Antimicrobial resistance profiles of Extended-Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli isolated from waste water, poultry, and swine samples at the animal enviroment interface in Kampala, Uganda

Abstract

Antimicrobial resistance (AMR) is a growing global public health challenge that threatens the effectiveness of antimicrobial agents in both human and veterinary medicine. Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli are among the priority antimicrobial-resistant pathogens. This study aimed to determine the antimicrobial resistance profiles of ESBL-producing E. coli at the animal-environment interface in Kampala, Uganda. A cross-sectional study was conducted using 120 samples comprising wastewater collected from Bugolobi Sewage Treatment Plant and Kampala City Abattoir, poultry cloacal swabs collected from Kalerwe, Kasubi, Nakawa, and Nakasero live bird markets, and swine rectal swabs collected from Nansana Abattoir. Isolation and identification of E. coli were performed using standard microbiological and biochemical methods. Phenotypic confirmation of ESBL production and antimicrobial susceptibility testing were conducted using the Kirby–Bauer disk diffusion method in accordance with Clinical and Laboratory Standards Institute (CLSI) 2026 guidelines. Overall, E. coli was isolated from 79 of the 120 samples, giving an overall proportion of 65.8%. Recovery rates were highest in wastewater (78%), followed by poultry (65.0%) and swine (55.0%). Among the E. coli isolates, 32% were confirmed as ESBL producers. Poultry had the highest proportion of ESBL-producing E. coli (50.0%), followed by swine (32%) and wastewater (16.1%), with (p = 0.023). Antimicrobial resistance was common, with 79% of isolates resistant to at least one antimicrobial agent, while 34% exhibited multidrug resistance. Multidrug resistance was highest among poultry (46%) and wastewater (42%) isolates compared with swine (9%) (p = 0.01). The findings demonstrate that wastewater, poultry, and swine constitute important reservoirs of ESBL-producing E. coli within Kampala's animal-environment interface. Strengthening antimicrobial stewardship, improving wastewater treatment and abattoir waste management, and implementing integrated One Health surveillance are essential to limit the spread of antimicrobial resistance in Uganda.