Finding Candida auris in public metagenomic repositories

Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative e...

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Bibliographic Details
Published in:PloS one 2024-01, Vol.19 (1), p.e0291406-e0291406
Main Authors: Mario-Vasquez, Jorge E, Bagal, Ujwal R, Lowe, Elijah, Morgulis, Aleksandr, Phan, John, Sexton, D Joseph, Shiryev, Sergey, Slatkevičius, Rytis, Welsh, Rory, Litvintseva, Anastasia P, Blumberg, Matthew, Agarwala, Richa, Chow, Nancy A
Format: Article
Language:English
Subjects:
Analysis
Antifungal Agents - therapeutic use
Biotechnology
Candida - genetics
Candida auris
Candidiasis
Candidiasis - microbiology
Computation
Datasets
Disease control
Disease transmission
Drug resistance in microorganisms
Fungi
Genomes
Genomics
Health aspects
Humans
Hypotheses
India
Metagenomics
Monitoring systems
Mortality
Multidrug resistance
Pathogens
Phylogeny
Prevention
Prospective Studies
Risk factors
Single nucleotide polymorphisms
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Summary:Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0291406