Current Fungal Infection Reports

, Volume 11, Issue 2, pp 52–59

Harnessing Whole Genome Sequencing in Medical Mycology

Advances in Diagnosis of Invasive Fungal Infections (S Chen, Section Editor)

DOI: 10.1007/s12281-017-0276-7

Cite this article as:
Cuomo, C.A. Curr Fungal Infect Rep (2017) 11: 52. doi:10.1007/s12281-017-0276-7
Part of the following topical collections:
  1. Topical Collection on Advances in Diagnosis of Invasive Fungal Infections


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.


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.


Whole genome sequencing Human fungal pathogens Genome sequencing Medical mycology Fungal infections Review 

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Infectious Disease and Microbiome ProgramBroad Institute of MIT and HarvardCambridgeUSA

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