Reversible haploidisation and convergent genomic routes to antifungal resistance in the Candida parapsilosis species complex

Antifungal resistance is rising among non-albicans Candida, with outbreaks increasingly linked to drug-resistant Candida parapsilosis. Using large-scale experimental evolution under fluconazole and anidulafungin, coupled to phenotyping and genome sequencing, we define resistance strategies across C. parapsilosis, Candida metapsilosis and Candida orthopsilosis. Despite diverse genetic backgrounds, adaptation repeatedly converged on a shared genomic toolkit that combines protein-altering mutations in key regulators and drug targets (including MRR1 and FKS1) with copy-number changes, aneuploidy, as well as loss of heterozygosity driving resistance alleles to homozygosity. Strikingly, drug selection triggered recurrent but reversible haploidisation in C. orthopsilosis, revealing ploidy reduction as a transient, selectable survival strategy. Resistance, particularly after fluconazole selection, imposed fitness costs that promoted compensatory evolution and resistance loss after drug withdrawal. Together, antifungal adaptation in this complex affects convergent targets, while being plastic in its genomic routes, with implications for resistance surveillance and drug cycling therapies.