Genomic epidemiological patterns and antifungal resistance profiles of <i>Candidozyma auris</i> in China: Spatiotemporal dynamics and persistent colonization.

Candidozyma auris (C. auris) is an emerging multidrug-resistant fungal pathogen with major global public health implications. However, the clinical characteristics, clade-specific genomic variation, resistance-associated SNP patterns, and transmission dynamics of C. auris in China remain insufficiently understood. We retrospectively analyzed clinical data from 22 intensive care unit patients colonized or infected with C. auris and performed antifungal susceptibility testing and whole-genome sequencing (WGS) on 25 isolates. All isolates were resistant to fluconazole, and 80% were resistant to amphotericin B, whereas echinocandin susceptibility remained intact. Phylogenetic analysis assigned the isolates to Clade I (n = 19) and Clade III (n = 6). SNP analysis revealed marked clade-specific differentiation in resistance-associated genes, with ERG11 Y132F enriched in Clade I and ERG11 alterations, including VF125AL, enriched in Clade III. Additional variants in ERG2, CDR1, TAC1a, and TAC1b also showed clade-biased distributions and frequent co-occurrence. However, no significant association was observed between individual SNPs or mutation burden and antifungal susceptibility phenotypes. To investigate transmission dynamics, we conducted comparative genomic and phylogeographic analyses using 210 C. auris genomes. Major inbound introductions into China were inferred from Canada and South Korea to Guangdong and from Pakistan to Beijing, while phylogeographic modeling suggested that Beijing and Guangdong may have served as key nodes for subsequent domestic spread. These findings highlight the importance of integrated genomic surveillance for tracking C. auris dissemination and informing targeted infection control strategies.