Whole-genome sequencing uncovers chromosomal and plasmid-borne multidrug resistance and virulence genes in poultry-associated Escherichia coli isolate from Nigeria

Abstract Background Unregulated antibiotic use in poultry farming contributes to the emergence and spread of multidrug-resistant (MDR) bacteria, posing risks to human, animal, and environmental health. Whole-genome sequencing, 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, integron-related elements, 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 antimicrobial classes, consistent with an MDR phenotype. Hybrid Illumina-Nanopore sequencing generated a 5.33 Mb genome comprising one chromosome and four plasmid-associated contigs. Chromosomal antimicrobial resistance genes included aac(6’)-Ib-cr , bla CTX−M−15 , and bla OXA−1 , conferring resistance to aminoglycosides, fluoroquinolones, cephalosporins, and penicillins, alongside additional efflux, transport, regulatory, and membrane-modification determinants. Plasmid-borne genes extended resistance to aminoglycosides, trimethoprim, macrolides, sulfonamides, penicillins, and tetracyclines. Col156 and IncF-type replicons indicated substantial potential for horizontal gene transfer. A complete integron was detected only on plasmid-containing contig 2, whereas a cluster of attC sites lacking integron-integrase (CALIN) occurred only on the chromosome. This compartmentalized architecture suggests stable chromosomal retention of cassette material alongside a transferable plasmid-associated resistance platform. Virulence profiling identified chromosomal factors involved in adhesion, iron acquisition, and toxin production, including the pap fimbrial cluster, yagW/ecpD , ykgK/ecpR , enterobactin, yersiniabactin, aerobactin, heme uptake systems, and sat . The plasmid-borne senB gene encodes an enterotoxin associated with intestinal fluid secretion and diarrheal disease. Multilocus sequence typing identified the isolate as ST131, a globally disseminated high-risk lineage. Conclusions This study provides comprehensive genomic characterization of an MDR E. coli isolate from poultry, revealing extensive AMR determinants, a plasmid-associated integron, chromosomal CALIN, and a diverse ExPEC-associated virulence repertoire. Detection of ST131 in poultry waste highlights the potential for zoonotic, veterinary, and environmental dissemination of AMR. These findings support prudent antibiotic use, improved farm biosecurity, continuous monitoring, and integrated genomic surveillance across agricultural and environmental sectors within a coordinated One Health framework to limit transmission of high-risk clones.