Abstract
M.Tech. (Biomedical Science)
Escherichia coli (E. coli) is a rod-shaped Gram-negative bacterium that exists as a commensal indicator or as a pathogenic type. Intestinal pathogenic E. coli infect and cause diarrheal disease syndrome in the gastrointestinal tract, while extra-intestinal pathogenic E. coli causes disease in other systems. Furthermore, E. coli has a variety of strains, each with its genotype that differs from wild-type E. coli. The genotype will then influence the phenotype that is expressed and each strain's physiology and life cycle. As a result, various E. coli strains will live in different animals. At present intestinal pathogenic E. coli that have been identified includes Diffusely Adhering E. coli (DAEC), Enteroinvasive E. coli (EIEC), Enterotoxigenic E. coli (ETEC), Enteropathogenic E. coli (EPEC), Diffusely Adhering E. coli (DAEC), Enterohaemorrhagic E. coli (EHEC), Enteroaggregative E. coli (EAEC), Shiga Toxin (Stx) producing E. coli (STEC) and lastly the Adherent Invasive E. coli (AIEC). Uropathogenic E. coli (UPEC), Neonatal Meningitis Associated E. coli (NMEC), and Sepsis-Associated E. coli (SEPEC) are some of the extra-intestinal pathogenic E. coli strains. Intestinal pathogenic E. coli has been the contributing factor in children under five to cause diarrheal illness worldwide. There is a lack of adequate information regarding the genetic diversity of E. coli strains isolated from South Africa, which could have a mixture of virulence genes, antimicrobial resistance genes and other genes which might assist the bacteria in increasing its bacterial virulence and infectivity. Several methods are available for detection and enumeration of E. coli from different sources. These include genotyping methods such Pulsed-Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST), Next Generation Sequencing (NGS), including Whole Genome Sequencing (WGS). WGS is now a widely used technique for characterising the bacterial genome in terms of molecular epidemiology, virulence, and antibiotic resistance. It is important in describing and improving our understanding of bacterial evolution, transmission, and outbreaks...