Development of Candida auris microsatellite typing and its application on a global collection of isolates

Abstract

Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of healthcare facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting, therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a microsatellite typing assay for C. auris.\n\nShort tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay was highly reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis we identified five major different C. auris clusters, namely, South-America, South-Asia, Africa, East-Asia and Iran. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian clade. Comparison with WGS demonstrated that isolates with <20 SNPs are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers.\n\nAltogether, a highly reproducible and specific microsatellite typing assay for C. auris was developed, which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate outbreaks.\n\nImportanceCandida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and mainly causes hospital associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. While the former is costly and only available in few centers, AFLP is a complicated technique and standardization is not possible. We describe a novel simple microsatellite genotyping technique based on small tandem repeats in the C. auris genome. Further we show that this microsatellite based genotyping technique has been proven comparable to WGS. Overall, this work provides a novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris.