Diagnostic Process Flashcards
What are the steps in the diagnostic process?
- patient assessment
- pre-analytical
- analytical
- post-analytical
- Diagnosis!
What is the patient assessment?
- problem oriented approach
- integration of history
- presentation
- physical exam findings & lab data
- Is an infectious process ongoing? list of differentials?
What is pre-analytical?
- specimens selected & collected
- laboratory provided w/ all relevant info
- samples shipped to lab
- lab accessions samples & selects appropriate tests
What is analytical?
- direct examination of specimen
- preliminary report
- sample processing
- primary set of results (ex: culture) recorded
- secondary tests selected & conducted
What is post analytical?
- final lab results & report by diagnostician
- interpretation of report by veterinarian
What are the principles of sampling?
- obtain sample from site of infection, minimizing contamination (culture margins of an abscess where viable organisms are more likely to be present (middle filled w/ WBCs that are producing toxic free radicals); collect urine via cystocentesis rather than “free-catch” urine)
- collect sample at correct time (when is your suspected pathogen likely to be shed?)
- collect sufficient (but not excessive) quantity of sample (consider tests you’re requesting, how much sample is needed? can excess samples be stored w/o loss of integrity? CONSULT W/ THE LAB!)
- use an appropriate collection device (sample must be sterile; use containers/devices designed for sampling; make sure you have the correct device for the test - some products include inhibitory substances that may interfere w/ analysis; garbage in = garbage out!)
- handle/store samples appropriately (can sample be frozen; special transport media required?)
- obtain cultures before administering antibiotics (collect sample then treat (if possible); if samples are collected post-antibiotic, how will you interpret a negative test?)
- make smears in addition to cultures (cheap & quick adjunctive test to be done in-house; STRONGLY encouraged to do Gram stains)
- labelling is key! (unique & unambiguous labelling of sample; fill out sample requisition form as completely as possible)
- dont put yourself or others in danger (warn about suspected zoonoses & dont request dangerous tests)
How should samples not be collected?
ziploc bag, knotted glove
- hazardous for lab workers, accessing sample using a sterile technique is difficult, easy to contaminate workspace
Why should you not recap needles?
- needlestick injuries are common
- consequences are relatively rare, but serious tendon sheath infections (some resulting in finger amputations) have been reported
Sharp safety tips:
- if recapping is necessary, use 1 hand scoop method, or use forceps to hold cap
- dispose of needles in sharps after use
- make sharps containers widely available
- only use correct sharps containers
- dont overfill containers
- consider safe alternatives (ex: hinged syringe caps)
- dont walk around w/ needles
What is the lab going to look for, & what method is required to detect the target?
- bacteria - culture
- parasite related structures - microscopy
- DNA/RNA - PCR
- Ab or Ag - ELISA
- tissue structures - histological exam
- differential cell counts (blood)
- biochemical analysis (blood, urine)
To freeze or NOT to freeze?
- CHECK WITH THE LAB
- generally, for bacteriological/mycological culture - dont freeze, & for non-propagative tests - freezing is possible
- there are organism/sample specific exceptions: can freeze milk (cryoprotective), can freeze samples to be tested for L. monocytogenes
What should you do if you’re working-up a case for a disease that you’re not experienced w/ & you arent sure about the best diagnostic strategy?
- contact the lab for help
- they should be able to walk you through their test catalogue & give advice on which assay answers your question
How do you ship samples safely?
- shipping regulations depend on what you are sending
- this is YOUR responsibility!
- check w/ shipper/lab for more info
- general principles: watertight primary container, absorbent material, watertight secondary container, sturdy outer packaging
How does sample processing occur at the lab?
- sample received -> sample processed in biosafety cabinet -> (sample smears made & stained -> preliminary report (ex: Gram (-) rods seen in urine sample)) -> incubation 18-24hrs -> any bacteria grown are identified -> antimicrobial susceptibility testing (AST) -> AST incubated 18-24 hrs -> final report (ex: etiological diagnosis & susceptibility test results)
What is susceptibility testing?
- ultimate goal of diagnostic microbiology is therapeutic guidance
- there are a wide variety of antimicrobials available (lab can help you determine which is most appropriate; antimicrobial susceptibility testing provides CRITICAL information)
What is susceptible vs resistant?
- susceptibility report describes bacteria isolated through the lens of the patient
- susceptible: if an organism is susceptible to drug X, there is a high likelihood of clinical success when drug X is used according to label indication
- resistant: if an organism is resistant to drug X, clinical failure is predicted when drug X is used according to the label indication
What is resistance from the bug’s perspective?
- resistance can be subdivided into intrinsic & acquired
- intrinsic resistance is constitutive: naturally resistant to drug that isnt acquired, it’s a
feature of that bacterial species - acquired resistance is not inherent to the organism (these are the ‘superbugs’, they have a gene or mutation which differentiates them from the wild-type; this is the resistance we’re concerned w/ - it’s the emerging problem)
Describe intrinsic resistance in the SPICE organisms:
- SPICE (Serratia, Providentia, Indole positive Proteae (includes Proteus vulgaris & Morganella spp), Citrobacter, Enterobacter)
- produce AmpC B-lactamases (can become de-repressed (over-produced) w/ therapy)
- intrinsic resistance to B-lactams
- intrinsic 3rd generation cephalosporin resistance
- in veterinary context, recommended to avoid all B-lactams
What are susceptibility test methods?
- categorical methods (only tells you whether an organism is susceptible or not)
- quantitative methods (yields MIC (minimum inhibitory concentration) which describes exactly how susceptible or resistant an organism is: MIC is the lowest concentration of a drug inhibiting bacterial growth; by convention, MIC is reported as a number on a doubling scale (0.12 micrograms/ml, 0.25 micrograms/ml, 0.5 micrograms/ml, 1 microgram/ml, 2 micrograms/ml)
What is a categorical diffusion test?
Kirby-Bauer Disc Test
What is a categorical dilution test?
there isnt one
What is a quantitative diffusion?
Gradient strips (E-test)
What is a quantitative dilution?
- agar dilution or broth dilution
What is Kirby-Bauer disc testing?
antibiotic discs, measure around disc to measure resistance
What is a broth micro-dilution?
- 96 well plates w/ free-dried abx in each
- can figure out the lowest concentration necessary to inhibit growth
BIG PIC: Why should you not recap needles used in clinic/lab?
so you dont poke yourself. this is a good way to get an infection from a low level organism
BIG PIC: What is the difference btwn intrinsic and acquired resistance?
intrinsic is something normal, it is a feature of that group of organisms, acquired means the organism has gained a feature that it didnt previously have whether via a mutation or gaining a plasmid
What are SPICE organisms, & why is it important that you are aware of them?
They are resistant to B-lactams
