Genomics and Fungal Speciation: What Can We Expect in the Clinical Laboratory?

Fungal species concept has been evolving and different criteria have been used to define fungal species. Though molecular markers have been used to study human fungal pathogens for over 20 years, most clinical microbiology labs still rely on morphological and biochemical characters for fungal identifications. With increasing genetic and genomic information on fungal pathogens, such a practice is likely going to change. The rapid accumulation of genetic and genomic data, especially since the broad application of next generation DNA sequencing tools in the last few years, are providing unprecedented opportunities to identify signatures of fungal species, strains, and clinically important phenotypes such as antifungal drug susceptibilities. These advances will not only provide fundamental insights into fungal speciation, potentially unifying the different fungal species concepts, but also increase the sensitivity, specificity, and efficiency of clinical microbiology diagnosis.