Genomic profiling of extended-spectrum beta-lactamase-producing Escherichia coli isolated from poultry and poultry farm workers in Accra, Ghana

Antimicrobial resistance (AMR), driven by the extensive use of antibiotics in human and animal health, poses a significant global threat. In Ghana, the contribution of poultry farming to the high prevalence of AMR remains underexplored. This study investigates the genomic characteristics and prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in poultry and human populations. A total of 300 cloacal swabs from poultry and 60 stool samples from poultry farm workers in peri-urban Accra were collected from 20 poultry farms and cultured. Bacterial isolates were identified through MALDI-TOF-MS, with ESBL production confirmed using the double disk synergy test. Whole-genome sequencing of 17 multi-drug resistant isolates selected was conducted on the MiSeq Illumina platform to characterize resistance genes, virulence genes, and sequence types. ESBL production was detected in 84.8% (n = 123/145) in isolates from poultry and 67.5% (n = 27/40) in isolates from humans. All isolates were resistant to cefotaxime, with significant resistance to tetracycline and sulfamethoxazole-trimethoprim also recorded. The bla_CTX-M-15 gene was the most prevalent ESBL gene identified, with additional genes including bla_CTX-M-27, bla_OXA-1, bla_OXA-181, bla_TEM-1B, and bla_DHA-1 also identified. Sequence typing revealed multiple resistance-associated sequence types, notably ST10 and ST155. Plasmid replicon analysis identified IncF, Col, and IncI1 groups, many co-occurring with multiple resistance genes. Virulome profiling revealed the presence of avian pathogenic E. coli (APEC)-associated genes such as iroN, iss, ompT, and hlyF. This study highlights the prevalence and genomic characteristics of ESBL-producing E. coli at the human-poultry interface in Ghana, emphasizing poultry as a potential reservoir for multidrug-resistant bacteria. The findings provide actionable insights for small- to medium-scale poultry farmers, including the importance of prudent antibiotic use, enhanced hygiene, and biosecurity practices, and underscore the need for ongoing genomic surveillance to guide interventions aimed at reducing the spread of antimicrobial resistance in Ghana.