The genetic epidemiology of extended-spectrum beta-lactamase producing Escherichia coli within the Manawatū region : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Palmerston North, New Zealand

Hospital and community infections caused by antibiotic resistant bacteria are difficult to treat, can become severe, and increase mortality rates. Extended-spectrum beta-lactamase (ESBL)- producing Escherichia coli (E. coli) are increasing in New Zealand and commonly associated with multi-drug resistance (MDR) in urinary tract infections (UTIs). However, in New Zealand, there is limited information about antibiotic resistance and ESBL-producing E. coli found in the environment. This study aimed to characterise the antibiotic resistance phenotypes and genotypes of ESBL-producing E. coli within the Manawatū River and MidCentral District. Human clinical ESBL-producing Enterobacterales isolates were sourced from Medlab Central (August 2019 to March 2020 and June 2020 to January 2021), and environmental isolates were sourced from six locations along the Manawatū River over two sampling periods (August 2019 to March 2020 and July 2020 to January 2021). There were a total of 311 clinical and 86 environmental ESBL-producing E. coli collected from Medlab Central and the along the Manawatū River respectively. The environmental samples from along the Manawatū River consisted of water, sediment, stormwater and treated effluent. Whole genome sequencing was conducted on 189 of the clinical isolates, and on 45 of the environmental isolates. Sequencing results revealed both the clinical and environmental isolates have a variety of ESBL coding genes and other antibiotic resistance genes. The ESBL gene blaCTX-M-27 was most prevalent amongst clinical isolates and blaCTX-M-15 for environmental isolates. Additionally treated effluent and the point at which it flows into the Manawatū River is a source of these antibiotic resistant E. coli, which also had a high incidence of multi-drug resistance (MDR). Sequence type (ST) 131 was the dominant sequence type recorded for both the clinical and environmental isolates. Whole genome sequence analysis of these isolates suggested that there was sharing of the same strain between humans and the Manawatū River. The results from this study provide insights into ESBL-producing E. coli within the Manawatū River and MidCentral District. Knowing the genetic relatedness of ESBL producing E. coli and other associated antibiotic resistance will assist in understanding different transmission pathways relating to humans, animals, and the environment