Clade Differentiation of Candida auris (Candidozyma auris) Clinical Isolates from Korean Hospitals Using Multilocus Sequence Typing and Sequence-Based Identification.

Candida auris (Candidozyma auris) is an emerging multidrug-resistant yeast with distinct phylogenetic clades that differ in their epidemiological characteristics. Rapid and practical methods for clade differentiation are needed for effective surveillance and infection control. We performed clade differentiation of C. auris clinical isolates collected in 32 Korean hospitals between 1996 and 2024 using multilocus sequence typing (MLST). All isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with species confirmation via internal transcribed spacer (ITS) and D1/D2 region sequencing. We evaluated whether these sequencing methods could help reliably distinguish clade II from other clades. MLST helped classify 339 isolates into clade II (194 isolates from 16 hospitals, 1996-2024) and clade I (145 isolates from 22 hospitals, 2018-2024). All clade II isolates showed distinct ITS sequences compared to other clades (I, III-VI), supporting phylogenetic separation. In contrast, D1/D2 sequencing could not distinguish clade II from clade III. Nine clade II isolates from patients with candidemia were sporadically identified over time and across hospitals. In contrast, clusters of clade I candidemia cases, previously unreported in Korea, were identified at 11 hospitals (2022-2024), with isolates showing identical MLST and ITS/D1/D2 sequences. These findings suggest possible ongoing nosocomial transmission of clade I C. auris fungemia in Korea and demonstrate that ITS sequencing can aid in reliably differentiating endemic clade II from non-clade II C. auris isolates, offering a simpler alternative to MLST.