Candida auris in Singapore: Genomic epidemiology, antifungal drug resistance, and identification using the updated 8.01 VITEK^Ⓡ2 system

Objectives: Candida auris (C. auris) has globally emerged as a multidrug-resistant pathogen. While it is known that there are four geographic clades, little is known about its genomic epidemiology in the Southeast Asian region. Laboratory identification can be challenging but the VITEK^Ⓡ2 system (version 8.01 software) has recently updated its database to include C. auris. This study aimed to investigate the genomic epidemiology of C. auris isolated in Singapore and the susceptibility profiles in relation to ERG11 and FKS1 mutations.

Methods: Seven C. auris isolates from 2012-2018 were analysed using whole-genome sequencing, and antifungal susceptibility testing was performed. The performance of the updated VITEK^Ⓡ2 system in identifying C. auris was also evaluated using these C. auris strains together with five closely related Candida species.

Results: Three clades were identified: South Asian (71.4%), South American (14.3%) and East Asian (14.3%). Local transmission was unlikely as there was no obviously identified cluster and most cases were likely to be imported at different time points following overseas hospitalisation exposure. Three isolates (42.9%) were multidrug-resistant. All South Asian strains were resistant to fluconazole and harboured ERG11 mutations, which were clade-specific. No FKS1 mutation was detected. The VITEK^Ⓡ2 system was able to correctly identify most of the South Asian C. auris strains but misidentified the East Asian strain and gave a low discrimination result for the South American clade.

Conclusion: This study showed that the introduction of C. auris into Singapore was possibly over multiple episodes and from different sources. The VITEK^Ⓡ2 System version 8.01 software has limited abilities in identifying C .auris.