Multidrug resistant Escherichia coli on chicken farms in Arua District, West Nile, Uganda: prevalence, antimicrobial resistance patterns, and public health risks

Abstract

Background: Antimicrobial resistance in food-animals threatens public health and food security. Much as chicken farms harbour resistant E. coli, its epidemiology in Uganda is still not well understood. This study determined the prevalence of multidrug resistant E. coli, described the resistance patterns, and identified risk factors associated with carriage of multidrug resistance on chicken farms in Arua, west Nile region, Uganda. Methods: Fresh faecal droppings were randomly sampled from chicken farms. Additional data were obtained from farm owners using a semi-structured questionnaire. Samples were inoculated on MacConkey agar and presumptive colonies were sub-cultured on blood agar, subjected to gram staining and biochemical tests. Kirby-Bauer disc diffusion method was used to test for susceptibility and clinical breakpoints were interpreted as defined by the Clinical and Laboratory Standards Institute guidelines (CLSI) 2022 (version 32). Multidrug resistance was defined as resistance to three or more classes of antibiotics. STATA version 14.0 was used for data analysis. To assess associations, prevalence ratios (PRs) were computed using Modified Poisson regression model. Result: Overall, 158 fresh faecal droppings were sampled. Most (68%) farms were small scale (<100 chicken), majority (67%) keeping dual-purpose chickens with over 50% located in rural areas. Multidrug resistant E. coli prevalence was 62.7% (95% CI: 55.0 – 70.3). There were significant differences in prevalence of multidrug resistance by gender (p = 0.004) and farmer’s education status (p = 0.017). High resistance was observed against ampicillin 79.8% (95% CI: 72.7 – 85.4), tetracycline 72.8% (95% CI: 65.2 – 79.2), cotrimoxazole 55.7% (95% CI: 47.8 – 63.3), and ciprofloxacin 38% (95% CI: 30.7 – 45.9). Male compared to female farmers (adjusted prevalence ratio [aPR] = 0.72, CI: 0.55 – 0.93), secondary versus informal education (aPR=0.64, CI: 0.46 – 0.88), tertiary versus informal education (aPR = 0.60, CI: 0.47 – 0.75), and administration of recommended antibiotic doses versus not following recommended doses (aPR = 0.76, CI: 0.59 – 0.96) independently posed a lower risk of multidrug resistant E. coli carriage. Unlike farms with footbaths, farms without had higher rates of multidrug resistant E. coli (aPR=1.48, CI: 1.16 – 1.88). Significant interaction occurred between tertiary education and absence of footbath (aPR = 1.74, p = 0.01). Conclusion: Multidrug resistant E. coli and resistance to individual antibiotics were highly prevalent on the chicken farms. Footbath, male gender, secondary education or higher and adherence to recommended antibiotic doses protected against E. coli resistance while education with no footbath on farm posed a heightened risk. There is need for context-specific collaborative strategies, to address knowledge on biosecurity on farms, and prudent use of antimicrobials among chicken farming communities which considers gender dimensions.