Whole Genome Sequencing

At a glance

  • FungiNet is a global community of practice advancing fungal pathogen genomics to improve outbreak responses and surveillance.
  • Activities include expanding fungal whole genome sequencing, developing data analytic tools, and contributing genomic data to a public database.
  • Public health collaborators can learn how to participate by emailing
Microscopic images of candida auris and aspergillus with text: FungiNet

Advancing fungal pathogen genomics

FungiNet, launched in 2021, is a global network of laboratorians, bioinformaticians, and epidemiologists advancing fungal pathogen genomics in public health.

A lab professional working on whole genome sequencing
FungiNet is working to advance fungal pathogen genomics.

The FungiNet community of practice shares resources to help public health officials:

  • Detect fungal disease outbreaks earlier.
  • Investigate outbreaks more effectively.
  • Track the spread of antimicrobial-resistant fungal pathogens.

FungiNet Domestic includes participants from across the United States, including many collaborators with the Antimicrobial Resistance Laboratory Network.

FungiNet Global currently has participants in Colombia, South Africa, Spain, Bangladesh, and Argentina.

How to participate‎

Email to learn more and access the FungiNet channel on the communication application Slack ®

FungiNet activities

Participants generate and analyze whole genome sequencing data for Candida auris (C. auris) and other fungal pathogens. Collaborators are building capacity in laboratory and bioinformatic fungal genomic analysis by developing new tools for fungal genomic analysis.

FungiNet contributes genomic data to the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA), a publicly accessible database.

FungiNet resources

  • Oltean HN, Etienne KA, Roe CC, Gade L, McCotter OZ, Engelthaler DM, Litvintseva AP. Utility of Whole-Genome Sequencing to Ascertain Locally Acquired Cases of Coccidioidomycosis, Washington, USA. Emerg Infect Dis. 2019 Mar;25(3):501-506. doi: 10.3201/eid2503.181155. PMID: 30789132; PMCID: PMC6390764.
  • Chow NA, Gade L, Tsay SV, Forsberg K, Greenko JA, Southwick KL, Barrett PM, Kerins JL, Lockhart SR, Chiller TM, Litvintseva AP; US Candida auris Investigation Team. Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey. Lancet Infect Dis. 2018 Dec;18(12):1377-1384. doi: 10.1016/S1473-3099(18)30597-8. Epub 2018 Oct 4. PMID: 30293877; PMCID: PMC6556114.
  • Cuomo CA. Harnessing Whole Genome Sequencing in Medical Mycology. Curr Fungal Infect Rep. 2017;11(2):52-59. doi: 10.1007/s12281-017-0276-7. Epub 2017 Jun 9. PMID: 28904649; PMCID: PMC5570814.
  • Bagal UR, Phan J, Welsh RM, Misas E, Wagner D, Gade L, Litvintseva AP, Cuomo CA, Chow NA. MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. Methods Mol Biol. 2022;2517:215-228. doi: 10.1007/978-1-0716-2417-3_17. PMID: 35674957