Segmental duplications and supernumerary chromosomes drive antifungal drug resistance in Candida auris

Candida auris, a World Health Organisation-listed critical priority fungal pathogen, causes frequent multidrug-resistant outbreaks worldwide. While point mutations underlying antifungal resistance are well characterised, the contribution of structural genomic variation to antifungal responses remains poorly defined. Here, we integrate whole-genome sequencing, a genome-wide copy number variation (CNV) screen, electrophoretic karyotyping, and mutation-accumulation analyses to investigate the role of structural variation in antifungal susceptibility across a clinical cohort of C. auris isolates. We identify recurrent CNV hotspots, with segmental duplications representing a predominant mode of genome variation. Small duplications encompassing ERG11 arise at high frequency and frequently co-occur with drug resistance-associated ERG11 mutations, collectively enhancing azole resistance. In addition, large centromere-inclusive duplications of chromosome 1 generate supernumerary chromosomes, leading to paradoxical growth and reduced susceptibility to caspofungin, an echinocandin. At the population level, structural variants frequently arise in parallel to FKS1 mutations, suggesting multiple genetic mechanisms underlying reduced drug susceptibility. Together, our findings establish segmental duplication as a major, non-mutational driver of antifungal resistance, highlighting the need to consider structural genomic variation in both resistance surveillance and clinical susceptibility testing.