Azole-resistant Candida parapsilosis complex isolates from Kayseri, Türkiye: genomic, phenotypic, antifungal resistance, and virulence characteristics

Objectives: This study aimed to investigate the species distribution, molecular characteristics, antifungal susceptibility profiles, resistance-associated genes, and virulence properties of azole-resistant C. parapsilosis complex isolates in Kayseri, Türkiye. Methods: Thirty C. parapsilosis complex isolates, initially identified from clinical specimens by conventional methods and MALDI-TOF MS over a two-year period, were analyzed. Whole-genome sequencing (WGS) was performed for species-level re-identification, phylogenetic analysis, and resistance gene mapping. Antifungal susceptibility testing was conducted using broth microdilution and gradient strip methods in accordance with CLSI and EUCAST guidelines. Virulence-related phenotypes, including phospholipase, proteinase, and esterase activity, and biofilm formation, were evaluated. Results: Of the 30 isolates, 28 were re-identified as C. parapsilosis sensu stricto and two as C. orthopsilosis using WGS. Most isolates (84%) were obtained from intensive care unit (ICU) patients, predominantly in the pediatric age group (67%). Blood was the most common source of isolates (90%). Isolates were resistant to (100%) fluconazole and itraconazole, and (70%) voriconazole, and susceptible to amphotericin B and caspofungin. High rates of proteinase (92.8%), phospholipase (71.4%), esterase activity (64.3%), and biofilm formation (78.6%) were observed among isolates. The most frequently detected resistance-associated genes were ERG3 (60%), HOG1 (56.6%), PDR16 (53.3%), ERG5 (53.3%), ERG27 (50%), and FKS1 (46.6%). Phylogenetic analysis revealed genetic diversity, with evidence of close evolutionary relationships among some isolates. Conclusion: Universal fluconazole resistance and the high virulence potential of these isolates, especially in pediatric ICUs, highlight a critical clinical challenge. The presence of diverse resistance-associated genes, even in the absence of canonical ERG11 mutations in some strains, suggests complex, multi-pathway resistance mechanisms. WGS provided higher discriminatory resolution than conventional methods for distinguishing cryptic species within the C. parapsilosis complex. WGS data were analyzed to determine phylogenetic relationships and identify resistance-associated genes using the ResFungi database.