Diverse genetic pathways drive convergent fluconazole and caspofungin resistance phenotypes in Candida albicans

The emergence of antifungal resistance in Candida albicans is a major worldwide public health threat, particularly for immunocompromised patients. Antifungal resistance may arise through uniform resistance mechanisms or through variable evolutionary routes. The aim of this study was to investigate whether antifungal resistance arises in C. albicans through shared or isolate-specific mechanisms, in other words, following convergent or divergent adaptive pathways and genetic mechanisms. Six laboratory-induced fluconazole-resistant and six caspofungin-resistant isolates were analyzed using whole-genome sequencing coupled to phenotypic tests assessing pathogenicity characteristics. All fluconazole-resistant isolates showed increased ergosterol production and elevated ATP-binding cassette (ABC) transporter efflux pump activity, indicating conserved resistance adaptation mechanisms. Recurrent mutations included ERG24 variants and SOD6 S225P in all isolates while other mutations such as ERG11 T128K varied between isolates. Caspofungin-resistant isolates exhibited diverse CHS3 mutations causing variable chitin increases despite a shared resistance strategy. In addition, many isolates displayed decreased biofilm formation and virulence which suggests that increased resistance subjects virulence mechanisms to fitness trade-offs. Altogether, our laboratory-induced antifungal-resistant C. albicans isolates experienced convergent phenotypic adaptations that were the result of genetically diverse evolutionary routes. YMAP (Yeast Mapping Analysis Pipeline) observations also revealed large scale chromosomal rearrangements in our resistant isolates indicating that in addition to point mutations, rearrangements contribute to the acquisition of resistance. Our study highlights the complexity of resistance development and suggests that similar resistance outcomes may be driven by different genomic mechanisms.