One Health genomic surveillance identified high-risk carbapenem-resistant ST821 clones of Acinetobacter baumannii in Nigerian clinical and community settings.

Acinetobacter baumannii is a Gram-negative opportunistic pathogen increasingly implicated in severe hospital and community-acquired infections. In Nigeria, widespread antibiotic use across human, animal and environmental sectors contributes to antibiotic selection pressures that drive the emergence and spread of high-risk multidrug-resistant lineages. This One Health genomic surveillance study investigated the prevalence, resistance mechanisms, genomic characteristics and reservoirs of A. baumannii across multiple sources in Kano, Nigeria. A total of 3,235 samples were collected from clinical samples, hospital environments, non-hospital environments and poultry droppings. A. baumannii isolates were identified by growth on MacConkey/CHROMagar and confirmed by bla OXA-51-like amplification. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method. Of all samples, 62 isolates were confirmed as A. baumannii, originating from clinical samples (n=24), hospital environments (n=33), non-hospital environments (n=2) and poultry droppings (n=3). Whole-genome sequencing of 27 select isolates was performed to characterize resistance and virulence genes, sequence types (STs), mobile genetic elements, genomic islands and SNP-based relatedness. Thirteen bla OXA-51-like and one bla OXA-58-like variants were detected. MLST revealed 21 STs using the Pasteur scheme and 14 using the Oxford scheme, many of which were susceptible to most antibiotics tested. In contrast, isolates N9, N13 and N16 (ST821) and N19 (ST625) were resistant to all tested antibiotics, including carbapenems. The highly resistant ST821 clones were isolated from a municipal dumpsite, hospital floors and a hospital bedside surface and separated by only 5-17 SNPs, indicating close relatedness and clonality. Previously reported ST821 strains from the UK, Pakistan, Germany and Nigeria were highly susceptible to antimicrobials. Although no plasmids were detected, complementary genomic islands were identified in N9, N13 and N16 containing blaNDM-1, tetA/tetR, folP, aac, aphA, dinB, cueR and trxC and therefore likely to confer resistance to antimicrobials. In conclusion, this study provides the first broad One Health genomic overview of A. baumannii circulating across human, environmental and poultry sources in northern Nigeria, revealing substantial genomic diversity and the identification of a closely related extreme drug-resistant ST821 lineage spanning hospital and community environments.