Antimicrobial Resistance Profiles and Genetic Characterization of Escherichia coli Isolated From Water in Athi River, Machakos

Abstract

Antimicrobial use in agriculture, livestock and in human health has increased over the years leading to increase in antimicrobial resistance among strains that can also find their way into the aquatic environments. Rivers can act as reservoirs of highly resistant strains and facilitate the dissemination of multidrug resistant (MDR) strains to animals and humans using the water. The objective of the study was to determine antimicrobial resistance profiles and genetic characterization of Escherichia coli isolated from water in Athi River, Machakos. The study design was cross-sectional. A total of 318 E. coli isolates (53 from each of the size site) were analysed for antibiotic susceptibility and characterized using polymerase chain reaction (PCR). Descriptive analysis using mean, frequency and proportion were used to analyse the data. Chi square test, odds ratio and confidence intervals (set at 95%) were used to assess drug susceptibility between the sites. Student’s t-test was also computed to compare the means of coliform count during dry and wet season. Sewage effluent site most highly contaminated (mean of 9.5x103 CFUs/ml) and virgin land with the least CFUs (mean 9.5x102 CFUs/ml). E. coli isolates were most resistant to ampicillin (63.8%) and most susceptible to gentamicin (99.4%). The prevalence of Multi drug resistant (MDR) strains (resistance to ≥3 classes of antimicrobials) was 65.4% in all sites. The prevalence of extended spectrum βlactamases (ESBLs) was 2.2% out of 318 and their distribution was not related to the sites. Based on PCR results, 22% had blaTEM, 33% had blaCTX-M and 28% had blaCMY. The prevalence of typical Enteropathogenic E. coli (EPEC) strains (carrying both eae and bfp genes) was 5% while the prevalence of atypical EPEC (carrying only eae) was 1.8%. The prevalence of Enteroaggregative E. coli (EAEC) carrying the aggR gene was 11%. The prevalence of Enterotoxigenic E. coli (ETEC) encoding only lt toxin was16 (5%) and while those carrying only st toxin was 6.9%. The prevalence of Enteroinvasive E. coli strains (EIEC) encoding as IpaH was 5% while that of strains, adherent invasive E. coli (AIEC), carrying adherent invasive gene inv was 8.7%. PCR analysis also showed that 36% isolates were positive for class 1integrons. It can be concluded that water from Athi River is not safe for human consumption and region near the sewage treatment plant requires most attention for decontamination. Better management of sewage treatment plant should be encouraged as well as reduction of anthropogenic activities near water systems.