Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines

Area of Science:

• Microbiology
• Genomics
• Public Health

Background:

• Candida auris is a multidrug-resistant fungus causing global health concerns.
• Healthcare-associated outbreaks and high antifungal resistance rates necessitate improved surveillance.
• Genomic surveillance is crucial for effective tracking and control of Candida auris.

Purpose of the Study:

• To establish a standardized benchmark dataset for validating Candida auris genomic analyses.
• To facilitate reliable comparisons of genomic data among international surveillance partners.
• To promote enhanced communication and collaboration in Candida auris surveillance networks.

Main Methods:

• Development of an empirical outbreak benchmark dataset comprising 23 Candida auris genomes.
• Inclusion of genomes from well-vetted studies with supporting epidemiological data.
• Validation of whole-genome sequencing data, phylogenetic trees, and epidemiological information.

Main Results:

• The benchmark dataset represents a polyclonal phylogeny with three distinct subclades.
• Genomic data, phylogenetic analysis, and epidemiological evidence were found to be in agreement.
• The dataset provides a standardized resource for comparing phylogenomic pipelines.

Conclusions:

• The established Candida auris benchmark set enables standardized comparisons of genomic analysis pipelines.
• This standardization is essential for ensuring mutual trust and understanding among surveillance partners.
• The dataset will ultimately foster more effective global collaborations for Candida auris control.