Molecular identification and antimicrobial resistance profiling of pathogenic E. coli isolates from smallholder livestock households in Central Ethiopia

Escherichia coli of different pathotypes are frequently involved in morbidity and mortality in animals and humans. The study aimed to identify E. coli pathotypes and determine antimicrobial resistance (AMR) profiles in Ethiopian smallholder livestock households. The pathotyping included 198 E. coli isolates identified from human and environmental samples collected from 98 households. AMR profiling was conducted on selected E. coli pathotypes from 89 households, along with known isolates from calf samples obtained from the same households. Morphological and biochemical tests were used to identify presumptive E. coli isolates. DNA was extracted and then singleplex PCR was used to amplify virulence genes. A disc diffusion test was applied for AMR profilings in E. coli pathotypes. Data were evaluated using chi-square tests and logistic regression. Calf (79.8 %) and human (73.7 %) samples were more likely to contain pathotypes (OR 3.2; 95 % CI: 1.7, 5.9; p = 0.001 and OR 2.3; 95 % CI: 1.2, 4.1; p = 0.008, respectively) than the environmental samples (55.6 %). ETEC (32.3 %) and STEC (15.2 %) were the most common pathotypes detected in the study samples. Out of the 176 isolates selected for AMR profiling, 85 % were resistant to at least one drug and 36 % were multi-drug resistant (MDR). The MDR isolates were found in 44 households, with 11 sharing identical pathotypes and resistance profiles among the different samples. Thus, E. coli strains were likely circulated among humans, animals, and the environment. This in turn calls for a One-health approach to improve antimicrobial usage standards and promote proper waste disposal practices.