Next-Generation Sequencing in the Mycology Lab

New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.     

Harnessing Whole Genome Sequencing in Medical Mycology

Purpose of Review

Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens.

Recent Findings

Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host.

Summary

Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

     

Medical Mycology for the Hospital Epidemiologist

Healthcare-associated invasive fungal infections are increasing and are a cause of significant patient morbidity and mortality. Nosocomial infections due to Candida species, followed by Aspergillus species, are the most common causes of these infections in hospitalized patients. Hospital epidemiologists and infection control practitioners must recognize that similar to bacterial pathogens, fungal infections can be the cause of hospital outbreaks, and issues of resistance are increasing. Efforts to best identify patients at risk for developing fungal infections or those at risk of having a resistant organism are ongoing. Better diagnostics and tools to aid prevention are needed in addition to usual infection prevention and control standards.