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

## TL;DR

This study characterizes antibiotic-resistant Escherichia coli from a poultry farm in South Africa, highlighting the risk of resistance spreading through food and the environment.

## Contribution

The study provides genomic insights into multidrug-resistant E. coli in a South African poultry system and their global phylogenetic links.

## Key findings

- 74% of confirmed E. coli isolates were multidrug-resistant, with high resistance to tetracycline, ampicillin, and trimethoprim–sulfamethoxazole.
- Resistance genes were frequently associated with mobile genetic elements like plasmids and integrons.
- Predominant sequence types showed phylogenetic relatedness to poultry and environmental isolates from other African countries.

## Abstract

Background: Intensive poultry production systems can act as reservoirs for antibiotic-resistant and multidrug-resistant (MDR) Escherichia coli, posing a public health risk through food and environmental transmission. Methods: This study investigated the genomic characteristics of antibiotic-resistant E. coli 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 E. coli isolates were detected using the Colilert-18 system, cultured on eosin methylene blue agar, and genomically confirmed by quantitative PCR (q-PCR) targeting the uidA 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. Results: Of 150 presumptive E. coli, 70 were genomically confirmed as E. coli 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 qacI. 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 E. coli strains previously identified in South Africa and Ghana. Conclusions: The detection of diverse, mobile MDR E. coli 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.