Detection and Prevalence of Top 6 non-O157 Shiga Toxin-Producing Escherichia coli in Beef

Jessica Bannon Advisor: Dr. Keith Warriner University of Guelph, 2016 There has been an increased incidence of non-O157 Shiga Toxin Escherichia coli (STEC) with six serotypes (Top 6) being implicated in causing haemolytic uremic syndrome (HUS). Beef has been suggested to be a significant vehicle for non-O157 STEC although conclusive evidence has yet to be obtained. The following aimed to determine the prevalence of the Top 6 non-O157 STEC in beef processing using three different diagnostic platforms then characterize the recovered isolates. Hide, carcass and environmental swab samples (n = 120) were collected from beef processing facilities over a 12 month period. Enriched samples were screened using Biocontrol GDS, BAX or PALLgene molecular diagnostic tests. Presumptive non-O157 STEC positive samples were confirmed using conventional PCR and serology. STEC was detected by GDS (55% positive), BAX (85% positive), and PALLgene (93%). However, during confirmation testing only 18 of the 120 samples (15%) were found to harbour STEC. Interestingly, the presence of virulence factors in the recovered isolates was unstable and readily lost during subsequent sub-culturing. There is a low prevalence of Top 6 non-O157 STEC associated with beef although other serotypes are encountered. Yet, the instability of the virulence factors in recovered strains would question their clinical relevance. iii Acknowledgements It is an honour and a privilege to extend my deepest gratitude to Dr. Keith Warriner, my advisor, for his guidance, support, patience, and dedication to this project. You gave me the direction to assistance to navigate through this field of research, as well as the freedom to push past the limits of the accepted knowledge. Because of this, my passion for research has grown significantly, and I am honoured to have been one of your students. I would like to acknowledge Dr. Roger Johnson, for his valuable time, advice, help with the correcting of this thesis, and assistance with the direction and completion of this research. I would like to extend my thanks to Carlos Leon-Velarde, who provided a great deal of assistance throughout this processes both within and outside of the laboratory. I would also like to express my appreciation for Dr. Gisele LaPointe for her assistance with the completion of the thesis and support through the important final stages of my degree. I want to acknowledge Cleso Mendonça Jordåo Junior, who worked closely with me in the laboratory over the course of this investigation. Thank you for your tremendous amounts of support, assistance, and guidance over the past two years. I would like to thank Mido Melebari, who assisted with various aspects of this investigation. You were both excellent collaborators and friends, and I will be forever grateful for your involvement with my MSc. I would also like to acknowledge Azadeh Namvar and Fan Wu for their assistance and support. For all of the support outside of the laboratory environment, I would like to thank the University of Guelph Intramural Department, especially Sarah, Karley, Haley, and Erica. You provided a crucial balance to my experience here at the University, and the emotional support that accompanied our friendship has been so significant to me. I would also like to acknowledge the Lam family – Joe, Marilyn, Chris, Jenny, Mohan, and Toby. You supported me with academic advice, emotional support, fantastic meals, and encouraged me through to the next step in my career. Thank you for being my “Guelph Family”. I would like to extend an additional acknowledgement to Chris Lam. Despite being in a different department, you managed to provide me with monumental levels of academic and scientific advice throughout the entirety of my thesis. Furthermore, you have been such an important rock and companion, and the moral support I’ve received from you has been critical to my success, sanity, and happiness. For that, I will be forever grateful. To my parents, Sharron and Tim, I need to extend a huge amount of gratitude. Throughout each stage of my academic career, you have always played such a major role in providing me with the support necessary for me to succeed. I would also like to acknowledge my siblings, Marshall and Laura. Thank you for being such wonderful role models, always being there for me, and allowing me to get to where I am today. iv Table of