Microbiology
What this domain tests
Microbiology tests preanalytical choices, stain and culture interpretation, organism identification, and antimicrobial susceptibility reporting - with heavy emphasis on pathogen versus contaminant and on using current breakpoints.
Specimen and direct examination
- Sputum acceptability by the Murray–Washington criteria: 10 or fewer squamous epithelial cells and 25 or more polymorphonuclear cells per low-power field.
- CSF is never refrigerated; fastidious genital and rectal organisms also die with cold. Blood cultures: two to three sets, 20–30 mL total adult volume, because volume is the single biggest sensitivity factor.
- Coagulase-negative staphylococcus growing in one of four bottles usually represents skin contamination, not bacteremia.
- Gram stain is reported as observed: Gram reaction, shape, arrangement, plus accompanying cells.
Identification and susceptibility testing
- MALDI-TOF identifies colonies rapidly; biochemical panels and molecular methods (16S sequencing, NAAT) cover slow or fastidious organisms.
- MIC results from broth microdilution, Etest, or gradient strips are interpreted with current CLSI breakpoints, which are organism-, site-, and year-specific.
- Special tests: D-test for inducible clindamycin resistance in Staphylococcus aureus, ESBL confirmation, carbapenemase detection, cefoxitin screening for MRSA, and vancomycin resistance screening for enterococci.
Worked example
Escherichia coli from a urine culture with a ceftriaxone MIC of 2 µg/mL. Current CLSI Enterobacterales breakpoints are S ≤1, I 2, R ≥4, so the result is intermediate. Reasoning: report intermediate, note that higher-dose regimens apply only to specific high-exposure sites, and perform ESBL testing. A laboratory still using an obsolete breakpoint such as S ≤8 would call this susceptible and mislead therapy. Annual breakpoint review is part of the quality system.
Traps that cost marks
- Reporting with outdated breakpoints.
- Calling a single contaminated blood culture bottle a true bacteremia.
- Refrigerating CSF or genital specimens.
- Treating a preliminary Gram stain as a final result.
- Interpreting an MIC without the specimen source and the organism.