Whole-genome characterization of Candidozyma auris isolates from a Korean tertiary care centre: clade II predominance, partly unexplained fluconazole resistance and a clade I isolate

In South Korea, Candidozyma auris is dominated by ear-associated clade II isolates, but institution-based genomic data remain limited. We analysed 35 archived isolates from 29 patients at a tertiary care centre between 2017 and 2023 using antifungal susceptibility testing and whole-genome sequencing. Thirty-four isolates belonged to clade II, and one urine isolate recovered after inter-hospital transfer belonged to subclade Ib. Serial clade II isolates from the same patient clustered together and had lower pairwise SNP distances than different-patient pairs (median, 8.5 versus 181). Among the first isolates from 29 patients, 14 (48.3%) were fluconazole resistant. In first clade II isolates, recurrent curated coding variation was concentrated in TAC1B and ERG11 ; TAC1B F214S and W198C and ERG11 K143R occurred only in resistant isolates, but recognized coding variants did not account for all resistant isolates. Clade II isolates shared a broadly conserved subtelomeric deletion backbone, with variable chromosome 6 loss of selected glycosylphosphatidylinositol-anchor genes. The clade Ib isolate carried ERG11 Y132F, TAC1B A583S and a CDR1 V704L/E709D-like change and met CDC tentative breakpoints for resistance to fluconazole, amphotericin B and caspofungin. These findings refine the genomic profile of Korean clade II isolates and highlight the potential introduction of a distinct clade I lineage through healthcare transfer.