Genotyping, phenotyping and phylogenetic classification of environmental Escherichia coli isolates

Abstract: Surface water is not only an essential water source for many rural and peri urban South Africans but also a medium for the transmission of diseases. In some instances this water is the only water source available for drinking water. This poses a health risk to consumers taking into consideration that treated effluents are released into surface waters. Microbial water quality monitoring has been at the forefront for decades, however the methods developed for testing water is geared towards analysis for the presence of pathogens in water bodies which is guided by the presence of faecal indicator bacteria, Escherichia coli (E. coli). E. coli itself can however cause disease in humans and with the growing antimicrobial resistance crisis, a valuable addition to the knowledge base is the understanding of E. coli virulence, their antibiotic resistance profiles and their geographical distribution. Microbial water quality studies test a limited number of samples due to the time, cost and skills required and the research problem was that a methodology was needed to allow for the faster screening of E. coli to assist in better monitoring for virulence genes and antibiotic resistance profiles of the isolates. The aim of the study was then to develop a directed screening method to identify E. coli from water bodies and characterize them in terms of their genotypic, phenotypic and phylogenetic grouping...D.Tech. (Biomedical Technology