Antimicrobial use and resistance profiles of Escherichia coli and Campylobacter species from small-scale poultry farms in Central Kenya

Abstract

Globally, Escherichia coli (E. coli) and Campylobacter spp. are key foodborne pathogens and important indicators for antimicrobial resistance (AMR) surveillance in poultry. Our study assessed their occurrence, antimicrobial resistance profiles, and antimicrobial use in Kenyan small-scale poultry production. A cross-sectional study was conducted between August and December 2024 in 340 small-scale poultry farms across four sub-counties of Murang’a County. In each farm, cloacal swabs from five adult chickens were aseptically collected and pooled to form a composite sample, while data on antimicrobial use were collected using a semi-structured questionnaire. Isolation of E. coli and Campylobacter spp. was carried out using conventional culture procedures, and isolates were confirmed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Antimicrobial susceptibility testing was performed using the Kirby–Bauer disk diffusion method, as per the CLSI (2024) guidelines. Antimicrobial use was reported in 75.3% (n = 256/340) of the study farms, with tetracyclines 73.8% (n = 189/256) and sulfonamides 52.3% (n = 134/256) being the most commonly used classes. E. coli was detected in 99.4% (n = 338/340) and Campylobacter spp. in 61.4% (n = 209/340). Among the Campylobacter isolates, C. jejuni 58.8% (n = 123/209) was more prevalent than C. coli 41.1% (n = 86/209). The highest resistance among E. coli isolates was observed against tetracycline, 74.0% (n = 77/104), and sulfamethoxazole-trimethoprim, 65.4% (n = 68/104). Extended-spectrum β-lactamase (ESBL)-producing E. coli and phenotypic carbapenem-resistant E. coli were detected at 4.8% (n = 5/104) and 25.0% (n = 26/104), respectively. Campylobacter spp. exhibited the highest resistance to nalidixic acid 67.3% (n = 69/104) and tetracycline 65.4% (n = 68/104). Multidrug resistance (MDR) was identified in 58.6% (n = 61/104) of E. coli and 46.1% (n = 48/104) of Campylobacter spp. A significant correlation between antimicrobial use and E. coli resistance profiles was found in Kigumo sub-county (r = 0.72, p = 0.04), whereas no significant association was observed for Campylobacter. Extensive use of antimicrobials and high multidrug resistance among E. coli and Campylobacter spp. in small-scale poultry farms in Kenya pose a significant public health and food safety risk. Therefore, targeted strategies to reduce antimicrobial use and the emergence of AMR bacteria from poultry production are required in the region.