Detection and Characterization Methods
Core concepts
Know the culture-based approach (isolation, identification, susceptibility) and its limitations (fastidious or unculturable agents). Know direct detection methods: Gram stain, antigen tests (latex agglutination, EIA, immunochromatographic), and molecular methods (PCR, real-time PCR, multiplex panels, sequencing, whole-genome sequencing). Understand serology (antibody vs antigen detection, window period, cross-reactivity).
Know organism-specific considerations: bacteria (culture plus susceptibility), mycobacteria (AFB smear, culture on LJ/MGIT, NAAT), fungi (culture, antigen - galactomannan, beta-D-glucan, cryptococcal antigen - and molecular), parasites (microscopy, antigen, PCR), and viruses (NAAT, antigen, serology, viral load). Understand MALDI-TOF for rapid identification and next-generation sequencing for outbreak and resistance detection.
Traps to expect
- Assuming a negative culture rules out infection - prior antibiotics, fastidious organisms, and low burden matter.
- Confusing antigen with antibody detection and their timing.
- Overlooking that NAAT does not distinguish live from dead organisms.
- Forgetting that galactomannan is a marker for invasive aspergillosis, while beta-D-glucan is broader (many fungi, not Cryptococcus or Mucorales).
Worked example / rule of thumb
A neutropenic patient has fever and pulmonary nodules; serum galactomannan is positive. Rule of thumb: galactomannan supports invasive aspergillosis; combine with imaging and culture. Beta-D-glucan is broader but negative in Cryptococcus and Mucorales, so don't use it to exclude those.