Gut Instincts: Applied Epidemiology of Enteric Viruses, Bacteria and Parasites

Abstract

Hunter New England (HNE) Health Protection is responsible for prevention, surveillance and response to threats to human health in the Hunter New England Local Health District (HNELHD) region of New South Wales (NSW). From February 2023 to October 2024, I undertook my MAE field placement within HNE Health Protection. This thesis describes the projects I undertook during the field placement. The projects that fulfill the MAE competencies are: 1) a capture-recapture analysis of acute flaccid paralysis surveillance in the Australian Capital Territory, 2) a case-control study of Clostridioides difficile infection and antibiotic use at a large, regional hospital, 3) investigation of an increase in cryptosporidiosis notifications in the HNE region, 4) an evaluation of Salmonella Enteritidis human health surveillance in NSW and 5) teaching of epidemiological concepts to other MAE scholars and colleagues. This thesis also describes other public health activities I contributed to during the field placement, including: local and national foodborne outbreak investigations through OzFoodNet; a data analysis summarising Australian listeriosis outbreaks from 2012 to 2022; routine follow-up of notifiable diseases in HNELHD; ad hoc data analyses to inform surveillance of notifiable diseases in HNELHD; development of HNE Health Protection incident response management system and processes for highly pathogenic avian influenza; and amendments to HNE Health Protection's Standard Operating Procedures for cryptosporidiosis follow-up. These projects and activities fulfil the core requirements of the Australian National University Master of Philosophy (Applied Epidemiology) program.