Phenotype-genotype relationships of Escherichia coli O157 and O26 isolates from New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Manawatū, New Zealand

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen responsible for causing severe manifestations of gastroenteritis in humans worldwide. STEC is transmitted to humans through the consumption of compromised food and water, or direct animal contact. Escherichia coli (E. coli) O157 and E. coli O26 are considered to be among the important STEC serogroups worldwide due to their association with outbreaks and clinical cases of haemolytic uraemic syndrome and haemorrhagic colitis. This study is concerned with the application of phenotypic microarray technology and high-throughput sequencing technology to characterise E. coli O157 and E. coli O26 New Zealand isolates. In this study, 190 phenotypes of carbon sources utilisation were studied in isolates belonging to E. coli O157 and O26 serogroups. The isolates were divided into groups based on the fermentation of sorbitol and rhamnose in E. coli O157 and O26, respectively. All the isolates respired on approximately 40% of the carbon sources. The sorbitol positive E. coli O157 isolates respired on more carbon sources compared to the sorbitol negative E. coli O157, rhamnose negative and rhamnose positive E. coli O26 isolates. Genomic analysis showed that E. coli O157 isolates had shorter genomes compared to those of the E. coli O26 isolates. The core genome comparisons revealed differences between and within the E. coli O157 and O26 serogroups. Clustering of E. coli O157 and O26 isolates based on sorbitol and rhamnose fermentation, respectively, was observed. The results obtained from this study illustrated that phenotypic and genotypic differences existed within the E. coli O157 isolates. The findings of the current study also demonstrated that while the E. coli O26 isolates had similar phenotypic characteristics, genotypic differences existed within the isolates