Development of Candida auris Short Tandem Repeat Typing and Its Application to 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 health care 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 short tandem repeat (STR) typing assay for C. auris. STRs in C. auris were identified, and from an initial selection of 23 STRs, 12 were used to develop a STR typing assay. Having shown that the STR typing assay was 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 of South American, South Asian, African, East Asian, and Iranian origin. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the South Asian clade. Comparison with WGS demonstrated that isolates with <20 single nucleotide polymorphisms (SNPs) are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers. Altogether, a highly reproducible and specific STR typing assay for C. auris was developed; this assay distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing by >30 SNPs, as determined via WGS, are also separated. This new C. auris-specific genotyping technique is a rapid, reliable, and cost-effective alternative to WGS analysis to investigate outbreaks. IMPORTANCE Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly 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. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris.

A Cluster of Candida auris Blood Stream Infections in a Tertiary Care Hospital in Oman from 2016 to 2019

“…Candida auris is currently separated into five geographically restricted clades (East-Asia, South-Asia, Africa, Iran and South-America) [ 38 ]. In the present study, we typed 55 isolates, originating from India, Kuwait, Oman, South-Africa, Japan, Korea, Venezuela and Iran with STR genotyping [ 39 ], which showed that the Omani isolates belong to the South Asian clade and had a clonal nature. STR genotyping also agreed completely with a previous whole genome analysis study on C. auris [ 32 ].…”

“…For genotyping C. auris, microsatellite analysis was employed using the following reference strains of clade I (India: ARbank 389), clade II (Japan: ARbank 381), clade III (South Africa: ARbank 383), clade IV (Venezuela: B11245, B11247, B11243, B11244, B1124) and clade V (Iran: ARbank 1097 = IFRC 2087) [ 39 ]. Briefly, DNA was extracted and purified with the MagNA Pure LC instrument and the MagNA Pure DNA isolation kit III (Roche Diagnostics GmbH, Mannheim, Germany), according to the recommendations of the manufacturer.…”

“…The sample was then incubated for 15 min at 100 °C and cooled down to room temperature. Four multiplex PCR reactions, which amplify 12 STR targets with a repeat size of 2, 3, or 9 nucleotides, were performed for genotyping the Omani isolates, which were compared with a global collection [ 39 ]. Copy numbers of the twelve markers of all isolates were determined using GeneMapper Software 5 (Applied Biosystems).…”

Tracking a Global Threat: a New Genotyping Method for Candida auris

“…A new report in mBio by de Groot et al describes the development of an STR typing approach for Candida auris (10). STR markers were initially identified from a search across reference genome assemblies generated for each of the initially described four major clades (11).…”

Genotypic diversity in clinical and environmental isolates of Cryptococcus neoformans from India using multilocus microsatellite and multilocus sequence typing

“…[38][39][40] Recently, a novel MLMT typing for Candida auris showed that the technique is highly concordant with whole genome sequencing in identifying five different geographical clusters in C auris. 41 However, due to the lack of a MLMT global database as compared to MLST the former is not well acknowledged in genotyping of C neoformans.…”