Molecular Detection and Characterization of Fungal Pathogens

Abstract

The increasing use of molecular methods for the identification and epidemiological study of fungal pathogens will require accessible and reliable public databases containing comprehensive sequence data. The molecular detection of pathogenic fungi directly in clinical specimens (e.g., blood, tissue, bronchoalveolar lavage [BAL] fluid, and other body fluids) is most often accomplished through PCR-based DNA amplification using Taq polymerase, although alternative methods such as RNA detection or isothermal amplification have also been used. Even with the resolution of such technical issues, there remain several drawbacks in using BAL fluid for the diagnosis of invasive aspergillosis. First, except for in limited studies, BAL is typically performed at a late stage of clinical disease, when the patient already has pneumonia or prolonged fever of unknown origin. Second, some attempts have been made to differentiate carriage, reactivation, and infection for Pneumocystis pneumonia by calculating the ratio of Pneumocystis DNA to human DNA. Among endemic mycoses, genetic probes for culture confirmation of the most commonly encountered dimorphic systemic fungal pathogens, Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides immitis/Coccidioides posadasii, have been reported. Genotyping based on multilocus sequence typing (MLST) or microsatellite markers can help one gain insight into the genetic relatedness of fungal isolates. The current trend towards mass sequencing creates the possibility of getting more and more pieces of information on the genome of each microorganism.