Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated <i>Escherichia coli</i> from Nigeria

Abstract

ABSTRACT Background Unregulated antibiotic use in poultry farming drives the emergence of multidrug-resistant (MDR) bacteria, which can spread to humans through the food chain and environment, posing serious public health risks. Whole-genome sequencing (WGS), combined with antimicrobial susceptibility testing (AST), enables detailed characterization of resistance mechanisms and supports antimicrobial stewardship. This study investigated the phenotypic and genotypic antimicrobial resistance (AMR), plasmid content, and virulence factors of an MDR Escherichia coli strain isolated from chicken droppings in Enugu State, Nigeria. Results Disk diffusion AST showed resistance to six of seven antibiotics tested (cefotaxime, ampicillin, erythromycin, gentamicin, ciprofloxacin, and doxycycline). Broth microdilution confirmed elevated minimum inhibitory concentrations across multiple classes, indicating an MDR phenotype. Hybrid WGS (Illumina and Nanopore) produced a 5.33 Mb genome comprising one chromosome and four plasmid-associated contigs. Chromosomal antimicrobial resistance genes (ARGs), including aac(6’)-Ib-cr, bla CTX-M-15 , and bla OXA-1 , conferred resistance to aminoglycosides, fluoroquinolones, cephalosporins, and penicillins. Additional resistance determinants included efflux pumps, transport-associated genes, regulatory elements, and membrane modification genes. Plasmid-borne ARGs conferring resistance to aminoglycosides, trimethoprim, macrolides, sulfonamides, penicillins, and tetracyclines were also identified. The presence of Col156 and IncF-type plasmids indicates strong potential for horizontal gene transfer. Virulence profiling revealed numerous chromosomally encoded factors related to adhesion, iron acquisition, and toxin production. These included the pap gene cluster encoding P fimbriae; adhesion-associated genes ( yagW/ecpD, ykgK/ecpR ); multiple iron acquisition systems (enterobactin, yersiniabactin, aerobactin, and heme uptake); and sat , which encodes an autotransporter toxin. Additionally, the plasmid-borne gene senB encodes an enterotoxin that induces intestinal fluid secretion and contributes to diarrheal disease. Multilocus sequence typing identified the strain as ST131, a globally disseminated high-risk lineage. Conclusions This study provides a comprehensive genomic characterization of an MDR E. coli strain from poultry, revealing multiple chromosomal and plasmid-borne ARGs, and a diverse virulence gene repertoire. The detection of ST131 in poultry waste highlights a complex public health issue involving zoonotic transmission, veterinary impact, and environmental spread of AMR. These findings underscore the need for prudent antibiotic use, continuous monitoring, and integrated genomic surveillance across agricultural and environmental sectors, alongside improved antimicrobial stewardship and strengthened farm biosecurity measures.