Comparative genomics of Candida albicans isolates from Bogotá, Colombia: Phylogenetic insights and resistance-related mutations

Candida albicans is an opportunistic fungal pathogen, considered the second most frequent agent of fungal infections worldwide, responsible for high mortality in immunocompromised patients. While epidemiology and genetic diversity of this fungus have been extensively studied globally, genomic profiling in Colombia remains limited. In this study, we analyzed the genomic characteristics of 13 Colombian clinical isolates, focusing on ploidy, gene changes, structural variations, single-nucleotide polymorphisms (SNPs), and their phylogenetic relationships with major clades identified by Multi Locus Sequence Typing (MLST). These isolations were selected due to their antifungal susceptibility profiles. Our findings showed no changes in the karyotype, a low number of genes with copy number variations, and a high number of SNPs. The SNP analysis revealed known and new mutations causing amino acid changes in key resistance-associated genes in both susceptible and resistant isolates. Phylogenetic analysis revealed that the C. albicans isolates were distributed across various global clades, with 46% belonging to clade 9. Interestingly, one isolate, known for its resistance to fluconazole and intermediate sensitivity to caspofungin, clustered within a distinct and understudied clade. Although no well-characterized mutations explaining resistance were found, these results suggest that other mechanisms or new mutations in untested genes may be involved. Additionally, our findings indicate that C. albicans may only require minor changes to adapt to the host environment. In this study, we present the first complete genome sequence of Colombian C.