Genomic Characterisation of Antibiotic-Resistant Escherichia coli from an Intensive Poultry Production System in the uMgungundlovu District, KwaZulu-Natal, South Africa: A Snapshot

<b>Background</b>: Intensive poultry production systems can act as reservoirs for antibiotic-resistant and multidrug-resistant (MDR) <i>Escherichia coli</i>, posing a public health risk through food and environmental transmission. <b>Methods:</b> This study investigated the genomic characteristics of antibiotic-resistant <i>E. coli</i> isolated from an intensive poultry production system in the uMgungundlovu District, KwaZulu-Natal, South Africa. Chicken litter, wastewater, and floor swab samples were collected over three consecutive production cycles. Putative <i>E. coli</i> isolates were detected using the Colilert-18 system, cultured on eosin methylene blue agar, and genomically confirmed by quantitative PCR (q-PCR) targeting the <i>uidA</i> gene. Whole genome sequencing was performed using the Illumina MiSeq platform, followed by bioinformatic analyses to assess resistance genes, mobile genetic elements, and phylogenetic relationships. <b>Results</b>: Of 150 presumptive <i>E. coli</i>, 70 were genomically confirmed as <i>E. coli</i> and resistant to at least one antibiotic, with 74% exhibiting multidrug resistance. Resistance was highest to tetracycline (100%), ampicillin (94%), and trimethoprim-sulfamethoxazole (76%), while ciprofloxacin resistance was rare (3%). Genomic analysis identified multiple antibiotic resistance genes conferring resistance to fluoroquinolones, β-lactams, aminoglycosides, amphenicols, fosfomycin, and sulfonamides, as well as the disinfectant resistance gene <i>qacI</i>. These genes were frequently associated with mobile genetic elements, including plasmids, integrons, transposons, and insertion sequences. Predominant sequence types included ST155, ST48, ST1286, and ST602, with phylogenetic relatedness to poultry-associated isolates from Cameroon, Ghana, Nigeria, and Tanzania, as well as environmental <i>E. coli</i> strains previously identified in South Africa and Ghana. <b>Conclusions</b>: The detection of diverse, mobile MDR <i>E. coli</i> lineages in poultry environments clearly signals a substantial risk for resistance gene dissemination into the food chain and surrounding ecosystems. Immediate attention and intervention are warranted to mitigate public health threats.