Fecal carriage and molecular characterization of ESBL-producing Enterobacteriaceae among farmers in Mid-Western Uganda

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Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose a growing threat to public health due to resistance to β-lactam antibiotics. This study aimed to determine the prevalence, antimicrobial resistance patterns, and genetic characterization of ESBL-producing Enterobacteriaceae from stool samples of farmers in Kibimba Parish, Kabarole District, Mid-Western Uganda. A cross-sectional study among 250 farmers involved stool culture, ESBL detection via the double-disc synergy test, PCR for blaCTX-M, blaTEM, and blaSHV genes, and antibiotic susceptibility testing. Data were analyzed using STATA v14.2. The prevalence of ESBL-producing Enterobacteriaceae was 36.4% (91/250) among farmers and 34.29 (107/312) (95%CI: 29.22–34.76) among isolated organisms. Escherichia coli was the predominant ESBL-producing isolate at 70.4% (76/107). High resistance was observed to piperacillin (94.0%) and ampicillin (81.4%), while imipenem (96.5%) and chloramphenicol (94.0%) showed the highest susceptibility. Multidrug resistance (MDR) was noted in 49.4% of all isolates and 33.7% of ESBL producers. Among 107 confirmed ESBL producers, 80.4% harbored at least one ESBL gene; blaCTX-M (48.7%), blaTEM (34.9%) and blaSHV (16.4%). ESBL carriage was significantly associated with use of shallow well water (p < 0.009), goat farming (p < 0.036), and chronic illness (p < 0.012). Farmers showed high fecal carriage of multidrug-resistant ESBL-producing Enterobacteriaceae, linked to environmental and health-related risk factors.