Whole Genome Sequencing with FungiNet
Updated September 30, 2022
What is FungiNet?
FungiNet is a network for molecular surveillance and genomic epidemiology for fungal diseases.
FungiNet was launched in 2021 in partnership with the Antibiotic Resistance Laboratory Network, which supports nationwide laboratory capacity to rapidly detect, prevent, and respond to drug resistance.
The gold standard method for FungiNet is whole genome sequencing (WGS).
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” and the information generated from this process is the “genomic data.” WGS is a laboratory procedure that determines the order of bases in the genome of an organism in one process. CDC generates genomic data using WGS for a variety of fungal pathogens.
Learn more about how whole genome sequencing works and is used to prevent the spread of foodborne, waterborne, and environmental diseases.
Why is generating genomic data for fungal diseases important?
Fungal genomic data provide public health professionals with information that can help them:1, 2
- Monitor, detect, and prevent the spread of fungal pathogens.
- Trace how fungal pathogens move through populations in certain outbreak
- Understand how people became exposed to fungal pathogens.
- Learn how fungal pathogens are geographically distributed.
Current fungal diseases supported by FungiNet
Many types of fungi cause disease. FungiNet focuses on Candida auris (C. auris). C. auris is an emerging fungus that presents a serious public health threat.3 FungiNet supports the generation and analysis of C. auris genomic data to:
- Help monitor circulating strains and clades.
- Supplement control efforts (i.e., help identify new introductions and ongoing or undetected transmission).
- Learn more about mechanisms of antifungal resistance.
In the future, FungiNet will expand to include other fungal pathogens.
Access to FungiNet Sequence Data
WGS produces large amounts of data. FungiNet participants produce and submit WGS data to the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA), a publicly accessible database. Public access provides the scientific community with up-to-date and comprehensive information that may be used for public health action.
- Oltean HN, Etienne KA, Roe CC, Gade L, McCotter OZ, Engelthaler DM, Litvintseva AP. 2019. Utility of Whole-Genome Sequencing to Ascertain Locally Acquired Cases of Coccidioidomycosis, Washington, USA. Emerg Infect Dis 25:501-506.
- Cuomo CA. 2017. Harnessing Whole Genome Sequencing in Medical Mycology. Curr Fungal Infect Rep 11:52-59.
- Chow NA, Gade L, Tsay SV, Forsberg K, Greenko JA, Southwick KL, Barrett PM, Kerins JL, Lockhart SR, Chiller TM, Litvintseva AP, Team USCaI. 2018. Multiple Introductions and Subsequent Transmission of Multidrug-resistant Candida auris in the USA: A Molecular Epidemiological Survey. Lancet Infect Dis 18:1377-1384.