Antimicrobial Susceptibility Profiles and Molecular Characterization of Archived Isolates of Escherichia coli from the Gut of Healthy Food Animals and Environmental Sources in Selected Counties in Kenya

Abstract

Escherichia coli is present in the intestinal tract of both humans and animals and is released into the environment through fecal material. E. coli is a reservoir for antibiotic resistance genes. Some strains of E. coli are pathogenic by acquisition of different virulence factors. The aim of this study was to determine antimicrobial susceptibility profiles, the pathotypes and the proportion of ESBL producers and ESBL genes among archived isolates of E. coli from the gut of healthy food animals and environmental sources in selected Counties in Kenya (Kiambu, Nairobi, Kisumu, Mombasa and Kwale). A laboratory based cross sectional study design was used. The sample size encompassed 375 archived isolates of E. coli (non-duplicate) at the Center for Microbiology Research, Kenya Medical Research Institute. Antimicrobial susceptibility profiles were determined by disk diffusion technique, E. coli pathotypes were determined by PCR. Phenotypic ESBL detection and ESBL encoding genes detection were done by Double Disk Synergy Test and PCR respectively. Overall, 78.4% archived isolates of E. coli were resistant to at least one of the 13 tested antibiotics among which 28.8% showed multidrug resistance whereas 21.6% were fully susceptible. Resistance to tetracycline was 55.2%, co-trimoxazole 44%, trimethoprim 43.7%, ampicillin 28.8%, nalidixic acid 18.7%, azithromycin 14.9%, ciprofloxacin 10.1%, chloramphenicol 8.8%, imipenem 0.8%, cefotaxime 5.9%, ceftazidime 3.7%, cefuroxime 2.4%, and gentamicin 1.1%. The proportion of Enteroaggregative E. coli (harbouring aggR gene) was 88.3% and other pathotypes were not found. The proportion of ESBL producing E. coli was 8.8% (33/375) and the antimicrobial resistance was significantly different between ESBL producers and non ESBL producers (p ≤ 0.05). All ESBL producers harboured blaTEM, 18.1% harboured blaCTX-M and none had blaSHV. Archived isolates of E. coli were found to be reservoirs for resistance determinants and virulence factor genes. Stringent regulations governing the usage of antimicrobials in animal agriculture should be applied to curb the development antibiotic resistance. Homestead and barns should be kept clean to prevent the spread of resistant pathogens in the environment by arthropods.