Genomic insights into a clade-specific Candida tropicalis lineage with resistance to azoles and immune evasion traits.

Candida tropicalis is a leading cause of invasive candidiasis in the Asia-Pacific region with reported crude mortality rates exceeding 50%. The rising prevalence of azole-resistant strains presents a significant clinical challenge. We analyzed 1,016 C. tropicalis clinical isolates collected over nine years from 27 hospitals across North India. Fluconazole resistance was detected in 5.1% (n = 52) of isolates, with cross-resistance observed to voriconazole in 55.7% and itraconazole in 44.2% of isolates. Multilocus sequence typing (MLST) analysis of global 1,630 isolates including 208 Indian and whole-genome sequencing of 716 global isolates (139 Indian) confirmed the clonal emergence and persistence of azole-resistant MLST clade 4 strains in Indian hospitals. Phylogenomic analyses identified that Indian azole-resistant lineage was closely related to azole-resistant isolates from mainland China and Taiwan. The underlying mechanism of resistance involved hotspot mutations (Y132F) in the ERG11 gene along with its duplication, overexpression, and twofold high ergosterol content. Comparative transcriptomics of two clinical isolates exhibiting >512 fold difference in fluconazole susceptibility identified upregulation of virulence-associated genes, ALS7 gene (eightfold), SAP7 and SAP9 (1.6- and 2-fold, respectively) in azole-resistant isolate. Furthermore, azole-resistant isolates showed robust biofilm-associated metabolic activity (twofold), reduced β-glucan exposure, and greater survival in both neutrophil and macrophage killing assays. Notably, azole-resistant lineage exhibits several traits associated with adhesion and immune evasion that could possibly enable its spread in healthcare settings and signals the beginning of a greater spread of this clone. The urgent need for continuous genomic surveillance and antifungal stewardship is warranted to mitigate the spread of multidrug-resistant C. tropicalis.IMPORTANCEInvasive fungal infections affect 6.5 million people annually and are associated with high mortality rates. Despite being the leading cause of invasive yeast infections in the Asia-Pacific, this is the first comprehensive study of Candida tropicalis from India documenting the emergence of azole-resistant clonal lineage (clade 4) in several hospitals in India. Azole resistance is driven by mutations, gene duplication, and overexpression of its target gene ERG11. The Indian azole-resistant isolates showed high genetic relatedness with those from China. Also, resistant isolate showed overexpression of virulence-related genes and robust biofilm formation. Notably, reduced β-glucan exposure in fluconazole-resistant isolates may contribute to their decreased susceptibility to the innate immune system. Importantly, this study provides evidence for the emergence of azole-resistant C. tropicalis lineage in India, which exhibits several traits associated with adhesion and immune evasion that could possibly enable its spread in healthcare settings leading to a public health concern.