MicroStation System, MicroLog Version 4.2 - DTU Systems Biology ...

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Assess SIM for ID #1 Gram-negative aerobes Gram-positive aerobes What Should I Do About “No Identification”? Check the on-screen + and – signs for that MicroPlate. You can use these mismatch indicators to assess what happened. Interpreting Results 1. The chart below will help you clarify your identification by using SIM and DIST values: USING SIM AND DIST TO ASSESS IDENTIFICATIONS � must be > 0.5 at 16-24 hours incubation � must be > 0.75 at 4-6 hours incubation Anaerobic microbes � must be > 0.5 at 20-24 hours incubation Yeasts � must be > 0.75 at 24 hours incubation � must be > 0.5 at 48 or 72 hours incubation Filamentous Fungi (& select yeasts) � must be ≥ 0.90 at 24 hours incubation � must be ≥ 0.70 at 48 hours incubation � must be ≥ 0.65 at 72 hours incubation � must be ≥ 0.60 at 96 hours incubation Assess SIM for top IDs If SIMs for top IDs are < the SIM required AND all belong to the same genus AND if their total is ≥ the SIM required, you can be confident that the microbe is in that genus. MicroLog will give you a genus-level ID rather than a species-level ID. 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 � Good match to both species (some are quite close) � Gram stain, colony morphology, oxidase and/or catalase tests, additional tests (see Bergey’s Manual) 2. 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. • If there 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. See Section 8. • If the mismatches are all + or all –, you may have made a testing error. Refer to Table 6-1, and see Section 10. Table 6-1 will assist you in figuring out the cause of these mismatches: MicroStation System/MicroLog User Guide Apr 07 Section 6 � Page 3
Interpreting Results Mismatch Type What It Might Mean All + (your pattern is giving fewer positive reactions than the species you’re comparing it to) All – (your pattern is giving more positive reactions than the species you’re comparing it to) Under-inoculation A1 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. Over-inoculation (especially with enterics) A1 well is underfilled Contamination (mixed culture) TABLE 6-1. ASSESSING MISMATCHES FF database Perform a visual macroscopic and microscopic assessment of your isolate compared to the first three ID ranked species. Refer to MicroLog software photo library or mycology textbooks as references. Note: The A1 well is not used as a negative control in the FF database, therefore this well may not appear colorless. FF ID Workflow 1. Read daily (at 24, 48, 72 hours) until ID is called. 2. After an ID is called, verify the first three choice macro/microscopically 3. If no ID, re-incubate the MicroPlate 4. Read at 96 hours. If an ID is called, verify the first three choices macro/microscopically 5. If no ID, launch additional investigation. Check first three choices macro/microscopically. Section 6 � Page 4 MicroStation System/MicroLog User Guide Apr 07
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MicroStation System MicroLog Versi
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LICENSE AGREEMENT Notice: This is a
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Table of Contents Section Title 1.
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10. Frequently Asked Questions…
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Welcome Section 1 � Page 2 Connec
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2. Installation and Registration In
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Installation and Registration The A
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8. E-mail the User Key File to tech
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MicroStation System/MicroLog Overvi
Page 19 and 20: Follow directions closely to obtain
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Page 29 and 30: Preparing Samples Preparing an inoc
Page 31 and 32: Preparing Samples Recognizing fasti
Page 33 and 34: Preparing Samples Media shorthand:
Page 35 and 36: Preparing Samples Don’t forget to
Page 37 and 38: Preparing Samples b. Use a sterile
Page 39 and 40: Preparing Samples aids in liquefyin
Page 41 and 42: Preparing Samples Caution! Pipet th
Page 43 and 44: Preparing Samples Special Procedure
Page 45 and 46: Preparing Samples Initial culture m
Page 47 and 48: Reading MicroPlates Set Up tab Sele
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Page 51 and 52: Reading MicroPlates 2. Enter reacti
Page 53 and 54: Reading MicroPlates Entering sample
Page 55 and 56: Reading MicroPlates Select file nam
Page 57 and 58: Reading MicroPlates Naming Workshee
Page 59 and 60: Reading MicroPlates This arrow show
Page 61 and 62: Reading MicroPlates Using Worksheet
Page 63 and 64: Reading MicroPlates 4. Click Save t
Page 65 and 66: Reading MicroPlates Wells with high
Page 67 and 68: Reading MicroPlates Exiting When yo
Page 69: Interpreting Results Understanding
Page 73 and 74: Interpreting Results What are those
Page 75 and 76: Interpreting Results NOTE: A1 value
Page 77 and 78: Interpreting Results Slide the scro
Page 79 and 80: Interpreting Results VS. CURRENT MI
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Page 83 and 84: Data Management and Compiling Datab
Page 85 and 86: Combining Data Files Data Managemen
Page 87 and 88: OK, Out, Hold, Atypical Sorting lab
Page 89 and 90: Remember! When building your own da
Page 93 and 94: DATABASE WINDOW Data Management and
Page 97 and 98: Arrow indicates selected entry Data
Page 103 and 104: Export Help Mark this choice if you
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Page 117 and 118: 9. Technical Notes In this section:
Page 119 and 120: Making Biolog Universal Growth Agar
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� � � � Technical Notes Gen
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10. Frequently Asked Questions In t
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Q A Q A Q A Frequently Asked Questi
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Troubleshooting Symptom Cause Solut
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Troubleshooting Preparing Inocula S
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Troubleshooting MicroStation Reader
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Glossary Dendrogram Cluster diagram
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Glossary Spore, fungal Sterile, fun
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Culture Media Atmosphere Temperatur
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Appendices: Notes Notes: Section 13
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Appendix 4: Database Species Lists
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Appendix 5: Program Printouts Appen
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Appendix 5: Program Printouts 1�
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Appendix 5: Program Printouts Funga
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Appendix 5: Program Printouts Print
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Appendix 6: Dangerous Pathogens (DP
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