Candida auris


MicrobiType service:  CauMT1


The opportunistic yeast Candida auris has emerged in recent years as an important agent of healthcare-associated infection (HAI). This may reflect the ability of C. auris to colonize the skin of healthcare workers, from which it can be transmitted to patients. Additionally, it can survive on environmental surfaces for long periods, and can also colonize these surfaces through formation of disinfectant-resistant biofilms. C. auris HAI are of particular concern due to the capacity for this fungus to exhibit antifungal resistance, and relatedly its high mortality rates. Epidemiologic investigation of outbreaks with the highly clonal C. auris have been assisted by DNA-based typing, typically to the clade level (1,2). In the U.S., the predominant clade has been South Asia Clade I; less common or undetected have been East Asia Clade II, South Africa clade III, South America clade IV, and Iran clade V.


Multiple approaches have been applied to strain typing of fungal isolates, but the two that have been most widely applied have been multilocus sequence typing (MLST) and microsatellite analysis. MLST employs conventional PCR and Sanger sequencing to analyze single nucleotide polymorphisms (SNPs) in a set of 7 or so housekeeping genes. These genes are relatively conserved, and hence the multilocus requirement; this significantly increases cost and complexity. Microsatellite analysis is also PCR-based, but targets tandem repeats that vary in length due to their intrinsically high rates of insertions and deletions. To maximize resolution, lengths are determined by capillary gel electrophoresis requiring costly equipment, and again multiple microsatellites must be analyzed. Furthermore, length-based methods have intrinsically limited data portability; i.e., the ease and accuracy with which typing results can be compared from day to day and from lab to lab.


A third approach, whole genome sequence-based SNP analysis, can substantially enhance MLST resolution by expanding the number of loci examined from 7 or so to several thousand. However, WGS-SNP analysis poses signficant challenges with respect to costs of equipment and reagents, computational capacity, and requirements for bioinformatic expertise; for fungi, these challenges would be compounded by the ca. 10-fold larger genomes.


At MicrobiType, an alternative approach to typing C. auris isolates was developed that addresses issues of cost and complexity while providing the resolution required for initial epidemiologic investigation (3). Following PCR from heat-killed colony lysates and Sanger sequencing, PLST locus CauMT1 provided unambiguous assignment of clade and, in particular, resolution of predominant clade I into 11 alleles (dendrograms).


(1) Y Zhu  et al. (2020). J. Clin. Microbiol. 58:e01503-19.

(2) B. L. Wickes (2020). J. Clin. Microbiol. 58:e02083-19.

(3) S. Katiyar and T. Edlind (2020). J. Clin. Microbiol. 58:e01039-20. doi: 10.1128/JCM.01039-20.


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