Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study

Abstract

The emerging fungal pathogen Candida auris poses a serious threat to global public health due to its worldwide distribution, multidrug resistance, high transmissibility, propensity to cause outbreaks, and high mortality. We aimed to characterise three unusual Cauris isolates detected in Singapore, and to determine whether they constitute a novel clade distinct from all previously known Cauris clades (I-V). In this genotypic and phenotypic study, we characterised three Cauris clinical isolates, which were cultured from epidemiologically unlinked inpatients at a large tertiary hospital in Singapore. The index isolate was detected in April, 2023. We performed whole-genome sequencing (WGS) and obtained hybrid assemblies of these Cauris isolates. The complete genomes were compared with representative genomes of all known Cauris clades. To provide a global context, 3651international WGS data from the National Center for Biotechnology Information (NCBI) database were included in a high-resolution single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing was done and antifungal resistance genes, mating-type locus, and chromosomal rearrangements were characterised from the WGS data of the three investigated isolates. We further implemented Bayesian logistic regression models to classify isolates into known clades and simulate the automatic detection of isolates belonging to novel clades as their WGS data became available. The three investigated isolates were separated by at least 37 000SNPs (range 37 000-236 900) from all existing Cauris clades. These isolates had opposite mating-type allele and different chromosomal rearrangements when compared with their closest clade IV relatives. The isolates were susceptible to all tested antifungals. Therefore, we propose that these isolates represent a new clade of Cauris, clade VI. Furthermore, an independent WGS dataset from Bangladesh, accessed via the NCBI Sequence Read Archive, was found to belong to this new clade. As a proof-of-concept, our Bayesian logistic regression model was able to flag these outlier genomes as a potential new clade. The discovery of a new Cauris clade in Singapore and Bangladesh in the Indomalayan zone, showing a close relationship to cladeIV members most commonly found in South America, highlights the unknown genetic diversity and origin of Cauris, particularly in under-resourced regions. Active surveillance in clinical settings, along with effective sequencing strategies and downstream analysis, will be essential in the identification of novel strains, tracking of transmission, and containment of adverse clinical effects of Cauris infections. Duke-NUS Academic Medical Center Nurturing Clinician Researcher Scheme, and the Genedant-GIS Innovation Program.