Diversity of Multi-Drug Resistance Genes in Escherichia coli Isolated from Poultry in Southern Togo

Background and Purpose: The medical sector is facing therapeutic dead ends due to antimicrobial resistance (AMR), which leads to human death and economic losses for poultry farmers. This study aimed to investigate the diversity of resistance genes in Enterobacteriaceae on poultry farms. Methods: Illumina sequencing was used for the cultivation of 184 poultry fecal samples, identification using the API 10S Biomerieux gallery, antibiotic susceptibility testing by disk diffusion, and DNA extraction using the Biocentric Bruker automated system. Results: Among the 164 isolates, Escherichia coli was the most isolated species (84.78%, n = 156), followed by Klebsiella pneumoniae (3.26%, n = 06), and Salmonella spp. (0.01%, n = 02). Among 156 Escherichia coli strains, 10% (n = 18) were extended-spectrum bêta-lactamase (ESBL) producers. Among the 13 sequenced ESBL-producing E. coli strains, 53 resistance genes were identified with moderate variability and some were strain-specific. Co-localization of plasmids with virulence genes was also observed. Several blaTEM variants that encode beta-lactam resistance have been frequently detected. The ompK37 and ompK36 mutants coding for carbapenemase production were identified in one strain. One strain carried mcr-1.1 gene. Conclusion: Antibiotics used in poultry farming contribute to the selection of resistant and highly virulent clones. Strengthening regulations on antibiotic use in poultry farming is necessary.