Whole Genome Sequencing and Fungal Disease Outbreaks

Updated July 27, 2020

CDC uses whole genome sequencing (WGS) to help solve fungal disease outbreaks and learn more about how they make people sick. Whole genome sequencing provides detailed genetic information about fungi and other germs that cause illness.

We use whole genome sequencing to:1-2

  • Monitor, detect, and prevent the spread of disease-causing fungi
  • Understand how people became exposed to fungi that made them sick
  • Learn how disease-causing fungi are geographically distributed
  • Help find the source of outbreaks and trace how disease-causing fungi move through populations in certain outbreaks
  • Determine how disease-causing fungi evolve during an infection

Using whole genome sequencing to solve outbreaks of Candida auris infections
Candida auris is an emerging fungus that presents a serious global health threat. CDC uses whole genome sequencing to help solve C. auris disease outbreaks by:

  • Tracking cases and the spread of C. auris
  • Identifying clades (strains) of C. auris from different regions of the world

What is whole genome sequencing?
The genome, or genetic material, of an organism (e.g., bacteria, virus, fungi, or human) is made up of DNA. Each organism has a unique DNA sequence, which is composed of bases (A, T, C, and G). If you know the sequence of the bases in an organism, you have identified its unique DNA fingerprint, or pattern. Determining the order of bases is called sequencing. Whole genome sequencing is a laboratory procedure that determines the order of bases in the genome of an organism in one process.

A woman analyzing whole genome sequencing data on a computer screen

Analyzing whole genome sequencing data

Learn more about how whole genome sequencing works and is used to prevent the spread of foodborne, waterborne, and environmental diseases.

Storing whole genome sequencing data
The use of whole genome sequencing produces large amounts of data. These data can be stored in NCBI’s Sequence Read Archiveexternal icon, which is a publicly accessible database. As more fungal genomes are analyzed and their data become publicly available, they can serve as reference genomes during other investigations. Public access provides the scientific community the most up to date and comprehensive DNA sequence information to aid outbreak investigations.

  1. 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, USAexternal icon. Emerg Infect Dis. 2019 Mar.
  2. Cuomo CA. Harnessing Whole Genome Sequencing in Medical Mycologyexternal icon. Curr Fungal Infect Rep. 2017 Jun 9.
  3. Litvintseva AP, Hurst S, Gade L, Frace MA, Hilsabeck R, Schupp JM, Gillece JD, et al. Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections.external icon J Clin Microbiol. 2014 Sep.
  4. Chow NA, Gade L, Tsay SV, Forsberg K, Greenko JA, Southwick KL, Barrett PM, et al. Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey.external icon Lancet Infect Dis. 2018 Dec.