Phylogenomic analysis and genetic mechanisms of antifungal resistance in clinical isolates of <i>Candida glabrata</i> ( <i>Nakaseomyces glabratus</i> ) from across Canada, 2013–2020

<i>Candida glabrata</i> (<i>Nakaseomyces glabratus</i>) is an important cause of invasive fungal infections and may exhibit reduced susceptibility toward antifungal drugs. Here, we used whole-genome sequencing to investigate the genomic phylogeny and identify genetic determinants of antifungal resistance in a collection of 142 clinical <i>C. glabrata</i> isolates obtained from the 10 provinces of Canada between 2013 and 2020. Our study prioritized resistant isolates (<i>n</i> = 62, 43.7%) from invasive infections to better understand antifungal resistance and represents the largest national genomic survey of clinical <i>C. glabrata</i> isolates performed to date in Canada. Phylogenomic analysis based on single-nucleotide variants in the core genome revealed 15 genetically related clusters of <i>C. glabrata</i>. The largest cluster (cluster I, <i>n</i> = 29) was significantly associated with antifungal resistance (<i>P</i> value = 0.0112). Antifungal-resistant isolates were present in almost all clusters, suggesting that resistance most likely arises from selective pressure during antifungal therapy, rather than dissemination of resistant clones. Thirty-six unique <i>PDR1</i> variants were found in 38/52 (73.1%) fluconazole-resistant <i>C. glabrata</i> isolates, with more than half identified in this study as potential novel azole resistance variants. Well-characterized hot-spot variants in <i>FKS</i> genes (<i>n</i> = 5) were found in 12/13 (92.3%) micafungin-resistant <i>C. glabrata</i> isolates. Our genomic analysis highlights the diversity in strain types and sheds light on potential genetic mechanisms of resistance in Canadian isolates of <i>C. glabrata</i>.IMPORTANCE<i>Candida glabrata</i>, also known as <i>Nakaseomyces glabratus</i>, is a type of yeast that can cause infections in individuals with weakened immune systems. Invasive infections can be difficult to treat since some <i>C. glabrata</i> isolates may not respond well to common antifungals. We studied a large collection of <i>C. glabrata</i> isolates collected from across Canada to better understand how <i>C. glabrata</i> spreads and why this fungal pathogen sometimes resists treatment. Using whole-genome sequence analysis, we found that drug resistance appears in different strains independently, likely as a result of treatment, rather than spreading from a single clone. We also identified specific mutations that may be linked to resistance to commonly used antifungal drugs, such as fluconazole and micafungin. Our research shows how valuable whole-genome sequencing is for understanding the spread and drug resistance of <i>C. glabrata</i>, which can help improve treatment and infection control.