Phenotypic and molecular characterization of pathotypes, and antimicrobial resistance profiles of escherichia coli from food, water and livestock in selected informal settlements in Nairobi.

Abstract

Escherichia coli (E.coli) are globally recognised as important causes of diarrhoeagenic infections as well as other extra-intestinal infections in both animals and man. In developing countries, E.coli is the most important agent causing diarrhoeal diseases which results in significant economic losses. In veterinary medicine, domestic animals are indicated as an essential harbour of multidrug-resistant E.coli which can be transferred food animals to man. The global rise in antibiotic resistance and particularly multi-drug resistance (MDR) has made treatment of infections challenging. The objective of this research study was to determine the pathotypes, and antimicrobial resistance profiles of E.coli isolated from foods, water and livestock in selected informal settlements in Nairobi. The study was carried out in two informal settlements in Nairobi, namely Viwandani and Korogocho. It entailed reviving of previously isolated and biochemically confirmed E.coli isolates. These isolates were streaked onto MacConkey agar plates and then incubated overnight at 37ºC. Distinct pink colonies were then picked from MacConkey agar, streaked on Tryptone Soy Agar (TSA) and incubated for 24hrs at 37ºC to obtain pure colonies. The Kirby-Bauer disk diffusion method was employed to determine the phenotypic antimicrobial susceptibility of the isolates in accordance with the Clinical and Laboratory Standards Institute(CLSI) guidelines (CLSI 2014). Inoculated plates with Mueller Hinton Agar (MHA) were seeded with antimicrobial disks and the zone of inhibition measured after incubation. Each isolate was screened for antimicrobial susceptibility with twelve different antimicrobial agents of veterinary and human health importance. The reference organism used was Escherichia coli ATCC 25922. The highest resistance was shown to ampicillin where 79(45.4%) isolates showed resistance to the antimicrobial agents, while the least resistance (0%) was demonstrated to ceftriaxone where all the isolates were susceptible. For livestock isolates, 74.5% of the isolates were susceptiple to antimicrobial agents tested, 8% were intermediate, and 17.5 were resistant.The highest resistance in livestock isolates was shown to tetracycline at 53% and sulfamethoxazole/ trimethoprim at 53% while amoxicillin/clavulanate and ciprofloxacin showed the least resistance at 1%. Antibiotic resistance genes detected in food isolates included blaTEM (91%) and tetA31% while in livestock, the antimicrobial resistance profiles included blaTEM (35%), and tetA (15%).The most prominent pathotype in food isolates was enteropathogenic enteropathogenic E. coli ETEC estA with 2% of the isolates testing positive while enterohaemorhagic E.coli (EHEC) was the most prominent pathotype in livestock with 4%. This study also showed that Escherichia coli from Viwandani and Korogocho are pathogenic and resistant to antibiotics. Since most antibiotics are shared between animals and human, the detection of resistance E.coli strains points at a risk of spread of resistant strains to man. This calls for further research and collaboration of public health department in a one health approach.