Table 2.

Laboratory diagnostics.

Diagnostic method	Sample types	Notes
Fungal microscopy	Sputum, BAL fluid, tissue, bone marrow	•Varying sensitivity dependent on quantity of fungus in sample and experience of microscopist •Use of calcofluor staining enhances detection, or giemsa-staining of bone-marrow for Histoplasma
Fungal culture	Sputum, BAL fluid, tissue, blood, bone marrow	•Gives definitive diagnosis •Fungal growth can be very slow, 4 weeks in some cases; Coccidioides is faster, growing in a few days
Antibody detection	Serum	•Antibody development may take weeks •Less useful in early infection or in the immunocompromised •Cross-reactivity of antibodies reduces specificity
Antigen detection	Serum, BAL fluid, urine	•Beta-D glucan – a non-specific fungal biomarker, may be raised in Coccidioides, Histoplasma, Talaromyces and Paracoccidioides infections, less useful with Blastomyces, which produces lower levels •Antigen testing (including urinary) is available for Blastomyces and Histoplasma •An assay for Talaromyces is in use in China
NAAT	BAL fluid, tissue	•Pan-fungal PCR may be useful •Specific PCR tests are currently more limited to research

BAL = bronchoalveolar lavage, NAAT = nucleic acid amplification test, PCR = polymerase chain reaction.