Candida auris: Prevalence, Antifungal Resistance, and Genomic Diversity in Healthcare Settings in Abuja, FCT

Candida auris is a globally emerging multidrug-resistant fungal pathogen associated with life-threatening hospital outbreaks and extraordinary persistence in healthcare environments. This prospective analytical study determined the prevalence, antifungal resistance profiles, and genomic diversity of C. auris in patients and environments of two tertiary hospitals in Abuja, Federal Capital Territory, in the North Central geopolitical zone of Nigeria. Screening swabs from axillae, groins, and nares of 300 high-risk patients (ICU patients and those with prolonged hospital stay) and 200 environmental surface swabs were processed on CHROMagar Candida Plus medium with confirmatory MALDI-TOF mass spectrometry. Antifungal susceptibility was determined by EUCAST broth microdilution. Whole-genome sequencing was performed on confirmed C. auris isolates using Illumina NextSeq. C. auris was detected in 6.7 percent of patients screened and 8.5 percent of environmental samples. All isolates were resistant to fluconazole and 62.5 percent were resistant to voriconazole. Echinocandin resistance was detected in 18.8 percent of isolates. Whole-genome sequencing assigned all Nigerian isolates to Clade III, the South Asian lineage, with two distinct sub-clusters, suggesting possible independent introduction events. The study provides the first genomic characterization of C. auris from Abuja and urgently recommends routine C. auris surveillance, contact precautions, and environmental decontamination protocols in Abuja tertiary hospitals. Keywords: Candida auris, antifungal resistance, genomic diversity, Abuja, hospital outbreak.