V.2.1. Mycology
The detection of fungi at various human body site, their identification at the species level, the quantification of the fungal burden and the assessment of their in vitro susceptibility or resistance to anti-fungal drugs are collectively denoted as a mycological diagnosis in the clinical laboratory.
Conventional mycological diagnosis relies on the macroscopic and microscopic assessment of fresh and culture samples (96,97). Direct examination of fresh samples aims at recognizing characteristic features, such as fungal hyphae. Inoculation on fungal growth media, followed by a 5 to 7 days incubation yields colonies further identified at the species level using MALDI-TOF Mass Spectrometry and a specialized fungal reference spectra database (98). Additional examination and analysis can be achieved by microscopic (direct, optical, or electronic) and molecular methods.
Soluble fungal antigens can be detected in fluid samples. The most widely used are (1-3)-β-D-glucan, considered a pan-fungal cell wall marker, and galactomannan, mainly released during Aspergillus spp hyphal growth (99).