Genomic epidemiology of ESBL-producing <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> across the human-animal-environment interface in peri-urban pig farms in Yaounde, Cameroon

ABSTRACT Background Livestock production systems in peri-urban areas are associated with high levels of interaction between humans, animals, and the environment, which may contribute to the dissemination of antimicrobial resistant bacteria. However, genomic characterization of resistant bacteria in the interconnected systems of humans, animals, and the environment in low- and middle-income countries like Cameroon is very limited. Methods This study was undertaken to investigate the ESBL-producing E. coli and K. pneumoniae in the peri-urban pig production systems in Yaounde, Cameroon, through the application of the One Health genomic approach. A total of 338 samples were collected from humans, pigs, and the environment. Enterobacterales were isolated using standard microbiological procedures, followed by antimicrobial susceptibility testing of the isolated bacteria using the Kirby-Bauer disk diffusion method based on the EUCAST breakpoints. Ten multidrug-resistant Enterobacterales with similar resistance profiles were sequenced to identify their sequence types, resistance determinants, plasmid replicons, and virulence determinants. Results Enterobacterales were found in 187 samples, comprising 38 human, 98 pig, and 51 environmental samples. E. coli (166 isolates) was the most prevalent species, followed by K. pneumoniae (100 isolates). Whole-genome sequencing revealed eight E. coli and two K. quasipneumoniae isolates from human, pig, wastewater, and farm environmental samples. The E. coli isolates represented seven sequence types, including the globally successful ST410 lineage. Notably, E. coli ST3580 was found in human and environmental samples from the Afanoyoa farm in different sampling months, while K. quasipneumoniae ST1535 was found in human and pig samples from the Etoudi farm in different months. All genomes encoded ESBL genes, with bla CTX-M-15 being the most prevalent, accompanied by other resistance genes to various antibiotic classes and several plasmid incompatibility groups. Conclusions These results show the circulation of genetically diverse ESBL-producing E. coli and K. pneumoniae in human, animal, and environmental reservoirs in peri-urban pig farming systems and the potential for cross-reservoir persistence of particular lineages. Improved One Health antimicrobial resistance surveillance and stewardship are critical to address antimicrobial resistance in rapidly urbanizing environments.