Characterization of Antibiotic Resistance in Escherichia coli from Meat Products and Human Samples in Botswana Using Molecular and Whole-Genome Approaches
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Introduction: Botswana experiences high diarrheal illness rates in rural areas like the Chobe region, where E. coli from meat products and food handlers may contribute to antibiotic resistance (ABR) transmission, posing a potential threat to public health. Purpose: Characterize the ABR profiles of E. coli isolated from meat products and human feces to explore potential links between meat and human ABR transmission. Methods: Meat (chicken and beef) were collected from local grocery stores, and human fecal samples were obtained from food handlers in Kasane, Botswana. E. coli isolates were obtained by selective enrichment and plating on EMB and MacConkey agars. ABR profiles were determined for 12 antibiotics using the CLSI disk diffusion method. Whole-genome sequencing was performed on multidrug-resistant isolates using the Illumina Miseq platform and genomes were analyzed using Galaxy and BV-BRC. Results: E. coli was isolated from 66 of 124 meat samples and 230 of 507 human fecal samples, with 56.06% (37/66) of meat isolates and 43.04% (99/230) of human isolates showing resistance to at least one antibiotic. Multidrug resistance (MDR) was detected in 30.30% (20/66) of meat isolates and 11.74% (27/230) of human isolates. Disk diffusion testing revealed that tetracycline and trimethoprim/sulfamethoxazole were the most frequently detected resistances across both meat and human isolates. Whole-genome sequencing identified no shared sequence types (STs) between E. coli isolates from meat and human samples. However, both sources carried the same ABR genes, including sul2, blaTEM-1, tetA, and qnrS1, along with shared plasmid types (IncFIB, IncFII, IncX1), while integrons, detected only in meat isolates, suggest horizontal gene transfer through mobile genetic elements. Significance: The detection of shared antibiotic resistance genes and plasmid types between meat and human isolates underscores the importance of monitoring meat products to inform strategies for mitigating the transmission of antibiotic resistance in Botswana.
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