Genomics & Gastroenteritis - A Journey in Applied Epidemiology

Abstract

This thesis describes the work completed during my field placement undertaken as part of my Master of Philosophy in Applied Epidemiology (MAE). From February 2021 to December 2022, I attended a field placement jointly shared between OzFoodNet at the Victorian Government Department of Health (DH), and the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at the Peter Doherty Institute for Infection and Immunity. As part of my field placements, I completed four projects to meet the requirements of the MAE. I was involved in an investigation of an outbreak of campylobacteriosis at a wedding, where I performed a nested case control study to try to identify the source of infection. The results indicated that the duck breast canape was the most likely source of infection. This investigation is also presented as a manuscript that has been submitted to Communicable Diseases Intelligence for peer-review and publication. I completed a data analysis project which examined the genomic diversity of Salmonella Typhimurium in Victoria between 2018-2020, to inform the implementation of whole genome sequencing (WGS) as a tool for routine surveillance. As an outcome of this work, I was able to assist the OzFoodNet team at DH in implementing the system, as well as test its usefulness during an investigation of a small cluster of cases of Salmonella Typhimurium. This cluster of cases was found to be part of a wider contaminated chicken issue that affected multiple jurisdictions. My data analysis project was presented at the Communicable Diseases & Immmunisation conference in Sydney in June 2022. I delved into the world of antimicrobial resistance (AMR), utilising data linkage to conduct an ecological study. The aim of this study was to examine the prevalence and genomic profile of vanA vancomycin resistant enterococci (VRE) in Victorian health care facilities and compare this to patterns of patient movement between hospital networks. This study aimed to inform future studies on the transmission of vanA VRE and to provide valuable input into the work performed by the AMR team at DH to develop surveillance and response processes for VRE. I also assisted OzFoodNet in establishing harmonised enhanced national surveillance of Salmonella Enteritidis (SE). This project reviewed current jurisdictional surveillance systems for SE and provided recommendations for establishing standardised data collection, as well as integration of national genomic surveillance of SE using the AusTrakka platform. As well as my four major projects, I describe two teaching activities. I provided an exercise on using genomics for the surveillance of foodborne disease as a Lesson from the Field to my MAE peers and had the opportunity to teach first year scholars about genomics and AMR. The thesis also outlines additional public health experience and other minor competencies gained during my field placements. Collectively, the work in this thesis highlights the important role genomics and field epidemiology plays in the surveillance and investigation of foodborne disease and detection of AMR and demonstrates the knowledge and skills I have obtained through completing the MAE. Show more