Microbiology and Parasitology: specimen logic and endemic infections
Microbiology and Parasitology tests the organism, the host response, and the diagnostic or preventive step that follows. PLE items favor endemic Philippine infections, specimen selection, and interpretation of smears and serology.
Core rules
- Gram stain: thick peptidoglycan retains crystal violet in gram-positive bacteria; lipid A endotoxin sits in the gram-negative outer membrane.
- Culture clues: MacConkey lactose fermenters appear pink; Salmonella and Shigella are non-lactose fermenters. Tuberculosis requires Lowenstein-Jensen or liquid culture; AFB smear lacks sensitivity.
- Parasite diagnosis: thick smear detects malaria parasites, thin smear identifies species; Kato-Katz quantifies soil-transmitted helminths; stool concentration is used for Schistosoma japonicum, while urine filtration applies to S. haematobium, not the Philippine species.
- Dengue: NS1 antigen is useful early; IgM becomes useful later. Leptospirosis follows floodwater exposure and is confirmed by MAT or PCR.
Worked example
A 35-year-old rice farmer develops fever five days after wading in floodwater, with calf pain, conjunctival suffusion, jaundice, and rising creatinine. The exposure and conjunctival suffusion point to leptospirosis; jaundice and acute kidney injury fit severe disease. Dengue is less likely because conjunctival suffusion is atypical and jaundice with AKI suggests leptospiral hepatorenal involvement. Do not wait for convalescent serology to start treatment when the clinical picture is strong.
Traps
A negative AFB smear does not exclude tuberculosis. Distinguish specimen contamination from true infection. Early leptospiral serology may be negative, so timing matters. Do not diagnose malaria on a single thick smear without considering parasite density and treatment response.