Plates window which shows the status of each stack slot AorB gt Left A or right B stack column Entry in each box gt Gives sample identifiers Red with padlock gt Slot occupied by MicroPlate not yet read Do not use Green with hand icon gt OK to use this slot 3 Open Door Open the incubator reader door 4 Remove Tray and Insert MicroPlate s e Slide one tray out of its slot e Place tray on bench top e Insert 1 or 2 MicroPlates into that tray gt Make sure Biolog logo faces front of tray toward you gt Make sure A1 well is in right rear corner gt Make sure MicroPlate fits into slot and all four corners are well seated gt Make sure MicroPlate lid is securely in place 5 Replace Tray in Incubator Reader Slide the tray back into its exact slot in the incubator reader gt Make sure you do not put tray into wrong slot gt If you do put tray in the wrong slot the system will read it and identify it anyway but the identification will not match that correct sample identifiers OmniLog ID software cannot detect this kind of error This depends on whether the slot is entered in a worksheet 6 Repeat for all MicroPlates e Remove next tray to be lo
35. floridana Burkholderia like Pseudomonas fluorescens Pseudomonas fluorescens biotype A Pseudomonas fluorescens biotype C Pseudomonas fluorescens biotype F Pseudomonas fluorescens biotype G Pseudomonas fragi Pseudomonas fulva Pseudomonas fuscovaginae Pseudomonas group 2 Burkholderia like Pseudomonas huttiensis Burkholderia like Pseudomonas lundensis Pseudomonas maculicola Pseudomonas marginalis Pseudomonas mendocina Pseudomonas mephitica Pseudomonas mucidolens Pseudomonas nitroreducens azelaica Pseudomonas oleovorans Pseudomonas pertucinogena Pseudomonas pseudoalcaligenes ss pseudoalcaligenes Pseudomonas putida Pseudomonas putida biotype A Pseudomonas putida biotype B Pseudomonas resinovorans Pseudomonas savastanoi pv fraxini Pseudomonas savastanoi pv glycinea Pseudomonas savastanoi pv nerii Pseudomonas spinosa Burkholderia Pseudomonas straminea Pseudomonas stutzeri Pseudomonas synxantha Pseudomonas syringae pv aceris Pseudomonas syringae pv antirrhini Pseudomonas syringae pv apii Pseudomonas syringae pv aptata Pseudomonas syringae pv atrofaciens Pseudomonas syringae pv coronafaciens Pseudomonas syringae pv cunninghamiae Pseudomonas syringae pv delphinii Pseudomonas syringae pv eriobotryae Pseudomonas syringae pv glycinea Pseudomonas syringae pv helianthi Pseudomonas syringae pv lachrymans Pseudomonas syringae pv mori Pseudomonas syringae pv myricae Pseudomonas syringae pv oryzae Pseudomonas syringae
36. only a few In this section easy steps 2 Checking Unload Status gt Removing e Check the status of all MicroPlates to see which ones are MicroPlates ready to be unloaded Marking MicroPlates as e Make sure that IDs have printed out Done i 2 Understanding e Remove MicroPlates that are ready for unloading Naming Conventions e Check status again Checking Unload Status When MicroPlates are ready to be unloaded the footer bar will let you know by reporting X Plates Done X the number of MicroPlates finished During operation the Read window will be displayed during incubation and reading MicroPlates The Read window allows you to view the batches and the MicroPlate status imniLog 3 J T mn Pe EE prm sep ee mV QM rxewswewr uWmeenz vmi trema ss sd Once you tse ewewr 2 unions vrrz Nt Resa ve a Se onen s unimewnc vis NatReea v EE open the door onen fa unimsenp vita nored M e cn nen ed 3 050630 P 4Plstes Jun 29 2006 Jun 30 2008 12 31 PM 22Hrs Normal ID Mode User vgomed Prit f h 20 Strain Sampie Name Other Last Read_ inc Hr Species Prob Sim Dist you nave omooca ow eam rego fio ost 9 eefe cp coccug res __ 25 9 T2536 215 minutes to w ez cei fon _ ear ag 1 1 Leier ler
37. pv papulans Pseudomonas syringae pv persicae Pseudomonas syringae pv phaseolicola Pseudomonas syringae pv pisi Pseudomonas syringae pv porri Pseudomonas syringae pv primulae Pseudomonas syringae pv sesami Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide 25 Jun 06 Jj Zi Ei QOonOoooooococaaoaocaoooooocoocaacaocaoooocococaoaoooocococooooooocooaoaoaacaooooooocococooooooaoqQ N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT Test O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O Thio ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ Medium BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU BU
38. pyrrocinia GN NENT O N BUG Bt Air 30 101 Burkholderia vietnamiensis GN NENT O N BUG By Air 30 102 Buttiauxella agrestis GN ENT O Y BUG B Air 35 37 103 Buttiauxella brennerae GN ENT O Y BUG B Air 35 37 104 Buttiauxella ferragutiae GN ENT O Y BUG B Air 35 37 105 Buttiauxella gaviniae GN ENT O Y BUG B Air 35 37 106 Buttiauxella izardii GN ENT O Y BUG B Air 35 37 107 Buttiauxella noackiae GN ENT O Y BUG B Air 35 37 108 Buttiauxella warmboldiae GN ENT O Y BUG B Air 35 37 109 Capnocytophaga canimorsus GN FAS O Y CHOC 6 5 CO2 35 37 110 Capnocytophaga cynodegmi GN FAS O Y CHOC 6 5 CO2 35 37 111 Capnocytophaga gingivalis GN FAS O Y CHOC 6 5 CO2 35 37 112 Capnocytophaga granulosa GN FAS O Y CHOC 6 5 CO2 35 37 113 Capnocytophaga haemolytica GN FAS O Y CHOC 6 5 CO2 35 37 114 Capnocytophaga ochracea sputigena GN FAS O Y CHOC 6 5 CO2 35 37 115 Cardiobacterium hominis GN NENT O N BUG B Air 35 37 116 CDC group DF 3 Capnocytophaga GN FAS O Y CHOC 6 5 CO2 35 37 117 CDC group EF 4 Neisseria GN FAS O Y CHOC 6 5 CO2 35 37 118 CDC group EO 2 GN NENT O N BUG B Air 30 119 CDC group II E subgroup A GN NENT O N BUG B Air 30 120 CDC group II E subgroup B GN NENT O N BUG B Air 30 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 5 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Ty
39. suis serogroup 1 2 GP COCCUS C Y BUG B 6 5 CO2 35 37 S Y S Y Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 17 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 327 Streptococcus suis serogroup 7 GP COCCUS C Y BUG B 6 5 CO2 35 37 328 Streptococcus thoraltensis GP COCCUS C Y BUG B 6 5 CO2 35 37 329 Streptococcus uberis GP COCCUS C Y BUG B 6 5 CO2 35 37 330 Streptococcus vestibularis GP COCCUS C Y BUG B 6 5 CO2 35 37 331 Streptococcus waius GP COCCUS C Y BUG B 6 5 CO2 35 37 332 Tetragenococcus halophilus GP COCCUS C Y BUG B Air 30 333 Tsukamurella inchonensis GP ROD C Y BUG B Air 35 37 334 Tsukamurella paurometabola GP ROD C Y BUG B Air 35 37 335 Turicella otitidis GP ROD C Y BUG B Air 35 37 336 Vagococcus fluvialis GP COCCUS C Y BUG B 6 5 CO2 35 37 337 Vagococcus lutrae GP COCCUS C Y BUG B 6 5 CO2 35 37 338 Vagococcus salmoninarum GP COCCUS C Y BUG B Air 26 339 Virgibacillus pantothenticus GP RODSB C W N BUG M Air 30 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 18 25 Jun 06 Appendix 5 Program Printouts Appendix 4 Program ID Printout Reader printout sample 1 gt Program Omni Log ID 1 1 FG rev C Wn 95 223 Reader SN
40. the incubator reader Read Read in Progress and is busy Wait until Reader Idle appears in the Reader Status cell before you use any software features or try to send any additional commands to the incubator reader Error Messages Error messages are urgent They indicate that something has gone wrong and the incubator reader is not functioning as it should They include Cell Message Color What To Do Door Status Door Open Error Red Yellow The incubator reader is trying to move but cannot because the door is open As long as the door is open the warning bell will ring every second and the Interrupt light will illuminate Close the door and the OmniLog will continue normally Error Status Hardware Error Red Yellow See Section 13 Temperature Error Red Yellow See Section 13 Video Error Red Yellow See Section 13 Plate Error Red Yellow See Section 13 User Cancel Red Yellow See Section 13 Re trying Contact Red Yellow See Section 13 OmniLog System User Guide 25 Jun 06 Section 1 X Page 14 Introducing the OmniLog ID System If you are unable to clear up any of these errors call Biolog Technical Services The Math Behind the Software OmniLog ID software uses extensive computer algorithms to take the information from the observed pattern and compare it to the database In simple terms OmniLog ID software rapidly compares the positive negative borderline purple pattern in the Mi
41. the registration form Then click the Load Registration Key button to load the registration key file and process the registration Section2 X Page 5 Installation and Registration Wil Registration Form Load Registration Key 4 The Temporary Registration box on the Welcome screen should now read Registered and turn from red to gray 5 The Registration Button is no longer present Installing Biolog MicroLog Databases Installing a Biolog MicroLog database Install databases in any order e Gram Negative GN e Gram Positive GP e Dangerous Pathogens DP 1 Check to make sure you have the Biolog MicroLog database CD ROM 2 Putthe database CD ROM into the CD ROM drive 3 Click Start 4 Select Run Click on Browse Click on the CD ROM drive 5 The field should read D SetUp database exe If drive D is not your CD ROM drive then type in the correct drive letter OmniLog System User Guide Section2 X Page 6 25 Jun 06 Installation and Registration 6 Click OK 7 Follow the instructions on the pop up dialogs Make note of the drive and directory path into which the database is installed 8 To install the database into the OmniLog directory Biolog OLID_XX_XX click Finish If you chose a different directory for the OL software then type in the name of that same directory before clicking Finish OmniLog System User Guide Section2 Page 7 25 Jun 06 Launching the OmniLog ID Prog
42. you sure you want to do that 2 These pop up queries will time out after 2 minutes If you have walked away with the door open a message will appear saying Door Open An alarm will sound TIMING READINGS AND THE SNOOZE BAR The door is open and you are unloading loading MicroPlates The Next Read 5 Min message appears in the footer bar You click the Snooze bar Next Read 5 Min flashes again You click the Snooze bar again Next Read 5 Min flashes again You click the Snooze bar again Because the incubator reader reads on the hour and half hour it will skip one read The door is open and you are still unloading loading MicroPlates The Next Read 5 Min message appears in the footer bar You click the Snooze bar A message will appear asking Are you sure you want to do that You click Yes You are not quite done so you click the Snooze bar again You need something from another room so you leave The door is open A Door Open message appears An alarm sounds Using an Offline Incubator At times you may want to use a second incubator then place the Caution incubated MicroPlates into the incubator reader for immediate reading The majority of This is especially helpful in the following circumstances microbes grow at either 30 C or 359 e If your suspected microbe requires a special atmosphere C Do NOT set the such as 6 CO2 iL i ee reddis e If your suspected microb
43. 120 Operator read Restricted Access Mode 323 Worksheet IDS 120 020313 A Read Mode Nor mal ID Mode 43 Setup Ti me Mar 13 2002 2 45 PM 53 Read Ti me Mar 14 2002 12 32 PM Read Hour 22 o gt Position 2 B Plate Type GN2 Strain Type GN NENT OXI 73 Sample Number 984 Strain Name aci hau gen 2 Strain Number Other 823 Database Biolog o gt DB File C OMNI LOG 1 D 11 GN601 KID i v i Reactions 38 53 Dara Strate OK Original Source Reader Reader Type Omni Log 102 Current Source Ori ginal Edit Status OK Record Frozen Yes Data Modificr N A Modify Date N A Parent File DONA Key lt X gt Positive X Borderline X Negative X Less Than Al 119 lt X Positive ID Negative X Negative ID Positive 2 4 5 6 7 E 9 10 11 12 Peaanesaanwmeecntww mewn ewww ewe ewe meme enw www enw em ewww wwe ewe wee ewe a Al 0 62 70 lt 169 gt lt 222 gt 45 2 13 340 43 B 56 6 2 88 39 104 4 4 3 I 3 98 C 15 3 3 4 11 5 3 43 2 lt 306 gt lt 160 gt 123 D s16672 3 17 3407 55 2 4 3 5 2 234 322 27 E 13 21 x264 3187 1367x300 1657 1967 2010753417 24427 2512 F lt 226 gt 56 124 22 lt 240 gt lt 286 gt lt 139 lt 323 gt lt 314 gt lt 341 gt 2 16 G lt 272 gt lt 320 gt lt 146 gt 2 lt 226 gt lt 295 gt lt 287 gt 2 92 lt 213 gt 51 lt 284 gt H lt 308 gt 13 4 16 341 24 100 3 3 2 it 133 gt Specics ID Acinctobactcr baumannii genospecies 2 lt SPECIES PROB SIM DIST TYPE
44. 2 35 37 168 Ignavigranum rouffiae GP COCCUS C Y BUG B 6 5 C02 35 37 169 Jonesia denitrificans GP ROD C Y BUG B Air 35 37 170 Kocuria kristinae GP COCCUS C Y BUG B Air 30 171 Kocuria rosea GP COCCUS C Y BUG B Air 30 172 Kocuria varians GP COCCUS C Y BUG B Air 30 173 Kurthia gibsonii GP ROD C Y BUG B Air 30 174 Kurthia sibirica GP ROD C Y BUG B Air 30 175 Kurthia zopfii GP ROD C Y BUG B Air 35 37 176 Kytococcus sedentarius GP COCCUS C Y BUG B Air 30 177 Lactococcus garvieae GP COCCUS C Y BUG B 6 5 C02 35 37 178 Lactococcus lactis ss cremoris GP COCCUS C Y BUG B 6 5 C02 35 37 179 Lactococcus lactis ss diacetylactis GP COCCUS C Y BUG B 6 5 C02 35 37 180 Lactococcus lactis ss hordniae GP COCCUS C Y BUG B 6 5 C02 35 37 181 Lactococcus lactis ss lactis GP COCCUS C Y BUG B 6 5 C02 35 37 182 Lactococcus plantarum GP COCCUS C Y BUG B 6 5 C02 35 37 183 Lactococcus raffinolactis GP COCCUS C Y BUG B Air 30 184 Leifsonia aquatica GP ROD C Y BUG B Air 35 37 185 Leuconostoc carnosum GP COCCUS C Y BUG B Air 30 186 Leuconostoc citreum GP COCCUS C Y BUG B 6 5 C02 35 37 187 Leuconostoc fallax GP COCCUS C Y BUG B 6 5 C02 35 37 188 Leuconostoc gelidum GP COCCUS C Y BUG B Air 30 189 Leuconostoc lactis GP COCCUS C Y BUG B Air 30 190 Leuconostoc mesenteroides GP COCCUS C Y BUG B Air 30 191 Leuconostoc mesenteroides ss dextranicum GP COCCUS C Y BUG B 6 5 C02 35 37 192 Leuconostoc mesenteroides ss mesenteroides GP COCCUS C Y BUG B 6 5 C02 35 37 193 L
45. 4 lt 135 gt 4 4 4 eth Biolog pm 2 o ja a a eto a a a 3 4 eri cvrogemrieseoegout L 1 5 3 am 4 a 3 439 4 04 3 A tivi Reactions 2070 76 k F 3 4 la 3 3 lan 4 4 41432 3 3 4 SEM 7 a 3 2 o je 3 3 a 3 2 jan 11 1745 1 164 1 A 2 2 2 2 3 486 Corynebacterium ulcerans 100 0910 134 GP RODCAT Corynebacterium pseudotuberculosis 0 0000 400 QOP RODCAT Corynebacterium diphtheriae 0 0000 923 GP RODCAT a Corynebacterium kutscheri 0 0000 952 GP RODCAT zl Mark As Done Restore PLATE DATA WINDOW 2 Click Mark as Done That entry will now be marked as Done on the Read window listing To restore the entry click Restore 4 Click Done The program will return to the Read window OmniLog System User Guide Section9 X Page 4 25 Jun 06 Unloading MicroPlates Understanding Naming Conventions Before using the advanced data management functions available in the OmniLog software it is important to understand how worksheets and data files are named File names and pathways are created automatically They are keyed to the setup date of the worksheet and the worksheet code letter All worksheet and data files generated by the software will fall into this automatically defined and created path Table 10 1 shows these conventions TABLE 10 1 FILE NAME AND PATHWAY NAMING FORMATS File Type Automatic Coding Example Path Path Program project path data ID
46. 460 Sphingomonas sanguinis GN NENT O N BUG B Air 30 461 Sphingomonas terrae GN NENT O N BUG B Air 30 462 Sphingomonas yanoikuyae GN NENT O N BUG B Air 30 463 Stenotrophomonas maltophilia GN NENT O N BUG B Air 30 464 Suttonella indologenes GN FAS O Y CHOC 6 5 CO2 35 37 465 Tatumella ptyseos GN ENT O Y BUG B Air 35 37 466 Taylorella equigenitalis GN FAS O Y CHOC 6 5 CO2 35 37 467 Trabulsiella guamensis GN ENT O Y BUG B Air 35 37 468 Variovorax paradoxus GN NENT O N BUG B Air 30 469 Vibrio aestuarianus GN NENT O N BUG B Air 30 470 Vibrio alginolyticus GN NENT O N BUG By Air 30 471 Vibrio campbelli GN NENT O N BUG B Air 30 472 Vibrio carchariae GN NENT O N BUG B Air 30 473 Vibrio cholerae OI ATCC 25870 GN NENT O N BUG B Air 30 474 Vibrio cholerae O1 0139 GN NENT O N BUG B Air 30 475 Vibrio cholerae non O1 GN NENT O N BUG B Air 30 476 Vibrio cincinnatiensis GN NENT O N BUG B Air 30 477 Vibrio diazotrophicus GN NENT O N BUG B Air 30 478 Vibrio fluvialis GN NENT O N BUG B Air 30 479 Vibrio furnissii GN NENT O N BUG B Air 30 480 Vibrio harveyi GN NENT O N BUG B Air 30 481 Vibrio mediterranei GN NENT O N BUG B Air 30 482 Vibrio metschnikovii GN NENT O N BUG B Air 30 483 Vibrio mimicus GN NENT O N BUG B Air 30 484 Vibrio natriegens GN NENT O N BUG B Air 30 485 Vibrio ordalii GN NENT O N BUG B Air 30 486 Vibrio parahaemolyticus GN NENT O N BUG B Air 30 487 Vibrio proteolyticus GN NENT O N BUG B Air 30 488 Vibrio splend
47. 5 37 218 Kingella oralis GN FAS O Y CHOC 6 5 CO2 35 37 219 Klebsiella oxytoca GN ENT O Y BUG B Air 35 37 220 Klebsiella pneumoniae ss ozaenae GN ENT O Y BUG B Air 35 37 221 Klebsiella pneumoniae ss pneumoniae GN ENT O Y BUG B Air 35 37 222 Klebsiella pneumoniae ss rhinoscleromatis GN ENT O Y BUG B Air 35 37 223 Kluyvera ascorbata GN ENT O Y BUG B Air 35 37 224 Kluyvera cochleae GN ENT O Y BUG B Air 35 37 225 Kluyvera cryocrescens GN ENT O Y BUG B Air 35 37 226 Kluyvera georgiana GN ENT O Y BUG B Air 35 37 227 Lampropedia hyalina GN NENT O N BUG B Air 30 228 Leclercia adecarboxylata GN ENT O Y BUG B Air 35 37 229 Leminorella grimontii GN ENT O Y BUG B Air 35 37 230 Leminorella richardii GN ENT O Y BUG B Air 35 37 231 Listonella anguillarum GN NENT O N BUG B Air 30 232 Listonella pelagia GN NENT O N BUG B Air 30 233 Mannheimia granulomatis GN NENT O N BUG B Air 35 37 234 Mannheimia haemolytica GN NENT O N BUG B Air 35 37 235 Moellerella wisconsensis GN ENT O Y BUG B Air 35 37 236 Moraxella bovis GN FAS O Y CHOC 6 5 CO2 35 37 237 Moraxella canis GN FAS O Y CHOC 6 5 CO2 35 37 238 Moraxella caprae GN FAS O Y CHOC 6 5 CO2 35 37 239 Moraxella catarrhalis GN FAS O Y CHOC 6 5 CO2 35 37 240 Moraxella caviae GN FAS O Y CHOC 6 5 CO2 35 37 241 Moraxella cuniculi GN FAS O Y CHOC 6 5 CO2 35 37 242 Moraxella equi GN FAS O Y CHOC 6 5 CO2 35 37 243 Moraxella lacunata GN FAS O Y CHOC 6 5 CO2 35 37 244 Moraxella nonliquefaciens GN FAS O Y
48. 5 CO2 35 37 193 Haemophilus avium Pasteurella GN FAS O Y CHOC 6 5 CO2 35 37 194 Haemophilus ducreyi GN FAS O Y CHOC 6 5 CO2 35 37 195 Haemophilus haemoglobinophilus GN FAS O Y CHOC 6 5 CO2 35 37 196 Haemophilus haemolyticus GN FAS O Y CHOC 6 5 CO2 35 37 197 Haemophilus influenzae GN FAS O Y CHOC 6 5 CO2 35 37 198 Haemophilus paracuniculus GN FAS O Y CHOC 6 5 CO2 35 37 199 Haemophilus paragallinarum GN FAS O Y CHOC 6 5 CO2 35 37 200 Haemophilus parahaemolyticus GN FAS O Y CHOC 6 5 CO2 35 37 201 Haemophilus parainfluenzae GN FAS O Y CHOC 6 5 CO2 35 37 202 Haemophilus paraphrohaemolyticus GN FAS O Y CHOC 6 5 CO2 35 37 203 Haemophilus paraphrophilus GN FAS O Y CHOC 6 5 CO2 35 37 204 Haemophilus parasuis GN FAS O Y CHOC 6 5 CO2 35 37 205 Haemophilus segnis GN FAS O Y CHOC 6 5 CO2 35 37 206 Haemophilus somnus GN FAS O Y CHOC 6 5 CO2 35 37 207 Hafnia alvei GN ENT O Y BUG B Air 35 37 208 Herbaspirillum rubrisubalbicans GN NENT O N BUG B Air 30 209 Herbaspirillum seropedicae GN NENT O N BUG B Air 30 210 Hydrogenophaga flava GN NENT O N BUG B Air 30 211 Hydrogenophaga palleronii GN NENT O N BUG B Air 30 212 Hydrogenophaga pseudoflava GN NENT O N BUG B Air 30 213 Hydrogenophaga taeniospiralis GN NENT O N BUG B Air 30 214 Iodobacter fluviatilis GN NENT O N BUG B Air 30 215 Janthinobacterium lividum GN NENT O N BUG B Air 26 216 Kingella denitirificans GN FAS O Y CHOC 6 5 CO2 35 37 217 Kingella kingae GN FAS O Y CHOC 6 5 CO2 3
49. BIOLOG OmniLog ID System User Guide 2006 Biolog Inc All rights reserved OmniLog MicroPlate Streakerz and LongSwabs are trademarks of Biolog Inc Microsoft Windows Windows NT Windows XP and Microsoft Excel are registered trademarks of Microsoft Corporation Technical Service For technical or sales assistance contact your local distribution partner or us at Address 21124 Cabot Blvd Hayward CA 94545 U S A Tel 510 785 2564 M F 7 30 a m to 5 00 p m PST Fax 510 782 4639 email info biolog com or tech biolog com Website www biolog com Ordering Information csorders biolog com OmniLog ID System User Guide Part 90311 June 2006 OmniLog ID Data Collection Software Release 1 3 LICENSE AGREEMENT Notice This is a legal agreement between you an individual or entity Licensee and Biolog Inc Licensor By purchasing or using this software whether it is on a diskette or preinstalled on a computer you agree to be bound by this agreement If you do not accept this agreement please immediately return the unopened envelope containing the complete contents as well as any computer on which such contents were preinstalled to Licensor or other place of purchase License Licensor grants Licensee the right to use the enclosed copy of Licensor s OmniLog ID software the Software at the single microbiology laboratory at one physical location for which this license is gran
50. C Y BUG B Air 30 212 Microbacterium saperdae GP ROD C Y BUG B Air 30 213 Microbacterium terregens GP ROD C Y BUG B Air 35 37 214 Microbacterium testaceum GP ROD C Y BUG B Air 35 37 215 Microbacterium spp CDC A 4 GP ROD C Y BUG B Air 35 37 216 Microbacterium spp CDC A 5 GP ROD C Y BUG B Air 35 37 217 Micrococcus diversus GP COCCUS C Y BUG B Air 30 218 Micrococcus luteus GP COCCUS C Y BUG B Air 30 219 Micrococcus lylae GP COCCUS C Y BUG B Air 30 220 Paenibacillus azotofixans GP RODSB C N BUG M Air 30 221 Paenibacillus larvae ss larvae GP RODSB C W N BUG M Air 30 222 Paenibacillus macerans GP RODSB C W N BUG M Air 30 223 Paenibacillus pabuli GP RODSB C W N BUG M Air 30 224 Paenibacillus polymyxa GP RODSB C W N BUG M Air 30 225 Paenibacillus popilliae GP RODSB C N BUG M Air 30 226 Paenibacillus validus GP RODSB C W N BUG M Air 30 227 Pediococcus acidilactici parvulus GP COCCUS C Y BUG B 6 5 CO2 35 37 228 Pediococcus dextrinicus GP COCCUS C Y BUG B 6 5 CO2 35 37 229 Pediococcus pentosaceus GP COCCUS C Y BUG B 6 5 CO2 35 37 230 Pediococcus urinaeequi GP COCCUS C Y BUG B 6 5 CO2 35 37 231 Pediococcus urinaeequi like GP COCCUS C Y BUG B 6 5 CO2 35 37 232 Rathayibacter rathayi GP ROD C N BUG Air 30 233 Rathayibacter tritici GP ROD C N BUG Air 30 234 Rhodococcus australis GP ROD C Y BUG B Air 35 37 235 Rhodococcus coprophilus GP ROD C Y BUG B Air 35 37 236 Rhodococcus equi GP ROD C Y BUG B Air
51. CCUS C Y BUG B 6 5 CO2 35 37 302 Streptococcus infantis GP COCCUS C Y BUG B 6 5 CO2 35 37 303 Streptococcus infantarius ss coli GP COCCUS C Y BUG B 6 5 CO2 35 37 304 Streptococcus infantarius ss infantarius GP COCCUS C Y BUG B 6 5 CO2 35 37 305 Streptococcus iniae GP COCCUS C Y BUG B 6 5 CO2 35 37 306 Streptococcus intermedius GP COCCUS C Y BUG B 6 5 CO2 35 37 307 Streptococcus intestinalis GP COCCUS C Y BUG B 6 5 CO2 35 37 308 Streptococcus macacae GP COCCUS C Y BUG B 6 5 CO2 35 37 309 Streptococcus macedonicus GP COCCUS C Y BUG B 6 5 CO2 35 37 310 Streptococcus mitis GP COCCUS C Y BUG B 6 5 CO2 35 37 311 Streptococcus mutans ratti GP COCCUS C Y BUG B 6 5 CO2 35 37 312 Streptococcus oralis GP COCCUS C Y BUG B 6 5 CO2 35 37 313 Streptococcus parasanguinis GP COCCUS C Y BUG B 6 5 CO2 35 37 314 Streptococcus peroris GP COCCUS C Y BUG B 6 5 CO2 35 37 315 Streptococcus phocae GP COCCUS C Y BUG B 6 596CO2 35 37 316 Streptococcus pluranimalium GP COCCUS C Y BUG B 6 5 CO2 35 37 317 Streptococcus pneumoniae GP COCCUS C Y BUG B 6 5 CO2 35 37 318 Streptococcus porcinus GP COCCUS C Y BUG B 6 5 CO2 35 37 319 Streptococcus pyogenes GP A GP COCCUS C Y BUG B 6 5 CO2 35 37 320 Streptococcus salivarius GP COCCUS C Y BUG B 6 5 CO2 35 37 321 Streptococcus sanguinis GP COCCUS C Y BUG B 6 5 CO2 35 37 322 Streptococcus sobrinus GP COCCUS C Y BUG B 6 5 CO2 35 37 323 Streptococcus suis GP RST GP COCCUS C Y BUG B 6 5 CO2 35 37 324 Streptococcus
52. CHOC 6 5 CO2 35 37 245 Moraxella osloensis GN FAS O Y CHOC 6 5 CO2 35 37 246 Moraxella ovis GN FAS O Y CHOC 6 5 CO2 35 37 247 Morganella morganii ss morganii GN ENT O Y BUG B Air 35 37 248 Myroides odoratimimus GN NENT O N BUG B Air 30 249 Myroides odoratus GN NENT O N BUG B Air 30 250 Neisseria animalis GN FAS O Y CHOC 6 5 CO2 35 37 251 Neisseria canis GN FAS O Y CHOC 6 5 CO2 35 37 252 Neisseria cinerea GN FAS O Y CHOC 6 5 CO2 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 7 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 Species Name Neisseria denitrificans Neisseria elongata ss elongata Neisseria flava Neisseria flavescens Neisseria gonorrhoeae Neisseria lactamica Neisseria meningitidis Neisseria mucosa Neisseria perflava Neisseria sicca Neisseria subflava Neisseria weaveri Obesumbacterium proteus Obesumbacterium proteus biogroup 2 Oceanomonas doudoroffii Ochrobactrum anthropi Oligella ureolytica Oligella urethralis Ornithobacterium rhinotracheale
53. CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 6 5 CO2 35 37 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Air 30 Section 15 X Page 4 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 55 Aeromonas schubertii DNA group 12 GN NENT O N BUG B Air 30 56 Aeromonas sobria DNA group 7 GN NENT O N BUG B Air 30 57 Aeromonas trota DNA group 13 GN NENT O N BUG B Air 30 58 Aeromonas veronii DNA group 10 GN NENT O N BUG B Air 30 59 Aeromonas veronii sobria DNA group 8 GN NENT O N BUG B Air 30 60 Alcaligenes faecalis ss faecalis GN NENT O N BUG B Air 30 61 Alysiella filiformis GN FAS O Y CHOC 6 5 CO2 35 37 62 Aminobacter aminovorans GN NENT O N BUG B Air 30 63 Ancylobacter aquaticus GN NENT O N BUG B Air 30 64 Aquaspirillum autotrophicum GN NENT O N BUG B Air 30 65 Aquaspirillum dispar GN NENT O N BUG B Air 30 66 Aquaspirillum metamorphum GN NENT O N BUG B Air 30 67 Aquaspirillum peregrinum ss integrum GN NENT O N BUG B Air 30 68 Aquaspirillum peregrinum ss peregrinum GN NENT O N BUG B Air 30 69 Aquaspirillum putridiconchylium GN NENT O N BUG B Air 30 70 Bergeyella zoohelcum GN NENT O N BUG B Air 30 71 Bordetella avium GN NENT O N BUG B Air 35 37 72 Bordetella bronchiseptica GN NENT O N BUG B Air 35 37 73 Bordetella hinzii GN NENT O N BUG B Air 30 74 Bordetell
54. Closing the Com serial port will shut down all hardware contact with the incubator reader OmniLog System User Guide Section3 X Page 4 25 Jun 06 Program Administration 4 Program Administration The OmniLog software can be run in either Restricted Access or Ims secon Unrestricted Access mode gt What is Restricted Access e Restricted Access is the recommended mode 3 First ioris e Data file integrity of modified files cannot be guaranteed with and Setting Up an Unrestricted Access mode Administrator gt Administrator Functions What is Restricted Access Mode gt Options Tab Restricted Access Mode requires that only users with Administrator Functions privileges have the ability to oversee and control access to the gt Creating a User program List gt Interpreting the The Administrator will Log In Log e Assign User names and passwords for those who will use the Administration system Sugars e Assign access privileges to each user e Oversee the security of the system Restricted Access Mode requires all users to log in with a User ID and password when entering the program or changing users The program maintains files of the User List Log In Log and Log In Log Archive to keep track of registered users access privileges and log in out activity in the system All of these files are encrypted The Log In Log Archive files can be placed by the Administrator in the computer network location of the
55. H RETIA concn dee ad is ede e RP ee adds 3 Preparmg Inoculq io ui ner pits Staten lied ee eit cus ere ee cles tesque 4 Inaculatinis NIeroPIates cu eee de idt ae eem eese UA ton se san con e tasa e itus 5 Incubatme MICRO PI ALES terinin aee n Bero ee tai 5 OmniLog Inc bator Reader isse eninin ias 6 System aultres 1 Read V rification ouod heretical eaten atti S dah ec etu 1 Ch ckitig the Error DOES nrinn eni bey bere a a ee desyade Unc raas tenes 3 NSIT Tes Read o id as ig RR ate Osta CE Gide i CERE UR QM 5 Usine Wel i ol leena a a a eter a a a NINET 6 Field Service Vests ch soot ooi ct ine ie ga UEM Pe A E oe 7 Relocating the Omni Log sscsatesaneisaavoczsiiunceuestenvaiausageassanncceatteduaedoasaectasseceaenes 8 e UE T eh e D 1 APpPpEendiC sS e UM 1 Appendix 1 Release 1 1 Setup Flowchart eie teens 4 Appendix 2 OmniLog Sample Worksheet essen 3 Appendix 3 Database Species Lists and Their Characteristics 4 Appendix 4 Program ID Printout eeeeeeeeeseeeseee eene entente enne enne 19 Appendix 5 Dangerous Pathogen DP Database see 21 Safety C onsiderdtloTis uoi seule ses eii So duo cale naga ea ah sage dagen 21 Special Procedures for Dangerous Pathogens eese 21 Introducing the OmniLog ID System 1 Introducing the OmniLog ID System In this section gt How It Works The Identificati
56. O Air if required Inoculating fluid GN GP IF GN GP IF T GN GP IF T GN GP IF T GN GP IF Gf Al well is pos Gf Al well is pos add thioglycolate add salicylate Inoculum turbidity 5296 T 6196 T 20 T 2096 T 2896 T Turbidity standard GN NENT GN ENT GP COC amp GP GP COC amp GP GP ROD SB ROD amp GN FAS ROD amp GN FAS MicroPlate type ul per well GN2 GN2 GN2 GP2 GP2 150 150 150 150 150 Incubation time hours 4 6 16 22 4 6 16 22 4 6 16 22 4 6 16 22 4 6 16 22 Note Agricultural bacteria may be grown on BUG without blood OmniLog System User Guide 25 Jun 06 Section 5 X Page 13 Loading and Reading MicroPlates 6 Loading and Reading MicroPlates In this section gt Checking Load and Batch Status gt Setting Up a Worksheet gt Read Modes gt Choosing a Database to Search Loading MicroPlates into the Incubator Reader Once your MicroPlates are properly inoculated see Section 5 the next step is to enter information into OmniLog ID This information relates to organizing plate data on worksheets managing files and printing results Then you can load MicroPlates into the incubator reader OmniLog ID is an automated system that relies on proper record keeping at the start of each batch Be sure to proceed through these data entry tasks with care The incubator reader can hold up to 50 batches of MicroPlates with two MicroPlates per tray and one worksheet assigned to each batch
57. Pandoraea norimbergensis Pantoea agglomerans Pantoea citrea Pantoea dispersa Pantoea punctata Pantoea stewartii ss stewartii Pantoea terrea Pasteurella aerogenes Pasteurella anatis Pasteurella bettyae Pasteurella caballi Pasteurella canis stomatis Pasteurella dagmatis Pasteurella gallinarum Pasteurella langaaensis Pasteurella lymphangitidis Pasteurella mairii Pasteurella multocida ss multocida Pasteurella pneumotropica Pasteurella testudinis Pasteurella trehalosi Pasteurella volantium Paucimonas lemoignei Pectobacterium carotovorum ss atrosepticum Pectobacterium carotovorum ss betavasculorum Pectobacterium carotovorum ss carotovorum Pectobacterium chrysanthemi Pectobacterium cypripedii Pedobacter heparinus Photobacterium angustum Photobacterium damsela ss damselae Photobacterium fischeri Photobacterium leiognathi Photorhabdus luminescens ss luminescens Phyllobacterium myrsinacearum Phyllobacterium rubiacearum Plesiomonas shigelloides Pragia fontium Proteus mirabilis Proteus myxofaciens Proteus penneri vulgaris Providencia alcalifaciens Providencia heimbachae Providencia rettgeri Providencia rustigianii Providencia stuartii Pseudomonas aeruginosa Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide 25 Jun 06 Zi 3 E QOonOooooocococaoaocaooooocoococaoaoaaoaoooococoaaaoooocococoaoaaoaoooocooacaocacaoaooocoooococo
58. Port bar The bar to the right will turn green and read Serial Port Open this indicates that computer access has been enabled 8 Click the Initialize Reader bar The bar to the right will turn green Hr E and read Reader Initialized this indicates that the computer and OmniLog the incubator reader are communicating Incubator Reader The footer bar will say Cycle Off If any error messages appear see Section 13 OmniLog System User Guide Section3 X Page2 25 Jun 06 Launching the OmniLog ID Program 10 All the buttons in the Test area of the Reader Setup window will be enabled See Chapter 13 for instructions on using these functions 11 Click the Start Cycle Mode bar The bar to the right will turn green and read Cycle On this indicates that an OmniLog read cycle is ready 12 The footer bar will say Reader OK Idle Printer Status Printer and software status is displayed in the Printer area of the Reader Setup window See Section 13 for a full description 1 Click Test Print to verify printer operation This will print three of Reader Setup test pages functions Setting the Temperature In the Temperature area of the Reader Setup window use the New Target arrows to select the target temperature 1 Click Apply The New Target temperature will show as the Current Target temperature 2 Click Temp Log to access a graphical log of 1 14 days of actual temperature readings for the incubator reader The Tem
59. RCH 1 Use the Database to Search drop down list to select the database you want If you select a User or OmniLog User database the Database File dialog box appears 2 Select the desired database by choosing the file name 3 Click OK Note When you re conducting a OmniLog User database search a U will appear on the Species ID ranked list on the Data window to denote species in the User database Also you will see a ML user designation in the upper left corner of the organism choices Verify that all information on the Worksheet Setup screen is correct Once the Next button is clicked the worksheet will be locked OmniLog System User Guide Section6 Page 6 25 Jun 06 Loading and Reading MicroPlates 4 Click Next to continue entering the worksheet the Worksheet window will appear or click Back to return to the Load window OmniLog ID C Program Files Biolog OLID_13_01 OLID_IDS data_2006 06 IDS_243_060628_1 WaC Position Plate Type Strain Type Sampe Strainname Strane lote NI Worksheet File name Save As Page Up WORKSHEET WINDOW Table 6 4 Explains The Actions of Various Buttons on This Screen TABLE 6 4 WORKSHEET WINDOW BUTTONS Button Function Abort Ends worksheet process Page Up Allows you to view lower numbered entries Page Down Allows you to view higher number entries Add Entry Allows you to enter data for each MicroPlate Print Allows you t
60. S project data for March 2001 YYYY MM Data_ 4 digit C OLID_IDS data_2001 03 year 2 digit month Worksheet Project Code_Serial number_ worksheet for March 13 2001 A YYMMDD_worksheet code W4C 23 010313A WAC Note you ll never need letter Project code 3 digit Serial to access a worksheet file number 2 digit year 2 digit month 2 digit day X code letter Normal Mode Data Worksheet name I DAC Normal data for March 13 2001 010313AI D4C Note All plates in worksheet are saved into this file I 2 ID this is your record of how MicroPlates are identified Short Data Log Worksheet name S position Plate in position 5A on March 13 2001 Data DAC A 010313AS_05A D4C Note There will be a separate data file for each MicroPlate in the worksheet S Short Log This is a first and last read log of each read time period This mode is useful when collecting data for your own database Full Data Log Data Worksheet name L_ position Plate in position 15B on March 13 D4C 2001 A 0010313AL_15B D4C Note There will be a separate data file for each MicroPlate in the Worksheet L Log This is a full log of all readings This mode is also useful when collecting data for your own database OmniLog System User Guide Section9 X Page 5 25 Jun 06 Technical Notes 10 Technical Notes This section gives specific information regarding consumable m
61. System User Guide 25 Jun 06 Preparing Samples Fill the tips with the suspension Check to see that all tips are filling equally and the tips are not leaking Prime the tips by dispensing once back into the reservoir If you are using an electronic pipetter it will prime itself Fill all MicroPlate wells with 150uL well for both Gram negatives and Gram positives Take care not to splash from one well to another Avoid contamination Avoid touching the bottom of the wells which could transfer carbon sources If the fluid level in the tips gets low refill and continue dispensing until all wells are full The electronic pipetter will double beep signaling you to purge and refill if necessary Cover the MicroPlate with its lid Section5 X Page 11 Incubating MicroPlates Note Identification of Filamentous Fungi Anaerobes and Yeasts require the use of the OmniLog Plus system Refer to your MicroLog Manual for detailed procedures Preparing Samples As soon as you dispense the suspension incubate the MicroPlate using the appropriate temperature atmosphere and time conditions Table 5 3 and the Appendices will help you select the correct conditions Remember the OmniLog can only be set to one temperature per cycle MicroPlates requiring other incubation temperatures must be incubated offline TABLE 5 3 SELECTING CORRECT INCUBATING CONDITIONS Organism Type Temperature At
62. Tracking Program Program Create User Database Perform Identifications Manage Data Control OmniLog open view copy re ID Incubator Reader Create audit trails export data Create reports graphs Original Data is automatically saved to a Data File Import Data Files Data Files Original Data Copied Data OMNILOG DATA FLOWCHART e Program Locations The OmniLog ID program must be loaded onto the computer directly attached to the OmniLog incubator reader OmniLog System User Guide Section 4 X Page 8 25 Jun 06 Preparing Samples 5 Preparing Samples In this section gt Isolating a Pure Culture Gram Staining Characterizing Aerobic Bacteria Culturing Your Microbe 2 Preparing Inocula Special Procedures for Spore Forming Gram Positive Rods gt Inoculating MicroPlates 2 Incubating MicroPlates gt Sample Preparation Process As with any system the precision and accuracy of OmniLog ID results require proper sample preparation The most common identification problems result from improper lab technique and using non recommended media Using good sterile technique and the correct media greatly increase the likelihood of problem free microbe identification If you re thinking of using non recommended media don t The extensive OmniLog ID database was specifically developed using Biolog s carefully selected media Using non specified media causes changes in the physiology of mic
63. UBATION OmniLog System User Guide 25 Jun 06 3 Incubate at 30 C for 16 24 hours do not exceed 16 hours for fast growing strains 4 Use a wooden Biolog Streakerz stick to prepare cell suspensions Scoop a small mass of cells onto the tip of the stick Avoid the area enclosed by the dashed box The cells located outside the gray area above are the most active cells Section 5 X Page 8 This technique is called the Dry Tube Method The method is recommended for all mucoid or dry colonies OmniLog System User Guide 25 Jun 06 Preparing Samples e It is essential to only take colonies starting at the ends of the Plus sign to half way down the junction of the two lines constituting the Plus sign In other words never pick up the bacteria from the center or close to the center e Pick up colonies with a wood Streakerz not a swab Rub the colonies around the walls of an empty sterile dry glass tube once the glass becomes wet clumps are difficult or impossible to disperse until mucoid dry colonies or any other sticky particles have been broken Use circular and up and down motions to create a smooth even film along the inside surface of the tube e Add 5 ml GN GP IF to suspend the film Mix the suspension with a sterile cotton swab using an up and down motion to ensure that all the cells have been suspended in a homogenous mixture e Add the remaining fluid and adjust turbidity to match the turbid
64. UG Air 30 122 Curtobacterium luteum GP ROD C N BUG Air 30 123 Curtobacterium pusillum GP ROD C N BUG Air 30 124 Deinococcus grandis GP COCCUS C Y BUG B Air 30 125 Deinococcus proteolyticus GP COCCUS C Y BUG B Air 30 126 Deinococcus radiodurans GP COCCUS C Y BUG B Air 30 127 Deinococcus radiophilus GP COCCUS C Y BUG B Air 30 128 Deinococcus radiopugnans GP COCCUS C Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 14 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 129 Dermabacter hominis GP ROD C Y BUG B Air 35 37 130 Dermacoccus nishinomiyaensis GP COCCUS C Y BUG B Air 30 131 Dolosicoccus paucivorans GP COCCUS C Y BUG B 6 5 CO2 35 37 132 Dolosigranulum pigrum GP COCCUS C Y BUG B 6 5 CO2 35 37 133 Enterococcus avium GP COCCUS C Y BUG B Air 35 37 134 Enterococcus casseliflavus GP COCCUS C Y BUG B Air 35 37 135 Enterococcus cecorum GP COCCUS C Y BUG B Air 35 37 136 Enterococcus columbae GP COCCUS C Y BUG B Air 35 37 137 Enterococcus dispar GP COCCUS C Y BUG B Air 30 138 Enterococcus durans GP COCCUS C Y BUG B Air 35 37 139 Enterococcus faecalis GP COCCUS C Y BUG B Air 35 37 140 Enterococcus faecium GP COCCUS C Y BUG B Air 35 37 141 Enterococcus flavescens GP COCCUS C Y BUG B Air 35 37 142 Enterococcus gallinarum GP COCCUS C Y BUG B Ai
65. UTHORITY TO BIND SELLER TO ANY AFFIRMATION REPRESENTATION OR WARRANT CONCERNING PRODUCTS MADE BY SELLER IN NO EVENT SHALL SELLER BE LIABLE FOR LOSS OF PROFIT LOSS OF DATA DAMAGE TO OTHER EQUIPMENT USED IN CONJUNCTION WITH THE PRODUCTS WHETHER OR NOT USED PROPERLY OR ANY OTHER INCIDENTAL CONSEQUENTIAL OR SPECIAL DAMAGES YOU AGREE THAT SELLER S LIABILITY FOR DAMAGES IF ANY SHALL NOT EXCEED THE PAYMENTS MADE BY YOU FOR ANY DEFECTIVE PRODUCT Schedule of Current Pages Sections The current OmniLog ID System User Guide is composed of the following pages or sections dated as shown Page Section Date Cover Page 25 Jun 06 Technical Service 25 Jun 06 License Agreement 25 Jun 06 Schedule of Current Pages 25 Jun 06 Table of Contents 25 Jun 06 Section 1 25 Jun 06 Section 2 25 Jun 06 Section 3 25 Jun 06 Section 4 25 Jun 06 Section 5 25 Jun 06 Section 6 25 Jun 06 Section 7 25 Jun 06 Section 8 25 Jun 06 Section 9 25 Jun 06 Section 10 25 Jun 06 Section 11 25 Jun 06 Section 12 25 Jun 06 Section 13 25 Jun 06 Section 14 25 Jun 06 Section 15 Appendix Cover Page 25 Jun 06 Appendix 1 25 Jun 06 Appendix 2 25 Jun 06 Appendix 3 25 Jun 06 Appendix 4 25 Jun 06 Appendix 5 25 Jun 06 Table of Contents Section Title Page 1 Introducing the OmniLog ID System eere eee eere eene ne 1 GOW At W OURS Lei oon aa na a oE AAEE A d genu seat leet bd 2 The Identification Pro6essaeissictuos caido tes ea o at e aeae
66. Y BUG B Air 35 37 173 Escherichia coli 0157 H7 GN ENT O Y BUG B Air 35 37 174 Escherichia fergusonii GN ENT O Y BUG B Air 35 37 175 Escherichia hermannii GN ENT O Y BUG B Air 35 37 176 Escherichia vulneris GN ENT O Y BUG B Air 35 37 177 Ewingella americana GN ENT O Y BUG B Air 35 37 178 Flavimonas oryzihabitans GN NENT O N BUG B Air 30 179 Flavobacterium ferrugineum GN NENT O N BUG B Air 30 180 Flavobacterium flevense GN NENT O N BUG B Air 30 181 Flavobacterium hydatis GN NENT O N BUG B Air 30 182 Flavobacterium johnsoniae GN NENT O N BUG B Air 30 183 Flavobacterium mizutaii GN NENT O N BUG B Air 30 184 Flavobacterium mizutaii like CDC group II I GN NENT O N BUG B Air 30 185 Flavobacterium resinovorum GN NENT O N BUG B Air 30 186 Flavobacterium tirrenicum Chryseobacterium GN NENT O N BUG B Air 30 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 6 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Test Thio Medium Atm Temp Zi 3 Ei 187 Francisella philomiragia GN FAS O N CHOC 6 5 CO2 35 37 188 Francisella tularensis GN FAS O N CHOC 6 5 CO2 35 37 189 Gilardi unnamed rod group 1 GN NENT O N BUG B Air 30 190 Haemophilus actinomycetemcomitans GN FAS O Y CHOC 6 5 CO2 35 37 191 Haemophilus aegyptius GN FAS O Y CHOC 6 5 CO2 35 37 192 Haemophilus aphrophilus GN FAS O Y CHOC 6
67. a holmesii GN NENT O N BUG B Air 30 75 Bordetella parapertussis GN NENT O N BUG B Air 35 37 76 Bordetella pertussis GN NENT O N BUG B Air 35 37 TI Bordetella trematum GN NENT O N BUG B Air 30 78 Bordetella like species GN NENT O N BUG B Air 35 37 79 Brenneria rubrifaciens GN ENT O N BUG Bf Air 30 80 Brenneria salicis GN ENT O N BUG B Air 30 81 Brevundimonas diminuta GN NENT O N BUG B Air 30 82 Brevundimonas vesicularis GN NENT O N BUG B Air 30 83 Brucella melitensis abortus GN FAS O N CHOC 6 5 CO2 35 37 84 Brucella melitensis abortus melitensis GN FAS O N CHOC 6 5 CO2 35 37 85 Brucella melitensis melitensis GN FAS O N CHOC 6 5 CO2 35 37 86 Brucella melitensis suis canis GN FAS O N CHOC 6 5 CO2 35 37 87 Brucella melitensis suis GN FAS O N CHOC 6 5 CO2 35 37 88 Budvicia aquatica GN ENT O Y BUG B Air 35 37 89 Burkholderia andropogonis GN NENT O N BUG Bt Air 30 90 Burkholderia caryophylli GN NENT O N BUG B Air 30 91 Burkholderia cepacia GN NENT O N BUG B Air 30 92 Burkholderia gladioli GN NENT O N BUG B Air 30 93 Burkholderia glathei GN NENT O N BUG B Air 30 94 Burkholderia glumae GN NENT O N BUG B Air 30 95 Burkholderia mallei GN NENT O N BUG Bt Air 30 96 Burkholderia multivorans GN NENT O N BUG B Air 30 97 Burkholderia phenazinium GN NENT O N BUG B Air 30 98 Burkholderia plantarii GN NENT O N BUG B Air 30 99 Burkholderia pseudomallei GN NENT O N BUG Bt Air 30 100 Burkholderia
68. aded e Place it on bench top e Insert 1 or 2 MicroPlates into that tray e Load into incubator reader 7 Watch the time Do not allow MicroPlates to sit on bench top for more than 20 minutes 8 Close Door WHAT ARE OMNILOG ID S IDENTIFICATION CRITERIA An OmniLog ID is made when two consecutive readings with acceptable SIM values have the same ID call exception Immediate read An ID made during the 4 6 hour read will be saved and readings will stop for that MicroPlate Normal Mode If no ID occurs in the 4 6 hour window reads will begin again at 16 hours Readings will occur every 30 minutes until the 22 hour read is complete or an ID is made If an ID is made during the 16 22 hour read it will be saved and readings will stop for that MicroPlate OmniLog System User Guide Section6 X Page 11 25 Jun 06 Loading and Reading MicroPlates HOW OFTEN DO READINGS TAKE PLACE Reads occur at 4 6 hours and at 16 22 hours OmniLog ID reads every 30 minutes These intervals occur every 30 clock minutes at the hour and the half hour not 30 minutes from the time you loaded MicroPlates Only MicroPlates that fall within these guidelines will be read MOVING THE CAMERA WHEN LOADING MICROPLATES In the normal course of operation the camera in the incubator reader moves from slot to slot as it reads MicroPlates When not in use it usually parks itself at the top row of the stack slot 25 Occasionally it will park at slot 1
69. and in our technical bulletin MicroLog Minutes Gram Stain Identification Since Gram stain readings start the chain of steps leading to an OmniLog identification it s essential to perform them according to standard lab protocol and to interpret results correctly v View the smear with a light microscope using the oil immersion objective Gram positive bacteria appear blue or violet gram negative bacteria appear pink or red v Gram negative bacteria may appear gram positive if the smear is too thick and decolorization is incomplete Gram positive bacteria may appear gram negative if the smear is over v decolorized This can also occur if the culture is not fresh and has reached stationary phase some Bacillus species are gram positive for only a few divisions after spore germination In addition gram positive bacteria will appear gram negative if the integrity of their cell walls is damaged To prevent misidentification prepare light smears of young actively v growing cultures Use known gram positive and gram negative controls When you re determining organism morphology perform Gram stains from liquid medium Solid agar can affect the appearance of the organism OmniLog System User Guide Section 12 X Page 1 25 Jun 06 Troubleshooting Symptom Cause Solution Gram variability Smear is too thick Make a single cell layer smear Run positive and negative controls All smears appear Over warming of slides A
70. as oryzae pv oryzicola GN NENT O N BUG Air 30 513 Xenorhabdus bovienii GN ENT O N BUG B Air 30 514 Xenorhabdus nematophila GN ENT O N BUG B Air 30 515 Yersinia aldovae GN ENT O Y BUG B Air 35 37 516 Yersinia bercovieri GN ENT O Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 11 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 517 Yersinia enterocolitica ss enterocolitica GN ENT O Y BUG B Air 35 37 518 Yersinia fredericksenii GN ENT O Y BUG B Air 35 37 519 Yersinia intermedia GN ENT O Y BUG B Air 35 37 520 Yersinia kristensenii GN ENT O Y BUG B Air 35 37 521 Yersinia mollaretii GN ENT O Y BUG B Air 35 37 522 Yersinia pestis GN ENT O Y BUG B Air 35 37 523 Yersinia pseudotuberculosis GN ENT O Y BUG B Air 35 37 524 Yersinia rohdei GN ENT O Y BUG B Air 35 37 525 Yersinia ruckeri GN ENT O Y BUG B Air 35 37 526 Yokenella regensburgei GN ENT O Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 12 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Gram Positive Aerobic Bacteria Species Name Type Test Thio Medium Atm Temp 1 Actinomyces bovis GP ROD C Y BUG B 6 5 C02 35 37 2 Actinomyces cani
71. aterials you ll need to perform microbial identifications as well as instructions for how to prepare isolation media and inoculating fluid In this section Materials List Media Preparation Materials List Item Description Media BUG B Growth medium for gram negative and gram positive bacteria BUG M Growth medium for gram positive spore forming rods BUG Growth medium for agricultural bacteria CHOC Growth medium for fastidious gram negative bacteria Inoculating GN GP IF Inoculating fluid for gram negative and gram positive bacteria Ed Salicylate Inoculating fluid additive for some microbes Thioglycolate Inoculating fluid additive for some microbes available in droppers Miscellaneous Streakerz Sterile 6 pointed streaking sticks PHUDES LongSwabs Sterile 7 cotton tipped swabs Transfer pipettes Sterile 9 disposable pipettes graduated tip 5 ml Reagent reservoirs Sterile reservoirs Pipette tips Sterile racked for repeating multichannel pipetter MicroPlates GN2 MicroPlates MicroPlates for gram negative bacteria GP2 MicroPlates MicroPlates for gram positive bacteria Media Preparation Biolog can provide you with all the pre made media you will need for microbe identification However you can also prepare your own media using Biolog s formulas OmniLog System User Guide 25 Jun 06 Section 10 X Page 1 Technical Notes Making Biolog Universal Growth Agar blood BUG
72. bacter genospecies 14 Acinetobacter genospecies 15 Acinetobacter haemolyticus genospecies 4 Acinetobacter johnsonii genospecies 7 Acinetobacter junii genospecies 5 Acinetobacter lwoffii genospecies 8 9 Acinetobacter radioresistens genospecies 12 Actinobacillus capsulatus Actinobacillus equuli Actinobacillus hominis Actinobacillus indolicus Actinobacillus lignieresii Actinobacillus minor Actinobacillus muris Actinobacillus pleuropneumoniae Actinobacillus porcinus Actinobacillus rossii Actinobacillus salpingitidis Actinobacillus seminis Actinobacillus suis Actinobacillus ureae Aeromonas allosaccharophila Aeromonas caviae DNA group 4 Aeromonas encheleia Aeromonas enteropelogenes Aeromonas eucrenophila DNA group 6 Aeromonas hydrophila DNA group 1 Aeromonas hydrophila like DNA group 2 Aeromonas hydrophila like DNA group 3 Aeromonas ichthiosmia Aeromonas jandaei DNA group 9 Aeromonas media DNA group 5b Aeromonas media like DNA group 5a Aeromonas salmonicida ss achromogenes Aeromonas salmonicida ss masoucida Aeromonas salmonicida ss salmonicida Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide 25 Jun 06 3 saf Ss z AQAQAQAQQAQQAQQAQAAQAAQAAQAQAQAAQAQAQAQQAQAAAQAAAQAQQAQAQAQAQAAQAQAAQAQAAQAAQAQAQAQQAQAQAQAAAQAQAQAQAQQAQAQQ N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N NENT N
73. before the next reading e Remove a MicroPlate from a worksheet if an error has occurred in the preparation of that MicroPlate e Perform an immediate read if you have incubated MicroPlates in a secondary offline incubator e Exit the program in special circumstances Using the Snooze Bar OmniLog System User Guide 25 Jun 06 At times you may wish to gain a few extra minutes before the next reading If for example the incubator reader door is open and you are still loading and or unloading MicroPlates the footer bar may begin to blink red and say Next Read 5 Min Just below that entry the Snooze bar will appear in yellow Edit privilege is required OmniLog ID Welcome Load EIE J ER TIT punc uum uU TURN UR e em acum mas sr Name Number Omer LestRead mers _ Species Prob Sm ps rapeea sesoncar aus __Nareadvat 565 NL _ 1 8 Gr2 Ge RoD car 356a L Mva 50535 EIE 1 1 LL SERTER SERE Snooze bar Min Until Read 4 45 Reset READ WINDOW WITH SNOOZE To gain extra time 1 Click Snooze The Snooze bar will disappear You will have 2 more minutes You can click the Snooze bar two more times for increments of 5 minutes each time through one read time If you try to click Snooze after a first skipped read OmniLog ID will allow it but make it more difficult for you Clicking Section 7 X Page 1 Special Functions Snooze again will result in a pop up window asking Are
74. ccus simulans GP COCCUS C Y BUG B Air 35 37 280 Staphylococcus warneri GP COCCUS C Y BUG B Air 35 37 281 Staphylococcus xylosus GP COCCUS C Y BUG B Air 35 37 282 Streptococcus acidominimus GP COCCUS C Y BUG B 6 5 CO2 35 37 283 Streptococcus agalactiae GP B GP COCCUS C Y BUG B 6 5 CO2 35 37 284 Streptococcus alactolyticus GP COCCUS C Y BUG B 6 5 CO2 35 37 285 Streptococcus anginosus GP COCCUS C Y BUG B 6 5 CO2 35 37 286 Streptococcus bovis GP D GP COCCUS C Y BUG B 6 5 CO2 35 37 287 Streptococcus canis GP COCCUS C Y BUG B 6 5 CO2 35 37 288 Streptococcus constellatus GP COCCUS C Y BUG B 6 5 CO2 35 37 289 Streptococcus criceti GP COCCUS C Y BUG B 6 5 CO2 35 37 290 Streptococcus cristatus GP COCCUS C Y BUG B 6 5 CO2 35 37 291 Streptococcus downei GP COCCUS C Y BUG B 6 5 CO2 35 37 292 Streptococcus dysgalactiae ss dysgalactiae GP COCCUS C Y BUG B 6 5 CO2 35 37 293 Streptococcus dysgalactiae ss equisimilis GP COCCUS C Y BUG B 6 5 CO2 35 37 294 Streptococcus equi ss equi GP COCCUS C Y BUG B 6 5 CO2 35 37 295 Streptococcus equi ss zooepidemicus GP C GP COCCUS C Y BUG B 6 5 CO2 35 37 296 Streptococcus equinus GP D GP COCCUS C Y BUG B 6 5 CO2 35 37 297 Streptococcus ferus GP COCCUS C Y BUG B 6 5 CO2 35 37 298 Streptococcus gallolyticus GP COCCUS C Y BUG B 6 5 CO2 35 37 299 Streptococcus gordonii GP COCCUS C Y BUG B 6 5 CO2 35 37 300 Streptococcus hyointestinalis GP COCCUS C Y BUG B 6 5 CO2 35 37 301 Streptococcus hyovaginalis GP CO
75. cheduled to read at a maximum of 4 times during the 4 to 6 hour incubation time window with readings occurring every half clock hour They are then scheduled to read at a maximum of 12 times during the 16 to 22 hour incubation time window The scheduled readings stop when an ID is made a file is saved to disk and the ID Report is printed If no ID is found the last read 22 hour is saved and the ID Report is printed When an identification is made the MicroPlate is marked on the computer screen as finished The MicroPlate can be removed freeing up the position in the incubator reader Immediate This mode is for Identification MicroPlates that are incubated off line All the MicroPlates in the worksheet will be read once immediately after loading is finished The system will not wait for the next half clock hour This single reading will be automatically saved to the computer disk and the ID Report is printed out The MicroPlates are marked as finished and can be removed When using this mode be sure to use the correct setup time there is an option in the setup time dialog that will automatically choose the previous day s date and time Short Data Logger Full Data Logger This mode is useful for building a user database MicroPlates are read 4 times during the 4 to 6 hour incubation time window with readings occurring every half clock hour The first 1 and fourth 4 reading are saved as separate files Then the MicroPla
76. chnique with Bacillus species 1 Isolate a pure culture When the culture is pure subculture on BUG M T 0 25 maltose swabbed with thioglycolate To add thioglycolate to the agar plate OmniLog System User Guide Section 5 X Page 7 25 Jun 06 Preparing Samples Before streaking the bacterium add precisely 8 drops from a thioglycolate dropper into 3 ml of sterile water Dip a sterile swab into the solution to moisten the cotton tip Spread a thin film of liquid across the entire surface of the agar medium once Allow time approximately 5 minutes for the Thioglycolate to dry on the agar Do not use wet plates as the cultures will spread This will stimulate cells into vegetative growth phase and decrease cell clumping 2 Using Biolog s sterile Streakerz sticks touch a colony and make a plus sign on the center of the agar media going across each of the two lines one or two times with the following exceptions If the organism is a fast grower and spreads make a very thin plus sign once to avoid excess growth and sporulation If the organism is a very slow grower multiple agar plates 2 3 may need to be inoculated The goal of this streaking technique see the diagram below is to restrain cell growth to two thin lines so that the cells along the edges have a good supply of food This keeps the cells in an active state and decreases sporulation STREAKING METHOD CELL GROWTH AFTER INC
77. cified incubating temperatures see Section 4 and Appendices If your unknown organism came from a cold or warm environment grow it first at its environmental temperature then try to grow it at 35 37 C 30 C or 26 C Add a pan of water to provide humidity in your incubator Incubate the MicroPlate at the same temperature as the growth plate Transfer a colony into a few ml of GN GP If or sterile water vortex for several seconds and streak out from the cell suspension onto a medium that aids the detection of subtle differences in colony morphology Take a single colony and streak for isolation on a separate plate Repeat as necessary until you have a pure culture Section 12 X Page 3 Preparing Inocula Troubleshooting Symptom Cause Solution Incorrect Turbidimeter out of Calibrate accurately turbidity calibration Inaccurate T measurements Trouble making a homogenous suspension Too few positive reactions in MicroPlates Use correct standards Make sure standards have not expired Tubes not properly blanked Once you blank a tube do not rotate it while making suspension Blank each suspension tube tubes are not optically precise and can vary tube to tube and with rotation Significant scratches or smudges on tube Nonuniform suspension of cells Mucoid or clumpy cells Detergent traces in tube Use suspension tubes only once then discard Visually inspect tubes before usin
78. croPlate to the species pattern in the appropriate database The patterns that most closely match your microbe s pattern are shown on the screen in ranked order Before making a decision on the result the software considers the possibility that even the first ranked choice may not be a good match It looks to see whether the first choice match is really close enough to be acceptable If not a No ID designation will result OmniLog ID uses a newly developed pattern matching method called Progressive ID PID This method accurately identifies species patterns by considering the progressive sequence in which purple wells are formed Typically microorganisms will use their favorite carbon sources most rapidly and completely resulting in dark purple wells that form quickly Less preferred carbon sources are consumed slowly or incompletely resulting in slower forming or lighter purple color The extra information considered by the PID matching method brings a higher level of consistency and accuracy representing another innovation in Biolog s technology OmniLog System User Guide Section 1 X Page 15 25 Jun 06 Installation and Registration 2 Installation and Registration in this section Installing the OmniLog Software a b gin s the 1 Insert the OmniLog Software CD into the CD ROM drive gt First Log In and 2 The OmniLog Software setup Windows Installer will initialize Setting Up an This will take a few moments t
79. ctory prefix The rest of the file will contain the 96 data vales The 1x96 selection will put all the data on one line The 8x12 format will put the file name on the first line and the 96 data numbers in an 8 row 12 column format as in a MicroPlate 13 Click Save Pic to save the original two MicroPlate video image to the disk as a bmp file You will be prompted for a file name Normally you will only do this if Biolog Technical Services requests it in the event of a problem reading MicroPlates 14 Click on the blank box labeled Auto Lighting right top corner of the screen The Auto Lighting box will have a check mark and function is on and ready for normal operations 15 Click Done to return to Reader Setup Note Contact Biolog Technical Support if any Read Verification tests fail Checking the Error Logs At times OmniLog ID may give you an error message These messages will appear in the lower left hand section of the footer bar All errors encountered by the OmniLog are stored in a log file which you can review The footer bar will contain a message if any error logs contain errors To clear these error messages you must enter the appropriate error log and zero the file Note Error messages appear in the footer bar according to a Hardware Video Temperature Plate hierarchy For instance if there OmniLog System User Guide Section 13 X Page 3 25 Jun 06 System Verification are current video and plate errors in the s
80. cycle mode Yellow Reader OK Busy Yellow The incubator reader is moving or reading cycle Green on reader busy Test Cycle On Yellow Reader is in Test Cyle mode Green Temperature Status Temp XX X Green This is the current incubator reader temperature which is in the target range Temp Error Red Temperature is out of range shows actual vs target Yellow temperatures Plate Status X Free Y in Use Green Number of positions free and number in use X Plates Done Red Number of MicroPlates ready to remove Yellow Current System Time Date and Time Green Date and time from operating system updated every second Month Day Year Hour Minutes AM PM User Name and Access User None Green No User is currently Logged in to the OmniLog Program User A User Name Green User is Logged in to the program User name appears in this box along with a one letter code signifying that users access level A Administrator S Setup User Unrestricted Access Red Administrator has set program to Unrestricted Access mode All Aspects of the software are available to all Users OmniLog System User Guide Section 1 X Page 12 25 Jun 06 Introducing the OmniLog ID System Time Until Auto Logout Blank Green No User is currently logged into the program mE Reset 12 Minutes before auto log out 15 1 countdown Green Red Reset button resets countdown to 15 minutes Auto Log out reset also occurs when program is in use W
81. data files are named automatically based on the setup date a Setup Code letter and a 3 character Project Code a The purpose of the Project code is to give the user the opportunity of organizing data under a specific project name or number If the user does not specify a Project code the default code of IDS will automatically be selected The purpose of the setup code letter is to differentiate between different worksheets set up on the same date 5 The worksheet setup menu will automatically enter the setup date as the current date and assign the next available setup code a You can manually change both the setup date and code by clicking on the Setup Date field and Setup Codes radio buttons The codes already used for the given date will be disabled 6 The default value in the Setup Time field is the current system time this refers to time of day the MicroPlates in the worksheet batch were set up a You can change this value by clicking on the Setup Time field While the plates are in the incubator reader the incubation time for the plates will be calculated by the current system time minus the setup time you entered for the MicroPlates All MicroPlates in a worksheet batch will have the same setup time OmniLog System User Guide 25 Jun 06 Section6 X Page 4 Loading and Reading MicroPlates Read Modes TABLE 6 3 PROGRAM READ MODES Mode Normal What It Does MicroPlates are s
82. e will use the User Name and Preliminary password given by the administrator The program will then automatically prompt them to create their own personal password This User determined password will be used for subsequent logins To Log in to the Program Click on the Log In box in the upper right hand corner of the Welcome Screen The Password Dialog will appear once that function is accessed Password Dialog x Enter Username Enter Password Cancel PASSWORD DIALOG WINDOW OmniLog System User Guide Section 1 X Page 5 25 Jun 06 OmniLog software has a predetermined time out period If the program is idle for more than 15 minutes the software will Introducing the OmniLog ID System Changing Users If the software is already open and it is necessary to change users 1 Click Log Out The button will change to Log In 2 Click Log In Now the new user will be allowed to Log in using the normal Log in procedure 3 A Password Dialog window will appear Enter the new user s name and password Press Enter Logging Out The Software is designed to automatically Log Out a user after 15 minutes of inactivity however to log out during a session 1 Click the Log Out button in the upper right hand corner Unauthorized Log In Attempts If someone enters an incorrect user name and or password the software will allow five attempts to enter the information correctly Subsequent attempts to open the pro
83. e Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 16 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics 325 Streptococcus suis serogroup 4 6 GP COCCU 326 Streptococcus suis serogroup 5 GP COCCU C C BUG B 6 5 CO2 35 37 BUG B 6 5 CO2 35 37 Species Name Type Test Thio Medium Atm Temp 261 Staphylococcus gallinarum GP COCCUS C Y BUG B Air 35 37 262 Staphylococcus haemolyticus GP COCCUS C Y BUG B Air 35 37 263 Staphylococcus hominis GP COCCUS C Y BUG B Air 35 37 264 Staphylococcus hominis ss novobiosepticus GP COCCUS C Y BUG B Air 35 37 265 Staphylococcus hyicus GP COCCUS C Y BUG B Air 35 37 266 Staphylococcus intermedius GP COCCUS C Y BUG B Air 35 37 267 Staphylococcus kloosii GP COCCUS C Y BUG B Air 35 37 268 Staphylococcus lentus GP COCCUS C Y BUG B Air 35 37 269 Staphylococcus lugdunensis GP COCCUS C Y BUG B Air 35 37 270 Staphylococcus lutrae GP COCCUS C Y BUG B Air 35 37 271 Staphylococcus muscae GP COCCUS C Y BUG B Air 35 37 272 Staphyloccocus pasteuri GP COCCUS C Y BUG B Air 35 37 273 Staphylococcus piscifermentans GP COCCUS C Y BUG B Air 35 37 274 Staphylococcus pulvereri vitulinus GP COCCUS C Y BUG B Air 35 37 275 Staphylococcus saprophyticus GP COCCUS C Y BUG B Air 35 37 276 Staphylococcus schleiferi GP COCCUS C Y BUG B Air 35 37 277 Staphylococcus sciuri GP COCCUS C Y BUG B Air 35 37 278 Staphylococcus sciuri ss rodentium GP COCCUS C Y BUG B Air 35 37 279 Staphyloco
84. e E E seid e cauce Sed accede Seema ch a ue cosa cs 5 Choosing a Database to SearcDiz es otim a edesgtuti eei eee uas Qo Re E sat eru ur Sages 6 Loading MicroPlates into the Incubator Reader eere 9 Special FUNC HOTS Mee PH E 1 Using the Snooze DIE oret ete reb a sedi E nta eta ends 1 Using arr Offline Incubator ices tese i Heo ec Ca tid tique quier ui lure NO dtd uns 2 Quite the Prostam ooo R toededul eiie cada piu A da ki e ee ant 3 Interpreting Results emet etit reir ra ceeds aree era ea eter Heic o ee uspa ese 1 Assessing the Accuracy of Your ID eise e loadcacaseceenseansoccdasna anvedeveanne 3 Pinning Down an Uncertain ID ses cies ie deeo tectis ts e ERES MES Lt idein 4 Unloading MicroPlates oie tee cete o each co Dro ase cte ce Pu ep eee Ee aene edens 1 Ch ckitig Unload SUUS s ses Codrus soi quier ferit eu te de HE Ud avrov vd eM aE 1 Removing Micro Plates 4a ooo e E E E Oe de cd R RNS 3 Marking MicroPlates AS Done is canine nnana a eias 4 Understanding Naming Conventions e sseessesesssessessessresressetsresressesstestessetseesreeseesee 5 Technical Notes d 1 Materials Tistori cia od E EE EREE RAE tute ce E s 1 Media Preparation suc onset e A E R O IRE 1 Frequently Asked Questions ccssscssscscssssssscscssssssccsssssssssccscsssssees 1 uenibiundippme e 1 Gram Stain Identification nin rds Debet teen ndi t eic due tad eua 1 Culturmg Nactoorp ams cose det atr sus te duds I
85. e Section 10 X Page2 25 Jun 06 Technical Notes General hints for culture media preparation Keep dehydrated media powder in original bottles with lids tightly closed to avoid water absorption and deterioration Use clean dry glassware that has been rinsed free of all soap residue IS Vv Add water to the vessel first then weigh agar powder and add it to the vessel Mix to obtain an even suspension Do NOT fill the vessel more than two thirds full to avoid boiling over during heating and autoclaving v1 Heat agar gently with constant stirring Making inoculating fluid GN GP IF Biolog supplies pre made inoculating fluid with the following composition 0 4096 sodium chloride NaCl 0 03 Pluronic F 68 e g Sigma P7061 0 02 Gellan Gum e g Phytagel Sigma P8169 However if you wish to prepare your own using Biolog s formula 1 Add 0 2 gm Gellan Gum to 1 liter of H2O 2 Heatto boiling stirring constantly until the Gellan Gum is completely dissolved 3 Turn off the heat but continue stirring 4 Add 4 gm NaCl and continue stirring until the NaCl is completely dissolved 5 Add 0 3 gm of Pluronic F 68 Continue stirring until the Pluronic F 68 is completely dissolved 6 Dispense the volume appropriate to obtain 19 ml post autoclaving into 20 x 150 tubes 7 Sterilize by autoclaving at 15 pounds of pressure and 121 C for 30 minutes Note Gellan Gum concentration of 0 01 0 02 is acceptab
86. e requires incubation at a at 32 C or 33 C temperature different from the current incubator reader hoping to cover temperature and you don t wish to reset the temperature both types The 1 Prepare samples according to Section 5 incubator reader MUST be set at the 2 Incubate MicroPlates in an offline incubator for the appropriate exact incubation length of time temperature 3 Load MicroPlates into the incubator reader as described in Section 6 OmniLog System User Guide Section7 X Page 2 25 Jun 06 Special Functions 4 Click the Normal Read radio button on the worksheet setup window to read the MicroPlate more than once 5 The Setup Time field will change to Read Time Enter the amount of time the MicroPlate was incubated in the secondary incubator 6 Enter sample information on the Worksheet Setup window as described in Section 6 7 Proceed with loading and reading as described in Section 6 OmniLog ID will immediately read MicroPlates marked as Immediate Read it will not wait until the next hour or half hour Quitting the Program Caution Quitting the program while there are pending reads will cause you to miss readings Except when data loss is unavoidable make sure the program and incubator reader are on while there are pending MicroPlates in the system OmniLog System User Guide 25 Jun 06 Since the computer you purchased with the system is dedicated to the OmniLog
87. ead Welcome Clar All User Entries osition Free _ Zero Pending Loads eave Plate emove Plate oad Plate amera Position E Start Unload Sequence UNLOAD WINDOW VIEW AS PLATES AND LOAD KEY Sequence 2 Click the Start Unload Sequence bar The Unload Plates window appears OmniLog System User Guide Section9 X Page 2 25 Jun 06 Unloading MicroPlates Removing MicroPlates Note The Snooze button can give you more time before the next read See Section 7 for details Caution It is up to you to remove the correct MicroPlates The incubator reader cannot detect if you are removing MicroPlates not listed as Done on the Unload Plates window OmniLog System User Guide 25 Jun 06 3 4 O ope rM 10 11 12 Open the incubator reader door Follow the list on the Unload Plates window to remove the correct MicroPlates OmniLog ID UNLOAD PLATE SCREEN PLATES DONE Remove only one tray at a time Slide the tray completely out of the incubator reader Place the tray on the workbench Remove the appropriate MicroPlate s from the tray Put the tray back into the same slot in the incubator reader If the camera has parked itself into slot behind a tray you wish to remove and you cannot get the tray out click Move Camera See Section 6 for details After you ve removed all the desired MicroPlates close the door Click Next in the lower r
88. eading MicroPlates TABLE 6 2 READ WINDOW DATA Column Explanation Position Number Shows batch slots as they are in the incubator reader Plate Type Shows Plate type entered Strain type Shows strain type entered Sample Number Shows sample number entered Strain Name Shows strain name entered Strain Number Shows strain number entered Other Shows the other text entered Last Read Shows the elapsed since data was taken Incubation Hours Shows how long the MicroPlate has been incubating Plate Status Shows those slots that are done and continuing reading Once you ve established current load status you must set up a worksheet for the new batch Remember each batch gets a separate worksheet OmniLog ID Jun 28 2006 95 eC G 90D NL Jun 28 2006 3 47 PM Worksheet setup window 1 Click the Start Load Sequence bar at the lower right side of the Load window 2 The Worksheet Setup window appears This window allows you to define a worksheet for the batch of MicroPlates you are about to load 3 Today s date automatically appears in the Setup Date field of the Worksheet Definition box You may change it to any date you wish OmniLog System User Guide 25 Jun 06 Section6 X Page 3 Remember Any selections you make on the Worksheet Setup window applies to ALL MicroPlates in that batch Loading and Reading MicroPlates 4 The worksheet and subsequent
89. er Guide Section X Page 7 25 Jun 06 Introducing the OmniLog ID System Loading and Reading MicroPlates Worksheets are the backbone of OmniLog ID you ll use them throughout the process of loading and reading MicroPlates They provide the organizational scheme for managing up to 50 MicroPlates and keeping accurate lists of identifications Each batch has its own worksheet Each worksheet can accommodate information of up to 50 MicroPlates If you have several batches of MicroPlates in the incubator reader at the same time you can view results for all worksheets by scrolling through the list on the Read window OmniLog ID Welcome Load 3 060630 M 4 Plates Jun 30 2006 8 40 AM gt Jul 01 2008 Siran Sample Nene number ow owewr i unimeena vitt ena oueur 2 unie e vitz rafon2 on ent 3 unie c viis ce ena oer a unimewno vits et Read Va pite Svan Samper Number Last Read nc Hr Species sim os ralor2 or roocajawan O eam arse ioo oso 124 s or2 oe coccus rezs __ aa em_ 210a A sore ss AUREUS 100 nes 235 nora eeu sez __ Ts p e oez anoo sa eri TL 25 ras 4 Plates Done READ WINDOW SHOWING STATUS OF BATCHES LOADED In order to make sure all worksheet information is correct OmniLog ID directs you through entering the following info
90. g Wipe outside of tubes with a tissue before placing in turbidimeter Use 7 swab to mix cells all the way to the bottom of the tube The light path that looks through the tube is only viewing the bottom of the tube For Spore Forming Gram positive Rods Follow the recommendations on pages 5 7 to 5 10 For Non Spore formers 1 Roll swab over young colonies in 3 and 4 quadrants 2 Mash colonies against side of a sterile tube above meniscus 3 Add several ml of inoculating fluid and wash the sides of the tube with a cotton swab 4 Mix well then examine for clumps If clumps are present allow them to settle 5 Transfer this concentrated inoculum into a fresh Inoculating Fluid tube until the recommended turbidity is reached Be careful not to transfer any colony clumps into the Inoculating fluid 1 For difficult organisms such as Gordonia or Tsukamurella suspend colonies as a dense suspension in a small amount of inoculating fluid as above 2 Incubate as needed at 35 C do not exceed 10 minutes Vortex if clumps still present pull off supernatant and repeat 3 Bring supernatant volume up to 18 ml and vortex until homogenous Use suspension tubes only once then discard Use of bad water OmniLog System User Guide 25 Jun 06 Use high quality purified water without preservatives Section 12 X Page 4 Inoculating MicroPlates Symptom Cause Troubleshooting Solution
91. g the System In the normal course of events the system will have been initialized during set up for continual operation However stopping the system maybe necessary for preventive maintenance of the operating system re boot or if you must move the OmniLog ID Follow the instructions below to re initialize the system 1 Double click the OL ID exe icon on your Desktop 2 The OmniLog software will initialize 3 Click the Log In button upper right corner 4 Enter Username and Password OmniLog System User Guide Section3 X Page 1 25 Jun 06 The Reader Setup window displays the set temperature and provides access to Open Close Com Port Initialize Reader Start Cycle Mode Temperature area Launching the OmniLog ID Program 5 Press Enter OmniLog ID Welcome Load Read Unload Exit Administration Print Hardware Status Save Hardware Status Com Not Open Set T 25 vs T 0 0 __ Reset WELCOME WINDOW 6 At the Welcome window click the Reader Setup bar The Reader Setup window will appear OmniLog ID Stop 3 Open Com Port Close Com Port Code MD Initialize Reader Stop Commands Bright Log qe Home Top Bes UN euncauen Test Read Menu D Park Bottom Admin Options Test Bell View Temp Log READER SETUP WINDOW 7 In the Initialize Reader area of the window click the Open Com
92. gram and log in using an incorrect user name or password will result in a warning tone and screen message just above the status bar noting unauthorized access has been attempted The message will remain until the Administrator Logs Into the program and clicks on the warning box If the Program Administrator cannot Log In contact Technical Services for assistance Log Out You Changing A Password _ ean prevent The Program will require users to change their password every three this logging off months but Users may change their passwords at any time by clicking OK when the 1 Click the Reader Setup button on the Welcome screen time out UH 2 Click Change Password on the bottom right corner of the Reader HARER Setup window OmniLog System User Guide Section 1 X Page 6 25 Jun 06 Introducing the OmniLog ID System OmniLog ID L7 CT Close Com Port Stop Commands Stop Cycle Mode P scu Font TestPrint Print Change Read Verification Change Password Password Initialize Reader Start Cycle Mode Test Read Menu T Park Bottom Test Bell READER SETUP WINDOW 3 In the Change Password Dialog window enter your old password new password and new password confirmation 4 Click OK Change Password Dialog x Re Enter Current Password Enter New Password Re Enter New Password Cancel CHANGE PASSWORD DIALOG WINDOW OmniLog System Us
93. hen box is red there are 5 minutes or less to auto log out Minutes Until Read Blank Green No MicroPlates to read OR there are more than 15 minutes until the next reading Min to Read 12 30 Green There are less than 15 but more than 10 minutes to the next read Min to Read 9 30 Yellow There are less than 10 but more than 5 minutes to the next read Min to Read 2 30 Red There are less than 5 minutes to the next read Read In Progress Red OmniLog is now reading Time of Next Read Blank Green There are no MicroPlates to read OR the next read is in more than 30 minutes Next Read X XX Green The next read is in less than 30 minutes AM PM Snooze Button The next read is in less than 5 minutes During normal operation some of these cells may flash this occurs because the footer bar cells are constantly updated as the software gets the latest status from the incubator reader Color coding will help you identify the nature of the entry as follows Caution Never dumdhe e In their normal OK state the cells will display in black software or reader letters on a bright green background off while the reader is busy This could e Warning messages show as black letters on a yellow green result in a flashing background mechanical jam that would require e Error messages show as white letters on a red yellow Biolog Technical flashing background Services to correct Typically all footer cells will be green with no warning or error me
94. iLog System User Guide 25 Jun 06 Section6 X Page 1 Start Load Sequence Caution Be sure to load MicroPlates into the incubator reader within 20 minutes after inoculating them Allowing MicroPlates to sit around can cause you to miss readings Loading and Reading MicroPlates amera Position En LOAD WINDOW AND LOAD KEY 3 Check the Load window to ascertain which slots are open for new MicroPlates The Footer bar will state how many slots are available 4 Click Read on the top menu bar The Read window will appear showing details for each MicroPlate currently in the incubator reader Check batch status by tracking the icons to the right of the Unload column ext BE no uo Unload Ext FEE mee MicroPlate status here 3 060650 M4 Plates Jun 30 2006 840 AM gt sui 01 2006 12 1 PM 22Hre Short Data Logger user vaome Print_ Piate Sirain Sampes Name Number Other uastRead net Species Pron Sm Dist afonajonenr 1 onnomnajyn T netreaayd em E S wa m 5m poe oesonca owem O aem ae oso ECAC __ _ r231em_ vez oen n2 a io Ll amp aye 4 Plates Done READ WINDOW Table 6 2 explains the columns on this screen OmniLog System User Guide 25 Jun 06 Section6 X Page 2 Setting Up a Worksheet Worksheet Identifiers Database to Search Loading and R
95. icd EE ESS 2 Easy to Use Softwate nie ib hui eee eee ade 4 User Eunetiolis 22e ren eheu ooh tee 5 GB IDEO taal i sla a air esae malen te Sume d LU MULUS 5 Changing Users HL 6 Loggins Outen e E E E TE RE E OEE O EE E M 6 Unauthorized Log In Attempts soian n a aS 6 Chang ing A Pass word c e sae eee ie alu eed eed 6 Loading and Reading MicroPlates sitos assess etches etos Isti hv 8 Interpreting Results 21st n isis seres are UR ek aera 9 Unloading MicsoPlIates ioh e eret bM d denen a f lesus 9 Using the Footer Barely i eo e ieee ose afa qute paciens 11 The Math Behind the Software 22 12 08 oerte e tesa tu teens 15 2 Installation and Registration e ssseseccssooccssssoccessssocecssoococcessoocessssoseeee 1 Installing the OmniLog SOf We noue le eb ortu mattis ae 1 First Log In and Setting up an Administrator eene 2 Registering Your SOPbWALe t nas ebbe ade A Boe sisse Uo ie t UD oes 4 Installing Biolog MicroLog Databases eene 6 3 Launching the OmniLog ID Program ecce ee ee ee ee eere enun 1 Initializing the Systemi es orit peii anid Sette le cee ates Satta ntu tM eei cd 1 Printer Statsion teed chee te ates oce E E ee ane qoa tudul da boc A Ohl ee cmt 3 Setting the Temperate ses eee tiae eee eos eal e eS 3 Shutting the System DOW sc esci dolet pebocd estet ite uia dod df raat 4 4 Program Administration eene ee
96. icroorganisms in MicroPlates In addition Biolog has carefully optimized the required inoculating fluids Don t deviate from Biolog s inocula preparation directions See pages 5 5 5 7 Step 4 Inoculate MicroPlates and place in the OmniLog Pipet the specified amount of cell suspension into each labeled MicroPlate put the lid on and place on trays in incubator reader Incubate MicroPlates using the same conditions of temperature and atmosphere used to culture the microorganisms Organisms requiring a microaerophilic atmosphere CO need to be incubated off line in this case you ll use the incubator reader for reading only Step 5 Obtain ID results from printer After an appropriate incubation time OmniLog ID automatically reads each MicroPlate The patterns formed in the wells are automatically entered into OmniLog ID software which searches the database and can provide an identification in seconds The printer automatically issues hardcopy results when an ID is complete Easy to Use Software OmniLog ID provides an easy to follow visual software interface to lead you through the identification process You ll spend most of your time using Worksheets with areas for entering sample identifiers sample number strain name strain number etc loading MicroPlates viewing current read status unloading MicroPlates and viewing microbial identifications Once you re familiar with the system you ll be able to prepare your samples
97. idus GN NENT O N BUG B Air 26 489 Vibrio tubiashii GN NENT O N BUG B Air 30 490 Vibrio vulnificus GN NENT O N BUG B Air 30 491 Vogesella indigofera GN NENT O N BUG B Air 30 492 Weeksella virosa GN NENT O N BUG B Air 30 493 Xanthomonas albilineans GN NENT O N BUG Air 30 494 Xanthomonas campestris pv begoniae A GN NENT O N BUG Air 30 495 Xanthomonas campestris pv begoniae B GN NENT O N BUG Air 30 496 Xanthomonas campestris pv campestris GN NENT O N BUG Air 30 497 Xanthomonas campestris pv carotae GN NENT O N BUG Air 30 498 Xanthomonas campestris pv corylina GN NENT O N BUG Air 30 499 Xanthomonas campestris pv dieffenbachiae GN NENT O N BUG Air 30 500 Xanthomonas campestris pv hyacinthi GN NENT O N BUG Air 30 501 Xanthomonas campestris pv juglandis GN NENT O N BUG Air 30 502 Xanthomonas campestris pv malvacearum GN NENT O N BUG Air 30 503 Xanthomonas campestris pv nigromaculans GN NENT O N BUG Air 30 504 Xanthomonas campestris pv pelargonii GN NENT O N BUG Air 30 505 Xanthomonas campestris pv phaseoli GN NENT O N BUG Air 30 506 Xanthomonas campestris pv poinsettiicola GN NENT O N BUG Air 30 507 Xanthomonas campestris pv raphani GN NENT O N BUG Air 30 508 Xanthomonas campestris pv sesami GN NENT O N BUG Air 30 509 Xanthomonas campestris pv tardicrescens GN NENT O N BUG Air 30 510 Xanthomonas campestris pv translucens GN NENT O N BUG Air 30 511 Xanthomonas campestris pv vesicatoria GN NENT O N BUG Air 30 512 Xanthomon
98. ight corner of the Unload Plates window The software returns you to the Read window This worksheet is no longer active If you wish to load new MicroPlates while the door is open complete unloading first Then load according to instructions in Section 6 Remember you have 20 minutes to complete an entire unload load cycle Section9 X Page 3 Unloading MicroPlates Marking MicroPlates As Done During normal operation the Read window will display As you track the progress of readings you may occasionally detect in your judgment a clearly erroneous identification by the OmniLog incubator reader This may occur if a sample has been mis prepared a MicroPlate incorrectly inoculated or incorrectly labeled Note To Mark MicroPlates as Done Users must have Edit privileges or Program Administrator Rather than proceed with a final reading of that MicroPlate you can clear it from its worksheet To clear a MicroPlate record during the read process in Restricted Access mode 1 Click on the appropriate row in the Read window The Plate Data window appears Plate Data Read Errors No Errors No Errors No Errors Temp Errors No Errors 243 Operator ledituser Restricted Acces IDS 243 060630 J Normal ID Mode Jun 30 2008 6 20 AM Jun 30 2006 11 31 AM fecocar PEE EPP CORN CON CON CN EEN o 3 3 594399 4004 014 4 4 2 B 3 3 4 3 69 4 4 4 4 86 2 c 1 3 59 35
99. ime e Str p 1031 Sample Number Micr oPlate m Information Strain Number ML DB File C YOMNILOG ID 110CYGN6 User DB File NA ivi Reactions 30 0 66 JOK 0 183 gt lt 182 gt 5 o o jo jo fo o o jo fofo o jo 0 0 0 2 0 0 0 0 0 1 83 80 Well by well 191 226 168 151 0 0 0 0 174 152 188 data values lt 231 gt 0 22 0 lt 182 gt lt 192 gt lt 192 gt lt 176 gt 0 6 0 lt 233 gt 194 0 0 0 234 216 195 ID Call SER RT GS 0 1 0 267 gt 0 240 186 215 206 217 0 0 213 0 0 0 0 0 212 0 0 0 0 0 o o NAME TYPE Alcaligenes faecalis ss faecalis m 0718 429 GNNENT OXI List of Closest 5 Ralstonia paucula 0000 1098 GN NENTOXI ip Matches Ralstonia eutropha m 0 000 1110 GN NENT OXI Statistical Aguaspirilum autotrophicum E 0 000 1132 GN NENT OX xi probabilities PLATE DATA WINDOW Unloading MicroPlates After the ID process is complete you ll unload MicroPlates Check the status on the Read window make sure all the IDs have printed out remove the MicroPlates and recheck the status The Unload window allows you to easily tell which MicroPlates are ready to be unloaded OmniLog System User Guide Section 1 X Page 9 25 Jun 06 Shows which MicroPlates are ready for unloading Introducing the OmniLog ID System OmniLog ID xj Welcome Load Read Unload Exit
100. imes Don t forget to add thioglycolate Caution Do not manipulate dropper any further as the plastic may when working with puncture causing injury GN Enteric 2 Invert the dropper for convenient drop by drop dispensing of GN Fastidious reagent Secs Reds 3 Dispense precisely 3 drops of concentrated thioglycolate into your inoculating fluid Do not use more than 3 drops per 18 20 ml This gives you a 5mM final concentration 4 Each dropper contains about 10 15 drops You can continue to use an open dropper for the rest of the day and then discard the remainder Adding sodium salicylate to inoculating fluid If gram positive non spore forming bacteria are false positive positive Al well even after you ve added thioglycolate to the inoculating fluid try adding sodium salicylate 1 Add thioglycolate as described above 2 Add 1 ml of sterile 100 mM sodium salicylate to 18 20 ml of GN GP IF This gives you a 5mm final concentration 3 Proceed with sample preparation OmniLog System User Guide Section5 X Page 6 25 Jun 06 Remember your microbes are alive Treat them with care Use fresh cultures Preparing Samples Preparing inocula Once you ve added thioglycolate if necessary prepare the inocula 1 Establish the appropriate turbidity range on your turbidimeter by adding and subtracting 2 T to the percent transmittance measured with the appropriate turbidity standard 2 Lift cells from the agar b
101. in descending order of date with the most recent date and log in first This log is non editable The Log In Log records the past 100 log in attempts For each log in attempt the Log In Log records the username date and time logged in whether the username is registered and the date and time the person logged out The Log also records which privileges registered users have as well as whether the program is in Unrestricted Access Mode This creates an audit trail in both Restricted and Unrestricted Access modes As log in records in excess of 100 drop from the list they are saved to a Read Only file Logins LoginLogXXXXX csv When this saved file contains 100 records subsequent records will be saved to a new file with a different date stamp XXXXX is a five digit date stamp OmniLog System User Guide Section4 X Page 5 25 Jun 06 Program Administration Drag column lines here to widen or narrow columns Jun 28 2006 15 45 never Yes Yes Jun 28 2006 13 29 Jun 28 2006 13 59 Yes Yes Jun 28 2006 13 29 Yes gomez never edituser Jun 28 2006 10 35 Jun2820061224 Yes Yes Save and Close Warning Only One Valid Administrator SAMPLE LOG IN LOG Interpreting the Log In Log Column Name Restricted Information Given If program was in Restricted Access mode when user logged in this entry will say Yes if program was operating in Unrestricted Access mode this entry will say No Entered Username
102. information in all fields marked with a in the User Entry Fields box 2 Click the Save User Key J 3 At prompt define a file name for the User Key File 4 E mail the User Key File to Tech Biolag com 5 We will e mail you back a Registration Key B When you get the Registration key go to the Registration Key tab Program Name Program Version Program Release Program Serial Number Windows Version Registration Date Company Institution Department ddress 1 iddress 2 ustomer Name ontact Phone Number ontact Fax Number Contact E mail Computer Make Model Re Enter Program Serial Number Win XP Service Pack 2 June 27 2006 Save User Key Fill out every line of the Registration Form Required Fields Click the Save User Key button A Save As window appears Type a file name for the User Key File in the File Name field The Save as Type field should show Text Files as the default file type Click Save The User Key will be saved as a text file Click Close E mail the User Key File to tech biolog com Follow the steps outlined below to load the Registration Key Biolog will e mail you a Registration Key Save the attached registration key file on your hard drive Biolog OLID_XX_XX certificates Once you have saved your Registration key open the OmniLog Software program and click on the Registration button to open the Registration Form Click on the Registration Key tab that is on
103. ion6 X Page 9 25 Jun 06 Loading and Reading MicroPlates OmniLog ID Unrestricted Access LOAD PLATE WINDOW 2 Check to make sure each MicroPlate is correctly labeled with a unique identifier Do not write on the side or top of the MicroPlate lid nor on the Biolog logo The best place to label the MicroPlate is on the front bottom edge Caution Do NOT open the incubator reader door when the footer bar shows 3 Load MicroPlates into the incubator reader according to the the message rules of thumb on page 6 11 Reader Busy 4 As you begin to load each tray check the position of the camera If the camera is on the position to be loaded click Move Camera Follow instructions below 5 When all MicroPlates and trays are in the proper slots close the door firmly 6 Click Finish in the lower right corner of the Load Plate window This brings you to the Read window Remember Do not take shortcuts when loading MicroPlates Do gt not remove more than one tray at a time Do not just pull trays out partially to insert MicroPlates Do not use trays that have been sitting at room temperature Trays must be kept at the set temperature of the incubator reader for accurate incubation OmniLog System User Guide Section6 X Page 10 25 Jun 06 Loading and Reading MicroPlates RULES OF THUMB FOR LOADING BATCHES 1 Assess Batch Is my batch going to incubate at 26 30 C Does my batch contain MicroPlates that are
104. ir choosing This allows the Administrator to place the files in a location that has secured access Why Restricted Access Mode Restricted Access Mode ensures that data integrity and security controls are implemented in accordance with the guidelines of 21 CFR Part 11 It assists in compliance with federal Current Good Manufacturing Practices CGMP by ensuring the integrity of program use and electronic files Security Features User List and Log in Log Notification of failed log in attempts User password change User privileges Session time out Password expiration OmniLog System User Guide Section4 X Page 1 25 Jun 06 Program Administration e Log in archive Electronic record integrity e Limiting access e Original record integrity e Documentation of changes by whom and when Audit trails What if don t work in a 21 CFR compliant environment No problem It is easy for the program Administrator to assign full access privileges to anyone in your organization who will be using the program This will give everyone the ability to use all of the system s features with the exception of the ability to access the Administration Options button Another option is simply to use the Administrator ID and password for all users thereby giving everyone equal access Note Original data files are automatically frozen when the data is generated Freezing files is performed manually only with copies of Original data files
105. ir dry slides completely before warming ram negative TENE Don t use a flame to fix slides Using old cultures Prepare slides from fresh log phase growth cultures Over decolorizing Repeat Gram stain using specified timing Run positive and negative controls Morphology unclear Growth on agar media Do a Gram stain from broth culture affects morphological appearance Too intense color Under decolorizing Use decolorizer made by same company that makes your stains Prepare decolorizer or acetone alcohol at several concentrations Test solutions at 5 10 and 15 seconds with known positive negative and weakly positive cultures Run positive and negative controls Additional differentiation techniques Make sure you re using proper Gram stain procedure If you still get ambiguous results use the following table as a guide Test Reactions Vancomycin sensitivity 30 ug disks Gram negative bacteria resistant Gram positive bacteria 9 most are sensitive Growth on MacConkey and CNA plates Gram negative bacteria 9 MacConkey CNA Gram positive bacteria 9 MacConkey CNA KOH test 3 Gram negative bacteria gt suspension becomes thick and stringy L alanine aminopeptidase activity use Gram negative bacteria gt commercially available test strips impregnated A ram positive bacteria gt with a colorimetric substrate for this enzyme G P For test procedures
106. is GN NENT O N BUG By Air 30 389 Pseudomonas syringae pv tomato GN NENT O N BUG Bt Air 30 390 Pseudomonas syringae pv zinaniae GN NENT O N BUG B Air 30 391 Pseudomonas taetrolens GN NENT O N BUG B Air 30 392 Pseudomonas tolaasii GN NENT O N BUG B Air 30 393 Pseudomonas viridiflava syringae GN NENT O N BUG Bt Air 30 394 Pseudomonas viridilivida GN NENT O N BUG B Air 30 395 Psychrobacter immobilis GN NENT O N BUG B Air 30 396 Psychrobacter phenylpyruvicus GN NENT O Y BUG B Air 35 37 397 Rahnella aquatilis GN ENT O Y BUG B Air 35 37 398 Ralstonia eutropha GN NENT O N BUG B Air 30 399 Ralstonia paucula GN NENT O N BUG B Air 30 400 Ralstonia pickettii GN NENT O N BUG B Air 30 401 Ralstonia solanacearum GN NENT O N BUG B Air 30 402 Raoultella planticola GN ENT O Y BUG B Air 35 37 403 Raoultella planticola ornithinolytica GN ENT O Y BUG B Air 35 37 404 Raoultella terrigena GN ENT O Y BUG B Air 35 37 405 Rhizobium like Cystic Fibrosis GN NENT O N BUG B Air 35 37 406 Rhizobium radiobacter GN NENT O N BUG B Air 30 407 Rhizobium rhizogenes GN NENT O N BUG Bt Air 30 408 Rhizobium vitis GN NENT O N BUG B Air 30 409 Riemerella anatipestifer GN NENT O N BUG B Air 35 37 410 Roseomonas cervicalis GN NENT O N BUG B Air 30 411 Roseomonas fauriae GN NENT O N BUG B Air 30 412 Roseomonas genomospecies 4 GN NENT O N BUG B Air 30 413 Roseomonas genomospecies 5 GN NENT O N BUG B Air 30 414 Roseomonas genomospecies 6 GN NENT O
107. ished click Done and your current worksheet will appear Click Print to print out the worksheet when you have completed the batch entry process OmniLog System User Guide Section6 Page 8 25 Jun 06 Loading and Reading MicroPlates Note Be sure to pr int GP COC CAT 11203 Name 14 Number 14 Other 14 your worksheet and s Seco CAT zo Nene 1B Number th Other 18 verify that all field information is correct M sos sun WORKSHEET WITH ENTRIES At this point it is a good idea to double check your worksheet for errors Make sure all required data is entered for each plate If there are corrections that need to be made simply click on the entry in the Worksheet window to be taken back to the Plate Information window for that plate At that point you may make your corrections Loading MicroPlates into the Incubator Reader The normal workflow for OmniLog ID is to prepare the samples inoculate the MicroPlates enter data into the computer then load the MicroPlates into the incubator reader Load with the worksheet in your hand or use the configuration on the Load window to guide you through correct placement of the MicroPlates See Section 7 if you ve incubated the MicroPlates in an offline incubator 1 After completing the worksheet and printing it out click Next to load the MicroPlates The Load Plate window appears At this point you can open the door without causing any error messages OmniLog System User Guide Sect
108. isteria grayi GP ROD C Y BUG B Air 35 37 194 Listeria innocua monocytogenes seeligeri welshimeri GP ROD C Y BUG B Air 35 37 Agricultural bacteria that maybe grown on Bug without load Found n the Dangerous Pathogen database OmniLog System User Guide Section 15 X Page 15 25 Jun 06 Appendix 3 Database Species Lists and Their Characteristics Species Name Type Test Thio Medium Atm Temp 195 Listeria ivanovii GP ROD C Y BUG B Air 35 37 196 Listeria ivanovii ss londoniensis GP ROD C Y BUG B Air 35 37 197 Listeria monocytogenes innocua seeligeri welshimeri GP ROD C Y BUG B Air 35 37 198 Listeria seeligeri innocua monocytogenes welshimeri GP ROD C Y BUG B Air 35 37 199 Listeria welshimeri innocua monocytogenes seeligeri GP ROD C Y BUG B Air 35 37 200 Macrococcus bovicus GP COCCUS C Y BUG B Air 35 37 201 Macrococcus carouselicus GP COCCUS C Y BUG B Air 35 37 202 Macrococcus caseolyticus GP COCCUS C Y BUG B Air 35 37 203 Macrococcus equipercicus GP COCCUS C Y BUG B Air 35 37 204 Microbacterium arborescens GP ROD C Y BUG B Air 35 37 205 Microbacterium esteraaromaticum GP ROD C Y BUG B Air 35 37 206 Microbacterium flavescens GP ROD C Y BUG B Air 35 37 207 Microbacterium imperiale GP ROD C Y BUG B Air 35 37 208 Microbacterium lacticum GP ROD C Y BUG B Air 35 37 209 Microbacterium laevaniformans GP ROD C Y BUG B Air 35 37 210 Microbacterium liquefaciens GP ROD C Y BUG B Air 35 37 211 Microbacterium maritypicum GP ROD
109. ity standard at 28 T 2 OD 0 55 e Cell suspensions must be free of mucus clumps or dry undissolved colonies e Prepare cell suspensions with a stick as swabs are too soft and will not be able to break up clumps Let the suspension stand for approximately 5 minutes to ensure that no solid particles remain If the suspension is not homogeneous pour the supernatant into another sterile tube and proceed with the next step Check the turbidity of the supernatant If it is too low incubate the test tube containing the sediment fraction unsuspended fraction for 5 minutes at 35 C Remove the tube from the incubator and vortex lightly until all matter is dissolved If necessary add extra fluid from the previously separated fraction supernatant to re suspend the culture Repeat this process until you reach the appropriate transmittance required for MicroPlate inoculation Inoculate a GP2 MicroPlate Incubate at 30 C for 4 22 hours Section5 X Page 9 NWN Preparing Samples General hints for handling Bacillus Always grow Bacillus species on BUG M T for identification Keep the incubation time as short as possible to reduce sporulation i e incubate for 16 rather than 24 hours if it s a fast grower If you have a strain that is difficult to disperse be sure you have carefully prepared the inoculum using the dry tube procedure Let the suspension stand for a 5 minutes to allow the clumps to settle to the bott
110. l to cancel the cycle process if you want to restart you must reinitialize the reader 9 Check Status to see if the test is cycling off or on 10 Click Done The software will return to the Reader Setup window Field Service Tests On the Welcome window you ll see a yellow box in the lower half labeled Field Service Only The Print Hardware Status and Save Hardware Status buttons are password protected and are only to be used by an authorized Biolog Field Service Technician LII f Welcome Load Read Unload Exit In the event of a hardware error contact Biolog Technical Services We may ask you to repeat the error and click the New Button for Hardware Status Menu has been placed on the footer bar upper left corner No normal customer use functional capabilities are on this screen This is used only on the instruction of Biolog authorized Technical or Field OmniLog System User Guide Section 13 X Page 7 25 Jun 06 System Verification Service Representative to assist in trouble shooting customer problems This menu has been improved to contain more information for troubleshooting purposes Hardware Status Menu contains 4 tabs 1 Hardware 2 Video 3 Data 4 Error Logs At the bottom of each page are 4 buttons 1 Close To close the Hardware Status Menu 2 Save as JPEG to save a JPEG image of the screen to e mail to Biolog representative 3 Save as BMP to save a BMP image of the screen t
111. le OmniLog System User Guide Section 10 X Page 3 25 Jun 06 Frequently Asked Questions 11 Frequently Asked Questions In this section gt Answers to Common Questions Q A How I should I store my MicroPlates Unpack MicroPlates as soon as you receive them and keep them refrigerated until use Biolog MicroPlates should be kept refrigerated not frozen MicroPlates are fairly stable at room temperature we suggest refrigeration because they must be kept cold for maximum shelf life At moderately warm temperatures they slowly begin to deteriorate Visually examine MicroPlates before using them You may see faint yellow brown or pink shades in wells when they are dry this is OK However if wells show significant color immediately after inoculating the MicroPlate with the cell suspension they have most likely been heat damaged Do I have to handle frozen or lyophilized cultures in a special way Yes Subculture frozen or lyophilized cultures two to three times before testing Our lab would really like to use our own media We know that our strains will grow on it Is that all right No However tempting it may be to use nonrecommended media using anything other than Biolog recommended media is a mistake The carbon source tests in our MicroPlates are configured for precise metabolic reactions The metabolic state of an organism has a profound influence on the resulting MicroPlate pattern that is the basis for ide
112. leted and returned by you within ten 10 days after the date of purchase Any product which is or becomes defective during said one year period shall be returned by you transportation custom duties and other fees prepaid in the original carton to Seller s principal facility in Hayward California or such other place which may be designated by Seller You must obtain prior approval from Seller before returning any product to Seller Transportation charges custom duties and other fees for return to you shall be paid by you and you shall bear all risk of loss or damage during transportation to and from Seller Seller shall reimburse you transportation charges custom duties and other crarges incurred by you in returning product pursuant to this paragraph only if a you have complied with all ofthese Terms and Conditions and b the returned product is defective in materials or workmanship and is covered by the limited warranty provided in this paragraph THERE ARE NO WARRANTIES WHICH EXTEND BEYOND THIS DESCRIPTION ON THE FACE HEREOF ANY COURSE OF DEALING CUSTOM OR USAGE OF TRADE OR COURSE OF PERFORMANCE NOTWITHSTANDING THE FOREGOING IS SPECIFICALLY IN LIEU OF ALL OTHER WARRANTIES EXPRESS OR IMPLIED INCLUDING THE WARRANTIES OF MERCHANTABILITY AND FITNESS OR USE FOR A PARTICULAR PURPOSE AND ANY WARRANTIES THAT THE PRODUCTS DO NOT INFRINGE THE PATIENT OR OTHER INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES NO AGENT OR REPRESENTATIVE OF SELLER HAS ANY A
113. lowing steps 1 5 on page 13 4 Clear Auto Restart Notice Welcome Read Unload Not Initialized 1 Auto Re Start Q Your computer might be at ri e This Restart Notice appears when an Auto Restart happens and will appear only on the Welcome Menu and must be cleared by clicking on it e You still will need to clear the Error Log Using Test Read AU Test Read is a method of recording information for analysis to determine if the incubator reader is reading correctly when using non Please let us assist standard MicroPlates or conditions Don t perform this test without the you in verifying the help of Biolog Technical Service OmniLog System Don t do this 1 From the Welcome window click Reader Setup Make sure the without the com port is open the reader is initialized and the cycle mode is assistance of Biolog off Click Test Read Menu Technical Service help OmniLog System User Guide Section 13 X Page 5 25 Jun 06 System Verification EH Save 8x12 Save BMP Pets fats TeTr 1s s hoje m m A m BB iB ic IC D D E E 3 T H ZEI rete nea uo nent Doun Read Ron Next Up Next Down BMP Bve Done oll Reset TEST READ WINDOW 2 PLATES 2 The Test Read window is similar to Read Verification The only difference is that instead of reading the MicroPlates versus a test mode the window displays the numeric values and positive borderline negative indicators of the Micr
114. mber of mismatches Technical Service ID Rules of Thumb SIM 1 0 gt a perfect match SIM 0 0 gt no match The closer to 1 0 the better the match e DIST of the first and second choices are nearly equal e There are many variable reactions more than 15 For additional assistance in interpreting results contact Biolog The chart below will help you clarify your identification by using SIM and DIST values USING SIM AND DIST TO ASSESS IDENTIFICATIONS Assess SIM for ID 1 Gram negative aerobes Gram positive aerobes must be gt 0 50 at 16 22 hours incubation must be gt 0 90 at 4 6 hours incubation Assess SIM for top IDs level ID If SIMs for top IDs are lt 0 50 AND all belong to the same genus AND if their total is gt 0 50 you can be confident that the microbe is in that genus MicroLog will give you a genus level ID rather than a species Assess DIST for top IDs If SIM is OK but DIST between ID 1 and ID 2 are very close If you remain unconfident of the ID try to differentiate organisms by performing one of these tests gt Good match to both species some are quite close gt Gram stain colony morphology oxidase and or catalase tests additional tests see Bergey s Manual OmniLog System User Guide 25 Jun 06 Section8 X Page 5 Unloading MicroPlates 9 Unloading MicroPlates Removing MicroPlates from the incubator reader requires
115. melitensis B abortus B canisB melitensis B suis Set up as Gram Negative Fastidious organism Grow in Chocolate agar media CO2 atmosphere Do not add Thioglycolate to GN GP IF Burkholderia mallei Burkholderia pseudomallei Set up as Gram negative Non Enteric organism Grow in BUG Blood Do not use TSA Blood Do not add Thioglycolate to GN GP IF Francisella tularensis Set up as Gram Negative Fastidious organism Grow in Chocolate agar media CO2 atmosphere Do not add Thioglycolate to GN GP IF Yersinia pestis Set up as Gram negative Non Enteric organism Grow in BUG Blood Do not use TSA Blood Do not add Thioglycolate to GN GP IF Special precautions should be taken when handling this group of organisms Processing specimens suspected to contain one of the above selected agents should only be handle by trained personnel under BSL2 for specimen processing BSL 3 for culture manipulation PRESUMPTIVE identifications with OmniLog stations should be interpreted with caution Please contact the local State health Department or CDC for confirmation of identification References Bioterrorism Implications for the Clinical Microbiologist Wolfgang F Klietmann et al Clinical Microbiology Reviews Vol 14 2001 p 364 381 CDC contacts www bt cdc gov www cdc gov ncidod hip CDC Emergency Response phone number 770 488 7100 OmniLog System User Guide 25 Jun 06 Section 15 X Page 22
116. mosphere Incubation Time Gram Negative Non Enteric 30 C Air 4 6 and 16 22 hours Gram Negative Enteric 35 C Air 4 6 and 16 22 hours Gram Negative Fastidious 35 C 6 5 CO 4 6 and 16 22 hours Incubate in secondary incubator Gram Positive Cocci 35 C or Air or 4 6 and 16 22 Gema Mosie Rab Car 30 C or 26 C if e if hours spore forming required q Incubate in secondary incubator if CO required Gram Positive Rods spore 30 C or Air 4 6 and 16 22 forming bacillus 55 C if required hours OmniLog System User Guide 25 Jun 06 Section5 X Page 12 Preparing Samples Sample Preparation Process Initial culture medium BUG B whatever media you usually isolate from can be used here Gram stain and observe cell morphology Gram stain results V Gram Negatives Gram Positives VV Characterization test Oxidase positive or requires 30 C Oxidase negative and TSIZA A or Requires CO or chocolate agar K A or lt mm colonies Characterization test Oxidase negative on BUG B or no and TSI K K or positive reactions K A when set up as ENT or NENT Strain type GN NENT GN ENT GN FAS GP COCCUS or GP ROD SB GP ROD spore forming bacillus Culture medium BUG B BUG B Chocolate BUG B BUG M T streaking Temperature Typically 30 C Typically 35 C Typically 35 C Typically 35 C Typically 30 C Atmosphere Air Air 6 5 CO Air or 6 5 C
117. n length and contains at least one number The password is case sensitive Click OK When the message Click on the Log In button at the top right to log in to the program appears click OK Click on the Log In box located in the upper right hand corner of the Welcome window A Password Dialog box will appear Section 2 X Page 3 Installation and Registration OmniLog Administrator Dialog software has a predetermined Please enter an Administrator username and 5 password For as long as it remains time out installed the program will recognize this user period If the as a program Administrator program is idle for more than Enter Username 15 minutes the soft tware will Enter Password Log Out You can prevent this logging off by clicking 2 OK when the time out E 7 Enter the Administrator username and password you set in Step 3 d Click OK appears 8 You will now be listed as the Original Administrator in the User List with full user privileges The message in the upper right hand of the Welcome screen will shows the Log In button Note 9 Click the Log In button to log in See Section 1 5 or section 3 1 Not all users will have 3 3 for Log In and Reader setup instructions full administrative privileges To learn more about assigning user names and passwords as well as setting up different levels of user access please refer to Section 4 Program Administration Password Dialog
118. ncubator reader Many borderline reactions on MicroPlate Wrong com port selected Review all sample preparation procedures for correctness and accuracy Choose correct com port Loose cable connection Turn incubator reader off Unplug cable then plug it back in Turn incubator reader on and try again Unknown cause MicroPlate mispositioned The incubator reader has its own error messages which should be self explanatory Call Biolog Technical Service if you need further assistance Make sure MicroPlate into place and is seated levelly Make sure MicroPlate lid is on Remove MicroPlate and reposition in incubator reader tray Make sure A1 well is at the right rear Verify that software is communicating with incubator reader Camera assembly is in the way Loose cable or incorrectly installed cable Loose or incorrectly installed cable Jam or failure Set and actual temperature out of range 2 C OmniLog System User Guide 25 Jun 06 Click Move Camera selection bar on the Load Plates window to move camera out of the way Make sure the serial cable is connected to serial port 1 on the incubator reader this will be the lower plug Click on the Video Error message on the footer bar If you get a message reading No Signal check the video cable at the back of the incubator reader The cable should go from a special plug at the back of the computer to the upper plug a
119. negative organisms Refer to a basic microbiology textbook if you are unsure of this procedure If the oxidase test is positive organism grows well aerobically you have a non enteric GN NENT microbe If the oxidase test is negative and the bacterium forms large colonies you most likely have an enteric GN ENT microbe Triple Sugar Iron TSI is an excellent method to confirm that your sample is GN NENT or GN ENT Setting up a TSI slant Prepare a TSI slant on oxidase negative microbes Refer to a basic microbiology textbook if you are unsure of this procedure If the TSI slant shows a K K alkaline alkaline or K A alkaline weak acid reaction your microbe is non enteric GN NENT If the TSI slant shows an A A acid acid or K A alkaline acid reaction your microbe is enteric GN ENT This is true with a few exceptions such as Pasteurella A A species or Acinetobacter A late A which can be weak oxidase positive Recognizing fastidious gram negatives OmniLog System User Guide 25 Jun 06 Fastidious gram negative bacteria are primarily isolated from the respiratory tracts of mammals Section5 X Page 3 Preparing Samples e These bacteria grow poorly or not at all on BUG B medium They grow much better on chocolate agar at 35 C in an atmosphere of 6 5 CO Note All microbes requiring a CO atmosphere must be incubated in a secondary or offline incubator before placing in the incubator reader for ide
120. ng the OmniLog ID System The OmniLog ID Microbe Identification Process Step 1 Isolate a pure culture on Biolog media Step 2 Do a Gram stain and determine testing le fe Kelere Step 3 Prepare inoculum at specified cell density Step 4 Inoculate MicroPlates and place in incubator reader Step 5 I Obtain ID results from printer Step 1 Isolate a pure culture on Biolog media Isolating a pure culture is not always easy Bacteria often have sticky Follow surfaces and cells sometimes stick together in clumps As a first step to directions accurate microbe identification streak agar plates using correct closely to techniques to generate well isolated colonies Always use Biolog obtain accurate recommended culture media and growth conditions See Section 5 for ES full culturing and incubation instructions Step 2 Do a Gram stain and determine testing protocol Proper Gram stain technique and interpretation are the important second step in the ID process See pages 5 2 and 12 1 12 2 OmniLog System User Guide Section 1 X Page 3 25 Jun 06 Introducing the OmniLog ID System Step 3 Prepare inoculum at specified cell density Microbiologists are sometimes trained to prepare cell suspensions in a casual manner often judging cell density by eye This practice will not yield accurate and reproducible results Cell density determines oxygen concentration a key parameter to control when testing m
121. ntification Characterizing gram positive microbes If your microbe is gram positive pay special attention to the cell morphology in the Gram stain Note the following e Determine whether the microbe is a coccus or a rod e If the microbe is a rod GP ROD determine whether it is spore forming bacillus GPR SB consisting of Bacillus and species formerly called Bacillus Spore formers require special handling and testing See pages 5 7 5 10 e It can be difficult to recognize Bacillus species from a Gram stain but most may be recognized by colony morphology They are often fast growers forming colonies that have unusual characteristic textures e g spreading slimy crusty dry embedded or forming skin like pellicles Performing a catalase test It is advisable to perform a catalase test 3 hydrogen peroxide on GP COCCUS and GP ROD isolates The catalase reaction can help you verify or narrow down the species identification If the organism is catalase negative this generally indicates a slow grower Subculture onto agar to obtain a lawn of growth using a swab or loop You may need more than one agar plate Refer to a basic microbiology textbook if you are unsure of this procedure Culturing Your Microbe Subculture onto the proper agar medium using a single isolated colony Most of the species in Biolog s database are relatively fast growers However if your microbe grows slowly you may need to streak subculture m
122. ntification Many species will give fewer positive reactions when grown on non recommended media Use Biolog recommended media only OmniLog System User Guide Section 11 X Page 1 25 Jun 06 Frequently Asked Questions Q Why is there a defined range for the turbidity of inocula It is essential to prepare inocula in a consistent and precise manner The A Biolog redox test chemistry is sensitive to oxygen concentration which is determined by cell density Use Biolog turbidity standards and calibrate your turbidimeter Q Are Biolog s Turbidity standards comparable to McFarland standards Biolog s Turbidity standards have different set points and are not pis comparable to McFarland standards Biolog s standards are set for cell densities at which the Biolog test performs optimally Use of Biolog standards is necessary to achieve consistent and accurate results Can I use one incubator for all my strains and set it at32 33 instead of Q having two incubators at 30 c and 35 37 c respectively Organisms grow better depending on the temperature of their environment A Biolog has chosen the temperatures at which the organisms in our database grow optimally Using different temperatures than those recommended will decrease the performance of your Biolog ID system We read our MicroPlates visually Occasionally we are unsure whether a O reaction is positive or negative How should we enter those wells Light purple reactions are con
123. o e mail to Biolog representative 4 Print to generate a printout of the screen Fax or e mail the complete print out to Biolog Technical Services The Test Bell button on the Reader Setup window will ring the system bell on the computer once The bell will ring continuously during a door open error This button helps you make sure you can hear the bell Relocating the OmniLog Caution Once the OmniLog ID system is set up it s best NOT to move it If for some reason you must move it call Biolog Technical Services first then follow these instructions OmniLog System User Guide 25 Jun 06 If you physically move the OmniLog you must first park the camera and make sure there s a tray in the bottom row as follows 1 On the Welcome window click Reader Setup Make sure the com port is open the reader is initialized and the cycle mode is off 2 Move the camera to the top or bottom of the reader using the Move Camera buttons The normal resting position for the camera is row 25 3 Before physically moving the incubator reader verify that an empty tray is in Row 1 Note It is standard practice to transport the reader with the camera at the top with a tray in the bottom row Click Park Wait until the footer bar Reader Status cell goes from Busy to Idle Quit the OmniLog software and turn off the OmniLog computer Section 13 X Page 8 System Verification It is advisable for weight considerations t
124. o prepare Administrator 3 The OmniLog Software Windows InstallShield Wizard will appear Click Next iz Install_OLID_13_01 InstallShield Wizard Registering Your Software Installing Biolog MicroLog Databases Welcome to the InstallShield Wizard for Install OLID 13 01 The InstallShield R Wizard will install Install OLID 13 01 on your computer To continue click Next WARNING This program is protected by copyright law and international treaties Important e The person installing the software must be logged in through 4 The License Agreement will appear Review the terms and select the Windows the I accept the terms in the license agreement radio button operating system Click Next as the 5 Carefully review the Readme Information Click Next Administrator 6 The next screen that appears gives you the option of where to a INTERN install the OmniLog root directory folders functions only on computers with Destination Folder The root directory OmniLog may be regional and installed anywhere on a stand alone PC or on a network drive If language options set you do install the directory on a network drive please remember uui that this program is currently not designed for multiple users at one time e The default suggested installation location is Program Files Biolog Click Next to accept this default location e To choose your own location click Change Select the Look In
125. o print current worksheet Next Locks down the current worksheet entered Save As To save worksheet under designated file name Load WS To Load Pre designated worksheet 5 Click Add Entry The Plate Information window appears OmniLog System User Guide Section6 Page 7 25 Jun 06 Clear Info Next Free Drop down lists e e x e e alalla You can edit a Loading and Reading MicroPlates OmniLog ID E N N GP ROD CAT X 248 238 228 218 208 198 185 175 168 158 148 138 125 118 108 58 55 48 38 25 Save Entry PLATE INFORMATION WINDOW Click Clear Info if you wish to clear all entries entered previously Select a position number by clicking anywhere on the tray stack or click Next Free for the next available position worksheet while you are working Select the correct Plate Type and Strain Type using the drop down on it by clicking lists on the position namber of the Type correct entries into the Sample Number Strain Name and entry you wish to j Other fields edit Click one of the following depending on what you want to do e Click Clear Info to clear the values you just typed in e Click Next Free to assign the next free tray position e Click Delete to delete the position entry e Click Save Entry to log the entry into the worksheet e Click Print Worksheet to print the worksheet Complete all entries for all MicroPlates in the batch Once you are fin
126. o remove all other trays from the incubator reader before transporting it Remember to re install all trays before using it again OmniLog System User Guide Section 13 X Page 9 25 Jun 06 Glossary In this section gt Definitions of 14 Glossary Terms Aseptic technique Standard lab procedures used to prevent contamination Carbon source utilization Basic process used to identify microbes based on the chemicals they can utilize Catalase test Additional test used to characterize gram positive bacteria Dendrogram Cluster diagram in the form of a branching tree Enteric Gram negative bacteria belonging to the group Enterobacteriaceae Freeze The act of converting a datafile into a Frozen and non editable format Gram negative Bacteria showing typical pink or red reaction on Gram stains Gram positive Bacteria show typical blue or violet reaction on Gram stains Histogram Visual representation of MicroPlate color distribution and thresholds Inocula Cell suspension used to inoculate MicroPlates Inoculating fluid Fluid used to prepare inocula Maltose A sugar added to BUG Agar Required for culturing spore forming gram positive rods e g Bacillus species MicroPlate Plate with 95 carbon source utilization tests one in each well with Al well as control MicroPlate reactions Positive negative and borderline color responses used to identify microbes Non enteric Gram negative bacteria not belonging to the group Ente
127. o seen PP sre 2126 105 0953 238 load and unload s MicroPlates If you need more time activate the Snooze bar 4 Plates Done READ WINDOW OmniLog System User Guide Section9 X Page 1 25 Jun 06 Unloading MicroPlates 1 When the Read window indicates that some MicroPlates are ready to be unloaded click Unload on the top menu bar The Unload window shows a picture of the tray stack indicating current status see Table 9 1 for explanation of symbols You can click on any row to see the Unload Key Check to ascertain which MicroPlates are ready for removal TABLE 9 1 UNLOAD WINDOW SYMBOLS Key Explanation Numbers along left and right edges Numbers correlate to tray numbers starting with number at the bottom through number 25 at the top A and B designations along left and right edges A left column of MicroPlates B right column of MicroPlates White slots with Slot empty of both MicroPlates and tray White slots with Slot contains tray but not MicroPlate Green background with red checkmark icon Slots that contain MicroPlates that have been read and are ready to be removed Yellow background with hand writing icon Slots containing MicroPlates that have been read but are not ready to be removed Data still saving Red background with clock icon Slots containing plates that have not been read yet o Tray Empty Pending ID D Continue Read late Done inetic R
128. oPlates Use the buttons as described on pages 13 1 13 3 Using Test Cycle The Test Cycle is a method to test the hardware mechanical cycle process and associated video mechanics You will only use this test to diagnose a hardware failure Don t perform this test without the help of Biolog Technical Service 1 From the Welcome menu click Reader Setup Make sure the com port is open the incubator reader is initialized and the cycle mode is off 2 Click Test Cycle The Test Cycle window appears xj Cycle type radio buttons II Ti Cycle length radio buttons Temp Log Reset IY TEST CYCLE WINDOW Operational controls OmniLog System User Guide Section 13 X Page 6 25 Jun 06 Please let us assist you in verifying the OmniLog System Don t do this without the assistance of Biolog Technical Service help System Verification 3 In the Cycle Type area of the window select the Move Only radio button to mechanically move the tray only or the Move and Video radio button mechanically move the tray cycle and capture the cycle on video 4 In the Cycle Length area of the window select the Single Cycle radio button to perform a single cycle through all trays or the Non Stop radio button to cycle repeatedly through all trays Click Start to begin the test cycle process If desired click Pause to pause the cycle process Click Stop to stop the cycle process om OM Click Cance
129. ogram Flexibility in Regulated Environments There are a number of features in the OmniLog program software that enhance utility and allow it to be easily integrated into a regulatory compliant lab It is important that the Administrator of the OmniLog software be aware of these features and their possible uses e Log In Log Storage The Log In Log will store the last 100 login attempts so that the administrator can easily see a history of program use After the 100 record limit is reached the program will move one record at a time to a file and location of the administrators choosing This Section4 X Page 7 Program Administration location should be secure and is specified on Options Page of the Administration screens e Accessing and Managing Data Original Data Including Species identification is automatically saved and cannot be manipulated in any way by any user However Datafiles can be used to perform a number of useful functions such as the creation of User databases and the tracking of strains for information on these functions and other data management features please see RetroSpect Trending and Tracking Software and MicroStation Software User Guides The chart below gives an overview of the creation and use of data Databases Biolog GN and GP and or User Created Current read data is Create compile manage compared to Databases User databases to establish identification RetroSpect Trending and OmniLog ID
130. om Carefully transfer the supernatant into another dry sterile tube to check the transmittance If necessary add more organism using the Dry Tube Method Bacillus cereus and Bacillus thuringiensis are considered indistinguishable by biochemical assays These two species are listed in the Biolog database as Bacillus cereus thuringiensis You may need to use more than one BUG M T agar plate for slow growing organisms Inoculating MicroPlates Caution Pipet the inoculum into a MicroPlate within 20 minutes Use sterile technique Inoculate the suspension into one of the following Biolog MicroPlates GN2 MicroPlate For all gram negative aerobic bacteria GP2 MicroPlate For all gram positive aerobic bacteria Pipet your inoculum into a Biolog MicroPlate within 20 30 minutes Waiting any longer may cause inaccurate identification When running a batch of MicroPlates set them up from preparing the inoculum to pipetting into the MicroPlate so you will not exceed the 20 minute deadline Inoculating protocol 1 Label the MicroPlate with the organism name number and plate type e g GN GP Label the side of the MicroPlate Itself not the lid 2 Using aseptic technique pour the cell suspension into a multichannel pipette reservoir 3 Firmly attach eight sterile tips to the pipetter Refer to the pipetter manual for further instructions OmniLog System User Guide Section5 X Page 10 25 Jun 06 OmniLog
131. on Process gt Easy to Use Software User Functions Using the Footer Bar The Math Behind the Software OmniLog System User Guide 25 Jun 06 The OmniLog ID System includes everything you need to incubate microbes and use all the features of OmniLog ID software OmniLog ID is a dedicated system for bacterial identification and includes the following components e Dedicated Windows based computer with preinstalled OmniLog ID software e OmniLog Incubator Reader e Printer e Turbidimeter e Electronic multichannel repeating pipettor OMNILOG ID SYSTEM OmniLog ID is an easy to use yet advanced tool for identifying and characterizing microorganisms Our combined databases include over 800 species of aerobic bacteria They contain nearly all of the significant species encountered in diverse practices of microbiology including pharmaceutical biotechnology cosmetic and medical device companies veterinary and clinical medicine agriculture and environmental science food processing spoilage and safety reference laboratories industrial microbiology and research and education Section 1 X Page 1 Introducing the OmniLog ID System OmniLog ID continues to expand and evolve to keep pace with progress in the field of microbiology Every month researchers discover new species of microorganisms and recognize their importance By using its patented technology with 95 carbon source utilization tests in a microtiter
132. onsistency of records OmniLog System User Guide 25 Jun 06 The Biolog OmniLog ID Data Collection MicroStation ID and RetroSpect Trending and Tracking software programs include software control features that ensure data integrity by limiting access ensuring that original data cannot be changed or deleted and providing audit trails These separate programs provide greater flexibility but they also require that the administrator control and synchronize all programs The administrator of the OmniLog program must integrate the software controls of each program into a regulatory compliant laboratory Usernames Access Levels and Passwords The Biolog ID programs have separate User Lists It is important to the administrator that these lists are consistent in order to create a reliable audit trail e When adding a user be sure to include a profile for that user in both programs Conversely if removing a User s Access privileges make the change in each program e Use identical user names in each program for a specific user e Instruct that when a user logs into a program for the first time that they Log In and establish their own passwords in both programs By doing this you will ensure that the User s passwords will expire at the same time and eliminate possible confusion e Instruct that if a User decides to change their password before the three month expiration period they make the change in each program OmniLog Pr
133. ooooooqQ N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N Z f Z N N N ENT N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N FAS N ENT N ENT ENT ENT ENT ENT ENT ENT N ENT N ENT N ENT N ENT N ENT N ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT ENT N ENT N ENT N ENT N ENT N ENT ENT ENT ENT ENT ENT ENT ENT ENT N ENT N ENT N ENT N ENT N ENT N ENT N ENT N ENT N ENT ENT Test O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O ZKKKKKKKKKZZZZZZZZZKKKKKZZZZZZZZZZZZZZZZKKKKK ZZ ZZZZZKKKKKKKKMKMKKK J e Medium CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC CHOC BUG B BUG B BUG Bt BUG B BUG B BUG B BUG B BUG Bt BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG Bt BUG Bt BUG Bt BUG Bt BUG Bt BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG B BUG Bt Atm Temp 6 5 CO2 35 37 6 5 CO2 35 37
134. ore than one agar plate Incubate according to Instructions on package insert For use GN2 and GP2 MicroPlates in general e Incubate most organisms for 24 hours Very slow growing species may require 48 hours OmniLog System User Guide Section5 X Page4 25 Jun 06 Preparing Samples e If using an offline incubator don t over incubate the culture Excess incubation can cause microbes to enter a stationary phase during which they lose viability and metabolic activity All culture plates will be grown in a secondary or offline incubator Table 5 1 and Appendix 1 will help you select the correct culture medium TABLE 5 1 SELECTING THE CORRECT CULTURE MEDIUM Organism Type Organism Culture Media Media Abbreviations shorthand Gram Negative Non Enteric GN NENT BUG B B blood Gram Negative Enteric GN ENT BUG B M maltose Gram Negative Fastidious GN FAS Chocolate T thioglycolate Gram Positive Cocci GP COCCUS BUG B Gram Positive Rods non spore GP ROD forming Gram Positive Rods spore forming GP ROD SB BUG M T bacillus Preparing Inocula Once your microbe is isolated and cultured prepare a liquid inoculum Refer to instructions enclosed with Biolog MicroPlates for detailed directions In general e The inoculum MUST be within the range specified by the STOP turbidity standards accompanying your database 2 T Is your e The inoculum MUST be uniformly suspended If an suspension i m organi
135. orrectly loaded row click Read Row Wait until the footer bar says that the reader is idle again The still video image of the two MicroPlates in that row will appear at the top of the window The Video Status area will show OmniLog System User Guide Section 13 X Page2 25 Jun 06 System Verification whether the camera detected a tray and MicroPlate If you selected No Tray or No Plate test modes a pass entry in Test Pass indicated a successful test The display under the still video image will show a well by well pass fail designation If a well passes it will contain a black check mark on a green background If it fails it will contain a black X on a red background In the All Zero and All Positive tests these designations will show for each well if that well was either zero for the All Zero test or positive for the All Positive test The Test Pass box will show pass only if all wells pass the test 9 Change the target row and click Read Row to test other rows you can also click Next Up or Next Down 10 Perform all four tests to fully test the incubator reader 11 Click Print to print out a report of the Read Verification test for that MicroPlate 12 Click Save 1x96 or Save 12x8 to save the actual data numbers for that MicroPlate to a comma delimited ASCII file You will be prompted for the name of the file The first entry in the ASCII file will be the file name without the dire
136. pe Test Thio Medium Atm Temp 121 CDC group II H GN NENT O N BUG B Air 30 122 Cedecea davisae GN ENT O Y BUG B Air 35 37 123 Cedecea lapagei GN ENT O Y BUG B Air 35 37 124 Cedecea neteri GN ENT O Y BUG B Air 35 37 125 Chromobacterium violaceum GN NENT O N BUG B Air 30 126 Chryseobacterium balustinum GN NENT O Y BUG B Air 30 127 Chryseobacterium gleum indologenes GN NENT O Y BUG B Air 30 128 Chryseobacterium indoltheticum GN NENT O Y BUG B Air 30 129 Chryseobacterium meningosepticum GN NENT O N BUG B Air 30 130 Chryseobacterium scophthalmum GN NENT O N BUG B Air 30 131 Chryseomonas luteola GN NENT O N BUG B Air 30 132 Citrobacter amalonaticus GN ENT O Y BUG B Air 35 37 133 Citrobacter braakii GN ENT O Y BUG B Air 35 37 134 Citrobacter farmeri GN ENT O Y BUG B Air 35 37 135 Citrobacter freundii GN ENT O Y BUG B Air 35 37 136 Citrobacter gillenii GN ENT O Y BUG B Air 35 37 137 Citrobacter koseri GN ENT O Y BUG B Air 35 37 138 Citrobacter murliniae GN ENT O Y BUG B Air 35 37 139 Citrobacter rodentium GN ENT O Y BUG B Air 35 37 140 Citrobacter sedlakii GN ENT O X BUG B Air 35 37 141 Citrobacter werkmanii GN ENT O Y BUG B Air 35 37 142 Citrobacter youngae GN ENT O Y BUG B Air 35 37 143 Comamonas terrigena GN NENT O N BUG B Air 30 144 Comamonas testosteroni GN NENT O N BUG B Air 30 145 Cytophaga fermentans GN NENT O N BUG B Air 30 146 Delftia acidovorans GN NENT O N BUG B Air 30 147 Edwardsiella hoshinae GN ENT O Y BUG B
137. perature Log window appears displaying black horizontal lines that represent the target temperature range 1 less and 1 more than set value The red line represents the actual temperature record Each vertical line represents one hour The medium thickness line represents noon and the thick line represents midnight OmniLog System User Guide Section3 X Page 3 25 Jun 06 Actual temperature red line Target temp and 1 black lines Launching the OmniLog ID Program Midnight OmniLog ID templogfile lg2 A 1 LL LL TEMPERATURE LOG WINDOW 3 Click Done The software will return to the Reader Setup window 4 Click Done The software will return to the Welcome window Shutting the System Down Caution To perform an emergency stop of the OmniLog while it is moving Click on the emergency Stop Commands button on the Status footer bar ol As long as there are no MicroPlates in the reader with pending reads you can exit the software by using the Exit menu or the X close button in the upper right of the screen However it s better to return to the Reader Setup window and shut down contact with the reader before you exit 1 Click Stop Cycle Mode 2 Click Stop Commands This halts new communication between the software and the incubator reader but commands already in progress will continue 3 To restore software contact with the incubator reader click Initialize Reader Note
138. plate format MicroPlate the Biolog microbial identification system can recognize over 4 x 10 possible metabolic patterns This provides room for future growth of the system so that the technology will remain state of the art How It Works Biolog s innovative patented technology uses each microbe s ability to use particular carbon sources to produce a unique pattern or fingerprint for that microbe As a microorganism begins to use the carbon sources in certain wells of the MicroPlate it respires This respiration process reduces a tetrazolium redox dye and those wells turn purple The end result is a pattern of purple wells on the MicroPlate that is characteristic of that microorganism This pattern is readable by a combination incubator reader instrument the OmniLog Incubator Reader The fingerprint data is fed into OmniLog ID software which searches its extensive database and can make an identification in seconds By developing a simple tool that allows 95 simultaneous carbon source utilization tests Biolog has accomplished its goal of producing an efficient easy to use powerful and reliable microbe identification system The Identification Process Microbial identification involves five basic steps These steps apply to all identifications A small number of species have peculiarities that may require an extra step or special handling techniques OmniLog System User Guide Section 1 X Page 2 25 Jun 06 Introduci
139. ppening when I get a hardware video temperature or plate error message Test Read is the incubator reader reading correctly for my uniquely altered MicroPlate Test Cycle are the hardware mechanical cycle process and associated video mechanics working correctly Field Service tests am I having a hardware error I cannot fix Relocating the OmniLog do I need to move the OmniLog to a different location Read Verification Please let us assist you in verifying the OmniLog System Don t do this without the assistance of Biolog Technical Service help OmniLog System User Guide 25 Jun 06 1 From the Welcome window click Reader Setup Make sure the com port is open the reader is initialized and the cycle mode is off Click Read Verification window appears showing two MicroPlates Click on the checked box labeled Auto Lighting right top corner of the screen The AutoLighting function must be off for system check Read Verification and Test Read The Auto Lighing function must be turned on in all other cases for normal use The Read Verification menu can check for four conditions No tray No MicroPlates All zero value plate Biolog s OmniLog Verification Kit is required for this test All positive plate Biolog s OmniLog Verification Kit is required for this test 5 Select a row other than the one where the camera is parked Section 13 X Page 1 System Verification Test mode radio b
140. pull down menu to browse for a location Select the location and click OK OmniLog System User Guide Section2 X Page 1 25 Jun 06 Note The Readme Information is not printable at the InstallShield Wizard window The file is located in the OmniLog Software root directory and is named readme rtf Go to this location to open and print the Readme information Installation and Registration 7 Now the InstallShield Wizard is ready to begin installation Choose Back to make any changes Cancel to exit the InstallShield Wizard and not install the program or Install to proceed with installation 8 The next screen that appears asks you to enter the serial number of your program found on the spine of the software jewel case Enter the serial number and click ok Program Serial Number DER Please Enter The Program Serial Number Printed On The Installation Disk Program Serial Number MM Cancel 9 The Installing OmniLog Software screen will appear while the installation is taking place Click Finish when the InstallShield Wizard Completed screen appears The following shortcut icon will now be installed on your desktop The OmniLog shortcut is the main program Click on this icon to open the main program Please remember that the OL DC program will count down for up to 60 days from date of software installation After 60 days the software will display a User Registration reminder within the program
141. r 35 37 143 Enterococcus hirae GP COCCUS C Y BUG B Air 35 37 144 Enterococcus malodoratus GP COCCUS C Y BUG B Air 35 37 145 Enterococcus mundtii GP COCCUS C Y BUG B Air 35 37 146 Enterococcus pseudoavium GP COCCUS C Y BUG B Air 35 37 147 Enterococcus raffinosus GP COCCUS C Y BUG B Air 35 37 148 Enterococcus saccharolyticus GP COCCUS C Y BUG B Air 35 37 149 Enterococcus solitarius GP COCCUS C Y BUG B Air 35 37 150 Enterococcus sulfureus GP COCCUS C Y BUG B Air 35 37 151 Eremococcus coleocola GP COCCUS C Y BUG B 6 5 CO2 35 37 152 Erysipelothrix rhusiopathiae tonsillarum GP ROD C Y BUG B 6 5 CO2 35 37 153 Exiguobacterium acetylicum GP ROD C Y BUG B Air 30 154 Gardnerella vaginalis GP ROD C Y BUG B 6 5 CO2 35 37 155 Gemella bergeri GP COCCUS C Y BUG B 6 5 CO2 35 37 156 Gemella haemolysans morbillorum GP COCCUS C Y BUG B 6 5 CO2 35 37 157 Gemella palaticanis GP COCCUS C Y BUG B 6 5 CO2 35 37 158 Gemella sanguinis GP COCCUS C Y BUG B 6 5 CO2 35 37 159 Geobacillus stearothermophilus GP RODSB C W N BUG M Air 55 160 Geobacillus thermoglucosidasius GP RODSB C W N BUG M Air 55 161 Globicatella sanguinis GP COCCUS C Y BUG B 6 5 CO2 35 37 162 Gordonia aichiensis GP ROD C Y BUG B Air 35 37 163 Gordonia bronchialis GP ROD C Y BUG B Air 35 37 164 Gordonia rubroprincta GP ROD C Y BUG B Air 35 37 165 Gordonia sputi GP ROD C Y BUG B Air 35 37 166 Gordonia terrae GP ROD C Y BUG B Air 35 37 167 Helcococcus kunzii GP COCCUS C Y BUG B 6 5 C0
142. r to select the proper media and MicroPlates for testing Bacteria Without a correctly identified Gram stain you will not get good ID results Once your initial culture has incubated sufficiently perform a standard Gram stain Determine the following e Is the microbe a bacterium or a yeast e Is the microbe gram positive or negative e Are the cells cocci or rods e Do the cells form spores Based on the source of the sample the initial growth conditions and the Gram stain you should know the basic type of microbe you have See Section 12 for specific Gram stain information Refer to a basic microbiology textbook if you are unsure of these procedures SectionS X Page 2 Preparing Samples Characterizing Aerobic Bacteria Enteric gram negative bacteria belonging to Enterobacteriaceae group Non enteric gram negative bacteria not belonging to Enterobacteriaceae group Gram negative and gram positive aerobes each require further investigations to determine proper handling and identification Characterizing gram negative microbes If your microbe is gram negative several additional tests will help determine whether your microbe is non enteric GN NENT enteric GN ENT or fastidious GN FAS and determine the proper setup protocol This has important implications in regards to choice of incubation temperature inoculum density and inoculating fluid Performing an oxidase test Do an oxidase test on all gram
143. ram 3 Launching the OmniLog ID Program In this section The OmniLog ID System is preloaded with the software package A gt Initializing Biolog service technician will help you set the system After that you the System will keep the computer and incubator reader on at all times The bias installation disks that come with your system are meant for back up atus Setting the only in the event of a system crash E Note OmniLog ID software works only on the computer supplied with PIOS te your OmniLog ID System Do not try to install the software on another System Down computer System requirements and recommendations I Biolog recommends the use of MicroSoft XP professional service pack 2 operating system as it has increased stability compared to previous MicroSoft operating systems versions 2 Power settings All power saving features must be turned off for operation of the system 3 The MicroSoft operating system must be reset re booted 2 to 4 times per month The OmniLog incubator reader does not need to be shut down This is to prevent possible system shutdown due to operating system stability factors 4 Users required to be admin level on Windows operating system If you ordered specific databases at the time of purchase those will have been factory installed The databases containing species information come on separate computer disks and are also intended for back up only in the event of a system crash Initializin
144. re are both and random mismatches this is probably a true mismatch If so this is probably a species not in Biolog s database You can add it to your own user created database using RetroSpect Trending and Tracking software Section8 Page 2 Interpreting Results e If the mismatches are all or all you may have made a testing error Refer to Table 8 2 and see Section 12 Table 8 2 will assist you in figuring out the cause of these mismatches Mismatch Type All your pattern is giving fewer positive reactions than the species you re comparing it to What It Might Mean Under inoculation A well is overfilled contains clumps or is cloudy Cells were mishandled too old cultured on wrong medium suspended in wrong inoculating fluid incubated at wrong temperature etc All your pattern is giving more positive reactions than the species you re comparing it to Over inoculation especially with enterics A1 well is underfilled Contamination mixed culture TABLE 8 2 ASSESSING MISMATCHES Dec 19 2001 t42 PM Dec 19 2001 6 43 PM PLATE DATA WINDOW Assessing the Accuracy of Your ID The OmniLog 1 X series software measures the goodness of the ID based on two criteria Match and Separation A value is derived for both of these concepts based on the Distance DIST The DIST value indicates how many mismatched reactions the test organism has
145. rmation about each MicroPlate in your batch e What date am I loading this batch e What unique code letter will I assign to this batch e Is this plate part of a project and if so what is the project code e When were the MicroPlates set up zero time for the incubation e Dol want to use normal read mode or a special read mode OmniLog System User Guide Section 1 X Page 8 25 Jun 06 Introducing the OmniLog ID System As incubation and reading progress the worksheets for all MicroPlates in the incubator reader will remain displayed on the Read window You ll be able to view in progress and final results for all MicroPlates and all worksheets When the ID process ends you ll automatically receive hardcopy results from your printer Interpreting Results As IDs show up on the Read window you can view more detailed information for any microbe listed The Plate Data Window shows a picture of the selected MicroPlates along with well by well readings and statistical information This information will help you assess the accuracy of the ID or pin down an uncertain ID using similarity index values and distances Plate Data jx Read Errors No Errors Plate Errors No Errors General Erro No Errors Temp Errors No Errors Read S 109 HH 1 ET E 5 PIE o E Well by well Still picture of MicroPlate reading of elolololololelelel MicroPlate IDs 109 D11219 K Read T
146. robacteriaceae Oxidase test Additional test used to characterize gram negative bacteria Pattern Color responses in MicroPlates OmniLog System User Guide Section 14 X Page 1 25 Jun 06 Glossary i Pleomorphic Having various distinct forms or shapes exhibited by a single strain or species Progressive ID PID Biolog Inc developed pattern matching method which considers the progressive sequence in which purple wells are formed Pure culture Culture containing only one microbe species Restricted Access mode Mode set by system administrator to prevent unregistered users from using system assign user names passwords and privileges to each user create an audit trail and freeze data files to maintain data integrity Salicylate Anticapsulate agent required as an addition to inoculating fluid for a few gram positive species Thioglycolate Anticapsulate agent required as an addition to inoculating fluid for gram negative enteric bacteria gram negative fastidious bacteria and gram positive cocci and rods Thresholds The optical boundaries between negative borderline and positive reactions TSI slant Additional test used to characterize gram negative bacteria Turbidity Measurement of cloudiness which is indicative of inocula cell densities Unrestricted Access mode Mode set by system administrator to allow any user to use all OmniLog software functions User Database Database produced by the User developed by using edited
147. robes Luxuriant growth and full metabolic activity are required for our system to work well The flowchart on page 1 3 provides an outline of the identification process The table on page 5 13 gives a comprehensive overview of the sample preparation process as does the flowchart in Appendix 1 Each shipment of Biolog MicroPlates comes with an Instructions for Use booklet Refer to these for more detailed instructions on how to setup your samples and troubleshooting tips Isolating a Pure Culture BUG Biolog Universal Growth Note Identification of Filamentous Fungi Anaerobes and Yeasts require the use of the OmniLog Plus system Refer to your MicroLog Manual for detailed procedures OmniLog System User Guide 25 Jun 06 Culture your sample on Biolog s general purpose culture medium Nearly all the species in the OmniLog ID database will grow on Biolog Universal Growth media BUG generally with the addition of either 5 sheep blood or 0 25 maltose If you have not purchased prepared media from Biolog prepare media according to the package insert See Section 11 for media preparation instructions Refer to the Instructions fo Use for detailed directions about how to grow a healthy culture In general Make certain you have a pure culture a single organism Incubate at optimal temperature Most bacteria should be grown at 35 C Some genera are grown at 30 C and a few gram positives at 26 C
148. rte eese e aee oen anco e ete n pear anao nun 1 What is Restricted Access Mode ceo eeasi redet oti senta age le iesu oen ei equat 1 First Log In and Setting up an Administrator esee 2 Administrator PUNCUONS 3i eret ce dert eig rit s statute ito Spin esista 2 Options Tab FUNCIONS S esu Medie o E ust ab ru ee aceon etie dev ose ras ML E 2 Create a User EISE scuta obit EE tetas a TOA TE R E E 3 Interpreting the Log In E09 chon aio C du eere pe tai p Cai Ub su fidt 5 Administration Suggestions 0 cdiscccesedsveseadedasnedasaseeseaspevadeadsaeedgaseseeatasdesaccaunasenvasedencees 7 5 Preparing Samples TATE E 1 Isolating a P re Culture nou bete Reid eisat a isa ia tn 1 Grami Stalin ge rie ES 2 Characterizing Aerobic Baeterta oiii aeo o qued opc ac oued E S 3 Cultariig Your Microbe es on ee edu eee e a eve 4 Prepare Tnocul C esh 5 Special Procedures for Spore Forming Gram Positive Rods sss 7 Inoculatitie Macro ates sooo eio eit obi Ouod edidi 10 Inc bating MicroPlates 2o quce pa E lu fica ie qula eut Depp 12 sample Preparation Process oret eto beca e tec bab epo ced dee ut ada eee eee 13 10 11 12 13 14 15 Loading and Reading MicroPlates eere reete 1 Checking Load and Batch St Uis uses te So RI Eee aa iU Beton va E Rgoea Por eue ERR BN bow 1 petting Upa Worksheet eie duod cod dueqias San ee ee a 3 Read Modes menan Sti
149. s Corynebacterium Enterobacter Pseudomonas Aeromonas Vibrio Acinetobacter Moraxella Clostridium and Candida www dsmz de bactnom is a good site for current bacterial nomenclature You can also link to this site through Biolog s web page www cbs knaw nl is a good site for current yeast and filamentous fungi nomenclature and information Remember you can always call Biolog Technical Services with any identification questions Our lab is interested in your quality control and validation procedures Where do we get this information Refer to the package insert and call Biolog Technical Services Request our Validation Package information Material Safety Data Sheets Quality Control organism information and Certificates of Performance OmniLog System User Guide Section 11 X Page 3 25 Jun 06 Troubleshooting 12 Troubleshooting In this section Carefully following the instructions in this guide will greatly minimize Gram Stain problems Occasionally however you may get stuck or encounter Identification difficulties This section addresses the symptoms causes and gt Culturing solutions to those occasional problems If you still can t figure out the oe ore cause of the problem call Biolog Technical Service We re always 2 Preparing Inocula glad to help 2 Inoculating MicroPlates gt Incubating MicroPlates gt OmniLog Incubator Reader Additional help can be found on Biolog s website at www biolog com
150. s GP ROD C Y BUG B 6 5 C02 35 37 3 Actinomyces hordeovulneris GP ROD C Y BUG B 6 5 C02 35 37 4 Actinomyces hyovaginalis GP ROD C W Y BUG B 6 5 CO2 35 37 5 Actinomyces naeslundii GP ROD C W Y BUG B 6 5 CO2 35 37 6 Actinomyces neuii ss anitratus GP ROD C Y BUG B 6 5 C02 35 37 7 Actinomyces neuii ss neuii GP ROD C Y BUG B 6 5 CO2 35 37 8 Actinomyces odontolyticus GP ROD C Y BUG B 6 5 CO2 35 37 9 Actinomyces radingae turicensis CDC E GP ROD C Y BUG B 6 5 CO2 35 37 10 Actinomyces viscosus GP ROD C Y BUG B 6 5 C02 35 37 11 Aerococcus christensenii GP COCCUS C Y BUG B 6 5 C02 35 37 12 Aerococcus urinae GP COCCUS C Y BUG B 6 5 CO2 35 37 13 Aerococcus viridans GP COCCUS C Y BUG B 6 5 CO2 35 37 14 Alloiococcus otitis GP COCCUS C W Y BUG B 6 5 CO2 35 37 15 Arcanobacterium bernardiae CDC 2 GP ROD C Y BUG B 6 5 CO2 35 37 16 Arcanobacterium haemolyticum GP ROD C Y BUG B 6 5 CO2 35 37 17 Arcanobacterium pyogenes GP ROD C Y BUG B 6 5 CO2 35 37 18 Arthrobacter cumminsii GP ROD C Y BUG B Air 30 19 Arthrobacter histidinolovorans GP ROD C Y BUG B Air 30 20 Arthrobacter ilicis GP ROD C Y BUG B Air 30 21 Arthrobacter woluwensis GP ROD C Y BUG B Air 30 22 Aureobacterium resistens GP ROD C Y BUG B Air 35 37 23 Bacillus alcalophilus GP RODSB C W N BUG M Air 30 24 Bacillus amyloliquefaciens GP RODSB C W N BUG M Air 30 25 Bacillus anthracis subgroup A GP RODSB C W N BUG M Air 30 26 Bacillus anthracis subgroup B GP RODSB C W
151. shows lt to indicate a mismatch where the database reaction is negative If you have a negative read with no brackets and database value for that well is positive the well will read indicating a positive reaction in the database At the time of a read the data is compared to the database to determine the ID The Read window gives the first ID choice for each microbe To see the top 10 choices for an ID click any row on the Read window The first four choices will show in the lower section of the Results window Scroll down to view all 10 If the answer to the following three questions is yes you can feel confident that ID 1 is accurate e Are the top ranked ID choices on the list all the same or closely related genera e Check the SIM similarity index value rating of ID 1 Is it 0 90 or above at 4 6 hours Is it 0 50 or above at 16 22 hours e Check the DIST distance rating of ID 1 Is it 0 50 or less Pinning Down an Uncertain ID If the top rated choices show any of the following results you may want to do some additional probing e The top rated ID choices on the list are random and unrelated genera e SIM is near 0 50 OmniLog System User Guide Section 8 X Page 4 25 Jun 06 Interpreting Results e DIST is greater than 5 00 Understanding the language of microbe identification within 1 PROB confidence probability of a called ID SIM calling criteria value DIST equivalent nu
152. sidered positive as long as the color is noticeable when compared to the Al reference well However if you re A still unsure enter these reactions as borderline If for example you enter 4 out of 95 tests as borderline OmniLog software will ignore the 4 borderline tests and base its identification on the remaining 91 tests This will give you far more accurate results than guessing wrong about reactions you re not sure of O What should I do if I get different ID results at 4 hours and at 24 hours OmniLog System User Guide Section 11 X Page 2 25 Jun 06 Frequently Asked Questions This is most often the result of having a mixed culture See Section 4 for recommended procedures and examine your culture carefully to see if it is mixed Also consider the similarity value at one incubation time vs the other Environmental strains will often grow a little differently than the lab strains used to make the databases Some strains may have a high similarity in our 4 hour database while others match our 24 hour database more closely Compare your similarity values to see which is a better match Are there any genera where the taxonomy is still undergoing change Taxonomists have not yet agreed upon how all species should be delineated and microbiology is an ever evolving science We update and expand our software library on a continual basis but at this point there are certain genera still undergoing revision These include Bacillu
153. sm forms clumps you will need to use special accurate Did techniques to achieve a homogenous suspension See Step you calibrate 4 on p 5 9 the bracketed bullets and Section 12 for the additional information turbidimeter X ES Oe Table 5 2 will help you decide which suspension medium to use Turbidity Standards OmniLogSystemUserGuide CS ection X Page5 25 Jun 06 Preparing Samples TABLE 5 2 SELECTING THE CORRECT INOCULATING FLUID TURBIDITY STANDARDS AND CELL DENSITY Organism Type Inoculating Fluid Turbidity Standards Inoculum Density Gram Negative Non Enteric GN GP IF GN NENT 52 T Gram Negative Enteric GN GP IF T GN ENT 61 T Gram Negative Fastidious GN GP IF T GP COC amp GP ROD 20 T amp GN FAS Gram Positive Cocci GN GP IF T GP COC amp GP ROD 20 T Gram Positive Rods non spore Sone forming Gram Positive Rods spore forming GN GP IF GP ROD SB 28 T bacillus Adding thioglycolate to inoculating fluid Some microbes see Table 5 2 require the addition of thioglycolate T to the inoculum Thioglycolate acts as an anticapsulate agent it decreases production of bacterial capsules so that strains give more consistent patterns Biolog s product line includes droppers of thioglycollate To add thioglycolate 1 Hold reagent dropper upright and point tip away from you Using a dissecting hemostat fully crush ampule close to its center one time only Tap the bottom on benchtop a few t
154. ssages However there are three general situations when the cells will change color and contain warning or error messages as follows OmniLog System User Guide Section X Page 13 25 Jun 06 Notice Messages Introducing the OmniLog ID System Notice message alert to OmniLog status but they do not require immediate action or necessarily mean the incubator reader is not operating normally Notice messages include Cell Message Color What To Do Door status Close Door Yellow Close the OmniLog door Green Plate Status X Plates Done Red Yellow It is time to remove X number of MicroPlates Temperature Not at Target Red Yellow If this occurs when there are no MicroPlates are Status Temperature in the incubator reader be sure to change or set temperature when the OmniLog is empty Wait until the incubator reader is at the new temperature this usually takes less than 2 hours before loading new plates Error Message Com Not Open Red Yellow During normal use keep the Com port open the Reader Not incubator reader initialized and the cycle mode Initialized on During system verification testing see Cycle Off Chapter 13 these error messages may occur Reader Busy Messages Reader Busy messages caution you not to take certain actions because the incubator reader is reading or about to read They include Cell Message Color What To Do Minutes Until 5 minutes OR Red Yellow Do NOT use the software while
155. t the back of the incubator reader Write down the message and call Biolog Technical Services If there is more than a 2 C difference between the temperature you set and the actual temperature of the incubator reader this message will appear This message will appear whenever you reset the temperature and remain in place until the temperature range has been reached The Not at Temp light at the front of the instrument will also illuminate until the temperature range has been reached Section 12 X Page 6 Symptom Cause Troubleshooting Solution Interrupt On light at front of incubator reader goes on You have tried to open the door while the camera assembly is moving OmniLog System User Guide 25 Jun 06 Shut the door immediately The incubator reader will reset To avoid making this error again keep an eye on the footer bar for the message Incubator reader Moving When this message shows do NOT open the door Section 12 X Page 7 System Verification 13 System Verification In this section Read Verification gt Checking the Error Logs gt Using Test Read gt Using Test Cycle 2 Field Service Tests gt Relocating the OmniLog OmniLog ID has built in utilities for testing the accuracy of readings and the functioning of the system These utilities include Read Verification is the incubator reader working correctly Error Logs what exactly is ha
156. te termination of this Agreement No copying or transmission of the Software is permitted LIMITED WARRANTY For one year after the date of the invoice from Seller Seller will either at its sole discretion repair or replace any product covered by such invoice purchased by you from Seller or Seller s authorized distributor which in Seller s judgment is defective in materials or workmanship or refund the amount paid by you for such product If the product is dated as to shelf life this limited warranty shall in no event extend beyond such shelf life In the case of third party computer operating system software this limited warranty shall extend only for thirty 30 days after the date of invoice and shall entitle you only to an exchange with no right to a refund This limited warranty does not cover a computer applications software which is governed by the Biolog Inc Software License Agreement b consumable or disposable items not dated by Seller as to shelf life including without limitation lamp assemblies bulbs fuses and batteries or c damage caused by batteries probes or electrodes This limited warranty does not apply to any product that has been misused neglected modified or repaired by anyone other than an authorized service facility or to any product requiring refrigeration or other special handling that is not properly refrigerated or so handled All warranty registration cards included with the products must be comp
157. ted the Site The Software shall include all related materials and documentation provided by Licensor The Software shall be used only in the conduct of Licensee s own business and Licensee shall not permit any third party to use the Software Licensee shall make available implementation computer equipment and software configurations approved by Licensor as adequate for implementation of the Software Ownership The Software and all modifications thereto and all copies thereof are proprietary to Licensor and title thereto remains in Licensor All applicable rights to patents copyrights know how trademarks and trade secrets in the Software and any modifications made thereto are and shall remain in Licensor Licensee shall not sell transfer publish disclose display or otherwise make available the Software or copies thereof to others Licensee agrees to secure and protect each module software product and related documentation in a manner consistent with the maintenance of Licensor s rights therein and to take appropriate actions by instruction or agreement with its employees or consultants who are permitted access to the Software to satisfy its obligations hereunder Any copies made by Licensee of the Software and other programs developed hereunder including translations compilations partial copies with modifications and updated works are the property of Licensor Violation of any provision of this paragraph shall be the basis for immedia
158. tes are read 12 times during the 16 to 22 hour incubation time window The first 1 and twelfth 12 reading are saved as separate files If an ID is called the reading is saved to file and the ID Report is printed The system keeps the MicroPlate as a pending read continuing to save all four 4 files until the last reading at 22 hours is taken This mode is useful for building a full progressive user database MicroPlates are read 4 times during the 4 to 6 hour incubation time window with readings occurring every half clock hour Four 4 reading are saved as separate files Then the MicroPlates are read 12 times during the 16 to 22 hour incubation time window Twelve 12 reading are saved as separate files If an ID is called the reading is saved to file and the ID Report is printed The system keeps the MicroPlate as a pending read continuing to save all sixteen 16 files until the last reading at 22 hours is taken OmniLog System User Guide Section6 X Page 5 25 Jun 06 Loading and Reading MicroPlates Choosing a Database to Search OmniLog software allows you to select which database you want to search If you have created User custom databases you can search the OmniLog databases the User database or both For information on creating a User database see RetroSpect Trending and Tracking Software OmniLog ID Jun 28 2006 Jun 28 2006 3 47 PM Biolog User Biolog User DATABASE WINDOW TO SELECT DATABASE TO SEA
159. to the reference organism in the database Match is a measure of how good of an absolute match the data is to the choices selected in the database The smaller the DIST the greater the match Separation is the difference in distance between the first choice and all of the other choices These two values are then multiplied together to get a final net ID score That final number is called SIM in the MicroLog and OmniLog systems OmniLog System User Guide 25 Jun 06 Section 8 X Page 3 Interpreting Results The match score itself constantly decreases with increasing distance The value for separation by itself is shown as PROB when an ID is called If the fist choice and the second choice were the exact same distance from the entered data then the PROB would be 0 5 The true separation PROB takes into account the other matches If the first three choices all had the same distance the PROB for all three would be 0 3333 and so on As the differences in the distances gets larger the PROB goes up At a difference in distances of 1 0 the PROB is 0 950 At a difference in differences of 2 0 the PROB is 0 997 If a well result does not match the result in the database for the organism in question plus minus mismatch indicators are visible on the screen and on the printout for the original read for that well If the read is positive on the MicroPlate lt gt and the database result for that well is negative the printout
160. tor can re enable Restricted Access Mode at a later time In addition the Administrator may select a destination directory other than the default for the Log In Log Save and Close Warning Only One Valid Administrator Restricted Access Mode Default is Restricted Access Mode check in the box Click on the checkbox to change the mode Destination Directory for LogIn Log files Shows the default directory where Log In Logs Archive files are saved Select the desired directory to place in the computer network location of your choosing You should select a secure location for example in a secure server or a password protected file folder Password Expiration Period Use the pull down menu to select either Three Months or One Minute The default is three months This requires all users to select new passwords after 3 months Select one minute to expedite validation testing only Time Out Period Use the pull down menu to select either Fifteen Minutes or 10 seconds The default is fifteen minutes Select 10 seconds to expedite validation testing only Creating a User List OmniLog System User Guide 25 Jun 06 Adding new users and Assigning Privileges On the Welcome window click the Administration selection bar and enter the Administrator username password The Log In Log will appear showing the history of program use Note Once the administrator adds a new user name to the user list that name can never be deleted or
161. using proper techniques read MicroPlates in batches prepare worksheets to organize information build your own database and analyze data using the advanced functions built into OmniLog ID software OmniLog System User Guide Section 1 X Page 4 25 Jun 06 Before you use the OmniLog software you must establish an ADMINISTRATOR user name and password Please see Section 2 Installation and Administration Introducing the OmniLog ID System The OmniLog ID ID Identification program operates the OmniLog Incubator Reader and identifies microbes Use of the RetroSpect Trending and Tracking Software program allows the user to edit compile manage and export the data created in the OmniLog ID program The ID program is structured to move automatically through the incubation and identification process Navigational tools include tabs to move from window to window drop down lists to choose from pre set choices selection bars and fields to type in specific data OmniLog ID performs the following functions e Guides you through loading and reading MicroPlates using worksheets e Guides you through unloading all or some MicroPlates when reading is complete e Identifies microbes and allows you to interpret results User Functions Logging In When the system is operating in Restricted Access mode all users must log in when attempting to perform certain functions When a User Logs on to the program for the first time he or sh
162. uttons Save 1x96 Save JPEG Save 8x12 Save BMP xanugggyaNEE m B S Save picture Target row appears here Move camera buttons Read TOW buttons READ VERIFICATION MENU WINDOW NO PLATES Note The camera will normally park at the home position of row Yo O A 25 The current parked location of the camera is listed in the lower right of the window Target Row Move the camera by scrolling the Remember number in the box to the left of the target row up and down Then click Row 1 is at the on To Row in the Move box You can also move the camera one row bottom of the up or down from the current row by clicking Next Up or Next Down in incubato i a the Move box reader row 25 is at the top 6 Select the desired test It is best to perform the same test for both MicroPlates in a row For each of the two MicroPlates click the desired item in Test Mode Note You can change the test mode after a reading 7 Place MicroPlates correctly depending on the test you re running as follows For the No Tray test remove the tray from the desired row For the No Plate test have a tray with no MicroPlates in the desired row For the All Zero Value Plate and All Positive Plate tests have all zero or all positive MicroPlates as described in the OmniLog Verification Kit instructions in the desired row and position 8 With the target row set to the c
163. y rolling the swab over the colonies rather than sliding across them Be sure not to pick up any agar 3 Twirl the swab against the inside surface of the tube above the fluid line to gently suspend the colonies 4 Dip the swab into the fluid and stir with a up down motion to the bottom of the tube to create a uniform suspension You can also use a sterile transfer pipet to mix without creating an aerosol Recap the tube and invert if using our GN GP IF 5 Adjust the inoculum density so it is within the specified turbidity range You can change the density by adding more cells to increase density or more inoculating fluid to lower density 6 Examine your suspension and make certain that it is homogeneous and free of clumps It is essential that the cell suspension does not contain clumps If there are only a few clumps allow them to settle to the bottom pouring off the supernatant If the bacterial suspension is not homogenous use the special procedures described in Step 4 on page 5 8 5 9 and in Section 12 Special Procedures for Spore Forming Gram Positive Rods Bacillus species are known for being difficult They start to sporulate within a matter of minutes of introduction to a growth limiting medium They also tend to form clumps crusts and pellicles skin like sheets when they grow on an agar surface making it difficult to prepare uniform cell suspensions Always use the following special swabbing and streaking te
164. ystem the footer bar will show only a Video Error Once you ve cleared the cause of that error the footer bar will show Plate Error Table 13 1 shows the types of error message you might receive TABLE 13 1 ERROR MESSAGE TYPES Error Type Problem This Error Could Cause Hardware Incubator reader may jam Video A problem reading a MicroPlate Temperature Incubating temperature may have spiked or dropped Plate Plate may be missing or left in the incubator reader 1 From the Welcome window click Reader Setup 2 Inthe Error Logs area click the error type you wish to view as listed in the footer bar warning HARDWARE ERRORS WINDOW 3 You can view or manipulate the list as follows Click Go to Start to see a description of the first error Click Page Up to see a description of the previous error Click Page Down to see a description of the next error Click Print to print the error list Click Zero File to delete the list need Edit privilege 4 Click Done The software will return to the Reader Setup window OmniLog System User Guide Section 13 X Page 4 25 Jun 06 System Verification 5 Click Done The software will return to the Welcome window Additional Footer Bar Notices Notice Meaning Restart Notice Power was interrupted to the unit Restart of Unit performed Service Warning Contact Tech Services unit may need routine preventative maintenance View and clear Notices by fol

User Guide - Ecologie Microbienne Lyon

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