Local Genomic Epidemiology of Acinetobacter baumannii Circulating in Hospital and Non-hospital Environments in Kano, Northwest Nigeria

Acinetobacter baumannii is a pathogenic bacterium of public health significance, capable of rapidly spreading within and between environments. The local epidemiology and transmission pattern of A. baumannii strains circulating in hospitals and non-hospital environments is rarely studied, and hence this is investigated in Kano, Nigeria. A cross-sectional study design was used to collect 172 samples from clinical, hospital, and non-hospital samples. Acinetobacter baumannii isolates were identified and confirmed using microbiological and molecular techniques. Variants of bla_OXA-51 were determined through amplicon sequencing, while whole genome sequencing was performed on 22 isolates to determine their allelic variants/sequence types (ST), resistance/virulence genes, insertion sequences, plasmids, single-nucleotide polymorphism (SNPs) and investigate phylogenetic relationships between the isolates. Twenty-seven A. baumannii were isolated from door handle and toilet floors of student hostels (14), soil and sullage samples (3 each), bed, chair, and drawer of hospital environments (9), and 1 from the urine of a patient. All these isolates belong to only 2 variants of bla_OXA51-like genes, 16 (48.8%) are bla_OXA-66 and 11 (33.3%) are bla_OXA-180. About 70% of the isolates were susceptible to many antibiotics, and 8 resistance genes encoding aminoglycoside, tetracycline, and sulphonamide resistance were acquired by only strains harbouring bla_OXA-66, and between 37 and 39 virulence genes were harboured by all the variants. Intrinsic bla_ADC-25 encoding resistance to β-lactams was found in all A. baumannii strains. The 2 variants had Pasteur scheme MLST allelic profiles ST2 and 267, which are not commonly reported in Nigeria. Few isolates from hospital and non-hospital sources form a cluster with SNPs number distances within the two clusters in the range of 85-100, suggesting a close relationship. The 2 variants circulate in both environments, suggesting transmission in both directions. Detection of ST267 (bla_OXA-180 variant) in a clinical sample indicates an environment-to-human transmission.