Integrative Phylogenomics of Candida auris Clades Circulating in Nigerian Intensive Care Units: Emergence, Transmission, and Antifungal Resistance Evolution

Candida auris is a globally emergent multidrug-resistant fungal pathogen with extraordinary capacity for nosocomial transmission and antifungal resistance, yet its genomic epidemiology and resistance evolution in Nigerian ICUs are entirely uncharacterized. This study performed integrative phylogenomics of C. auris isolates from tertiary hospital ICUs across three geopolitical zones to establish clade identity, transmission networks, and antifungal resistance evolution pathways in Nigerian healthcare settings. C. auris isolates were collected from blood cultures, skin swabs, and catheter tips of ICU patients at teaching hospitals in Lagos (South West), Benin City (South South), and Abuja (North Central) over 24 months. Whole-genome sequencing using Illumina NovaSeq was performed on 45 confirmed isolates. Clade assignment was determined by phylogenetic placement against the global C. auris reference dataset. Single nucleotide polymorphism-based transmission network analysis identified intra- and inter-hospital transmission chains. Antifungal susceptibility by EUCAST broth microdilution was correlated with ERG11, FKS1, and MRR1 resistance mutation profiles. Results confirmed the presence of Clade I (South Asian) in all three locations, with one Lagos hospital additionally harboring Clade III (South African) isolates. SNP-based analysis identified two inter-hospital transmission clusters involving Lagos and Abuja facilities, suggesting patient transfer-mediated transmission. ERG11 Y132F mutations conferring fluconazole resistance were present in 88.9 percent of isolates. FKS1 S639F echinocandin resistance mutations were detected in 4 isolates, representing the first confirmed echinocandin-resistant C. auris in Nigeria. These findings provide the first genomic characterization of C. auris in Nigeria and constitute an original contribution to global C. auris phylogeography. Keywords: Candida auris, phylogenomics, antifungal resistance, ICU outbreak, Nigeria.