Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda

SIMPLE SUMMARY: A paucity of information on antimicrobial resistance in animals in Rwanda prompted us to conduct this study, the objective of which was to estimate the prevalence of antibiotic resistance among Escherichia coli and Salmonella from the feces of cattle, goats, pigs, and poultry. We found that resistance to tetracycline, ampicillin, and streptomycin were the most frequent among non-type-specific E. coli isolates. Resistance to chloramphenicol, quinolone-based antibiotics, amoxicillin–clavulanic acid, and azithromycin were also observed among these bacterial isolates, but with lower percentages. Most of resistant E. coli, including multidrug-resistant strains, were isolated from poultry fecal samples. More than 30% of samples were positive for E. coli resistant to third-generation cephalosporins or quinolone-based antibiotics. All isolated Salmonella were pan-susceptible. These results give an insight into the status of antibiotic resistance in food animals in Rwanda, as well as a call for further research. Also, the findings indicated a need for antibiotic stewardship and antimicrobial resistance surveillance initiatives. ABSTRACT: In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) E. coli and Salmonella using plain culture media. In addition, we used MacConkey agar media supplemented with cefotaxime at 1.0 μg/mL and ciprofloxacin at 0.5 μg/mL to increase the probability of detecting E. coli with low susceptibility to third-generation cephalosporins and quinolones, respectively. Antibiotic susceptibility testing was performed using the disk diffusion test. Among 540 NTS E. coli isolates, resistance to tetracycline was the most frequently observed (35.6%), followed by resistance to ampicillin (19.6%) and streptomycin (16.5%). Percentages of NTS E. coli resistant to all three antibiotics and percentages of multidrug-resistant strains were higher in isolates from poultry. All isolated Salmonella were susceptible to all antibiotics. The sample-level prevalence for resistance to third-generation cephalosporins was estimated at 35.6% with all third-generation cephalosporin-resistant E. coli, expressing an extended-spectrum beta-lactamase phenotype. The sample-level prevalence for quinolone resistance was estimated at 48.3%. These results provided a baseline for future research and the development of integrated surveillance initiatives.