A Retrospective Molecular Epidemiology Study: Emergence and dissemination of Azole-Resistant Candida parapsilosis...

Candida parapsilosis sensu stricto has emerged as a major cause of healthcare-associated candidemia, with increasing reports of fluconazole resistance worldwide. This resistance is most commonly associated with amino acid substitutions in Erg11p, particularly Y132F; however, regional variation in resistance mechanisms and clonal dissemination remains not fully understood. This study investigated the molecular epidemiology and genomic landscape of fluconazole-resistant C. parapsilosis in Paraná, Southern Brazil, over a 10-year period. A total of 54 resistant isolates identified between 2014 and 2024 were retrospectively analyzed; 51 viable isolates were confirmed by species identification, antifungal susceptibility testing, and microsatellite genotyping. A subset of 18 representative isolates underwent whole-genome sequencing for phylogenomic analysis. Variants in genes associated with azole resistance, including ERG11, MRR1, TAC1, CDR1, MDR1, ERG3, and ERG6, were characterized. Fluconazole resistance emerged in 2018 and increased thereafter. Phylogenomic analysis revealed two geographically structured lineages: a dominant clone circulating across multiple healthcare institutions in the Curitiba metropolitan area and a second lineage restricted to the northern region of the state. The dominant clone showed minimal genomic diversity (0-5 SNPs), consistent with long-term persistence. A conserved resistance profile was observed, with 17 of 18 sequenced isolates harboring the K143R substitution in Erg11p, while all retained the wild-type residue at position 132. The single isolate lacking ERG11 mutations carried a novel C849Y substitution in the Mrr1p regulator. These findings demonstrate the emergence and persistence of a highly clonal fluconazole-resistant C. parapsilosis lineage in Southern Brazil, characterized by a conserved K143R substitution independent of Y132F. The detection of closely related isolates across different hospitals underscores the need for regional genomic surveillance of hospital-adapted fungal pathogens.