Genomic Characterisation of Virulence and In Vivo Pathogenicity of Azole-Antifungal Resistant Candida from HIV/AIDS Patients in Southeast Nigeria

Background: Oral candidiasis remains a common opportunistic infection among people living with HIV/AIDS, especially in low-resource settings. Rising antifungal resistance and systemic candidiasis complicate treatment. This study investigated the genomic features and virulence mechanisms of Candida species isolated from HIV-positive individuals in southeast Nigeria. Methods: Oral swabs (n=514) from HIV patients were collected and cultured on Chromogenic agar for Candida, with azole susceptibility assessed through the Kirby-Bauer disk-diffusion method. Representative isolates underwent whole-genome sequencing to identify virulence genes and mechanisms. A pathogenicity study was conducted on 16 rats, divided into four groups: Candida albicans, Candida glabrata, a mixed inoculum, and a non-inoculated control. Over 28 days, morbidity, mortality, weight changes, and organ infections were evaluated. Results: All sequenced strains belonged to Sequence Type 15 with conserved genomes. Key virulence genes (waaF, waaG, pilH, and pvdS) and housekeeping genes (argS, gyrB, ileS, nuoC, ppsA, recA, rpoB, rpoD) were consistently expressed, supporting biofilm formation, stress tolerance, immune evasion, and persistence mechanisms. In vivo, rats inoculated with C. albicans or mixed inoculum showed severe morbidity, high mortality (100% and 75% respectively), weight loss, and tissue necrosis, indicating systemic infection. Conclusion: Azole-resistant Candida species from HIV-infected individuals exhibit diverse genetic and phenotypic mechanisms that drive virulence and resistance. The findings emphasise their pathogenic potential and the challenges they pose for diagnosis and treatment. Genomic similarity among isolates indicates clonal expansion and potential interspecies gene exchange, underscoring the importance of integrated antifungal surveillance and stewardship in resource-limited settings.