Genomic epidemiology of Colombian resistant Candida auris isolates

Since 2016, Candida auris has been subject to mandatory reporting in Colombia due to its critical public health implications. In this context, a genomic characterization of clinical C. auris isolates collected between 2018 and 2024 through national surveillance led by the Instituto Nacional de Salud (INS) was conducted. Twenty-seven isolates from hospitalized patients across 14 departments were analyzed using next-generation sequencing (NGS) and bioinformatics tools (MycoSNP-nf v1.5, TheiaEuk BLAST, Python script, and MUSCLE, snp_phylogeny) to identify mutations associated with antifungal resistance. The patient group was predominantly male n = 18 (66.7%), with 48% (n = 13) for the older adult age group (>60 years of age). Antifungal susceptibility testing (anidulafungin, fluconazole, and amphotericin B) revealed that five isolates (18.5%) were resistant to a single antifungal, while 22 (81.5%) were resistant to two. All isolates belonged to clade IV (South America) and exhibited genetic divergence ranging from 5 to 127 single-nucleotide polymorphisms (SNPs). Mutations in the ERG11 gene were identified in 16 isolates, including Y132F (n = 11), G459S (n = 1), K143R (n = 2), and F444L (n = 1), along with a novel mutation, G445D (n = 1). Four of these 16 isolates also harbored mutations in the TAC1B gene (P595H, n = 3; S611P, n = 1), and one isolate carried a single TAC1B mutation (S195G). Additionally, three isolates presented the S639F mutation in the FKS1 gene. Notably, seven isolates showed phenotypic resistance without any known resistance mutations. These findings are concerning, as the antifungals involved are critical for treating invasive Candida infections. The study highlights the need for ongoing genomic surveillance to complement phenotypic testing and enhance strategies for antifungal resistance control, ultimately informing therapeutic decision-making and drug development.