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).