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Article

Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines

Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Author to whom correspondence should be addressed.
Academic Editor: John R. Perfect
J. Fungi 2021, 7(3), 214; https://doi.org/10.3390/jof7030214
Received: 10 February 2021 / Revised: 4 March 2021 / Accepted: 11 March 2021 / Published: 16 March 2021
(This article belongs to the Special Issue Candida auris 2.0)
Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations. View Full-Text
Keywords: Candida auris; emerging fungal diseases; drug-resistant fungi; genomic; whole-genome sequencing WGS Candida auris; emerging fungal diseases; drug-resistant fungi; genomic; whole-genome sequencing WGS
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MDPI and ACS Style

Welsh, R.M.; Misas, E.; Forsberg, K.; Lyman, M.; Chow, N.A. Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines. J. Fungi 2021, 7, 214. https://doi.org/10.3390/jof7030214

AMA Style

Welsh RM, Misas E, Forsberg K, Lyman M, Chow NA. Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines. Journal of Fungi. 2021; 7(3):214. https://doi.org/10.3390/jof7030214

Chicago/Turabian Style

Welsh, Rory M., Elizabeth Misas, Kaitlin Forsberg, Meghan Lyman, and Nancy A. Chow 2021. "Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines" Journal of Fungi 7, no. 3: 214. https://doi.org/10.3390/jof7030214

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