Journal Article

Finding Candida auris in public metagenomic repositories

Litvintseva, Anastasia P., Bagal, Ujwal R., Slatkevičius, Rytis, Blumberg, Matthew, Shiryev, Sergey, Lowe, Elijah, Morgulis, Aleksandr, Agarwala, Richa, Welsh, Rory, Sexton, D. Joseph, Mario-Vasquez, Jorge E., Chow, Nancy A., Phan, John

2024

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: 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