Molecular Characteristics of Archived Isolates of Escherichia coli from the Gut of Healthy Food Animals and Environmental Sources in Selected Counties in Kenya

E. coli is a reservoir of resistance genes encoding resistance enzymes including extended-spectrum beta-lactamases (ESBL) and carbapenemases. This study aims to determine the resistance pattern, the pathotypes, and the proportion of ESBL producers among archived E. coli isolates from healthy food animals and their immediate environments at the Center for Microbiology Research, Kenya Medical Research Institute. Of the 375 isolates, 78.4% isolates were resistant to at least one of the 13 tested antibiotics and 28.8% showed multidrug resistance. Resistance was higher to tetracycline (55.2%), co-trimoxazole (44%), trimethoprim (43.7%), and ampicillin (28.8%). The proportion of Enteroaggregative E. coli was 88.3% while other pathotypes were not found. The proportion of ESBL producers was 8.8% of which 100% harboured blaTEM, 18.1% harboured blaCTX-M; blaSHV was not found. E.coli isolates from healthy food animals were multidrug resistant and harboured virulence genes and ESBL genes. Risk assessment and management is necessary to protect farmers and the public in general. Keywords: Archived E. coli isolates, antimicrobial resistance, multidrug resistance, pathotypes, ESBLs