Adikwu, M. U. | bioRxiv Science

bioRxiv2025

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

BackgroundUnregulated 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. ResultsDisk 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, blaCTX-M-15, and blaOXA-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. ConclusionsThis 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.

microbiology↗

bioRxiv2025

Investigating the factors influencing antibiotic use practices and their association with antimicrobial resistance awareness among poultry farmers in Enugu State, Nigeria

BackgroundThe irrational use of antibiotics in poultry production has far-reaching consequences and continues to impact the fight against antimicrobial resistance (AMR) in Africa. In Nigeria, antibiotics are available over-the-counter and are widely used in food animal production for various reasons, including prophylaxis and growth promotion. While this practice may support animal production, it also drives the spread of AMR, posing serious health challenges due to close human-livestock interactions and the countrys high disease burden. This study examined poultry farmers knowledge, attitudes, and practices (KAP) regarding antibiotic use and AMR, aiming to highlight the public health risks and challenges in combating AMR in Nigeria. MethodsA cross-sectional survey of 200 poultry farms in Enugu State, Southeast Nigeria, was conducted to evaluate farmers KAP towards antibiotic usage and AMR. Using a validated, standardized, and self-administered questionnaire, data were collected from farmers responsible for key farm decisions, including input and feed management. The questionnaire comprised three sections: socio-demographic data, knowledge of AMR, and knowledge and practices regarding antibiotic use. Ethical approval was obtained, and participants gave oral consent based on their professional capacity. ResultsThe evaluation of poultrys farmers KAP regarding antibiotic usage and AMR revealed that the majority of farmers (90.5%) reported using antibiotics, primarily for treating infections (80.5%) or for feed enhancement, growth promotion, and prophylaxis (61%). Ampicillin (75%), ciprofloxacin (71.5%), and doxycycline (71%) were the most commonly administered antibiotics. Monthly administration was the most common (48%), and 89% of respondents believed that antibiotics promote poultry growth. Interestingly, a substantial proportion of respondents (65%) were unaware of AMR, highlighting a significant knowledge gap, with only 16% recognizing the risk of AMR infections. ConclusionOur study revealed that the surveyed poultry farmers heavily rely on antibiotics, primarily for treating infections and, to a significant extent, for growth promotion, despite their limited awareness of AMR. Ampicillin was identified as the most commonly used antibiotic, raising concerns due to its potential link to beta-lactamase selection amid the countrys carbapenem resistance issues. These findings underscore the urgent need for targeted education to address the AMR knowledge gap and reduce the misuse of antibiotics in poultry farming settings in Nigeria.

scientific communication and education↗