On Alert: Applied Epidemiology in Australia

Abstract

This thesis fulfills the requirements of the Master of Philosophy in Applied Epidemiology (MAE Program).

I completed the 22-month MAE Program placed in the Communicable Diseases Epidemiology and Surveillance Section (CDESS) in the Office of Health Protection at the Australian Government Department of Health and Aged Care (formerly known as the Australian Government Department of Health) . During my MAE Program, I completed four core projects and undertook additional public health surveillance and epidemiology activities. The first of these projects was an investigation of an acute public health threat, where I present a paper on the epidemiology of human cases in an outbreak of locally acquired Japanese encephalitis virus in Australia that occurred in 2021-2022.

The second is a routine surveillance report, where I analysed enteric disease databases and prepared the 2018 annual surveillance report for OzFoodNet. This report details the epidemiology and trends of foodborne diseases and foodborne disease outbreaks in Australia in 2018.

The third was the establishment of a new pilot surveillance system to detect potential outbreaks of salmonellosis by providing automated alerts to OzFoodNet epidemiologists working in CDESS. The Salmonella Serovar Alert System (SSAS) is a two-stage system that automatically assesses Salmonella serovars using alert criteria (stage one) and outbreak detection algorithms (stage two) to produce reports and detect unexpected serovar increases across multiple jurisdictions. The outbreak detection algorithms used to develop SSAS were tested and validated against known historical Multi-Jurisdictional Outbreak Investigations previously investigated by OzFoodNet. Following the pilot of SSAS I also undertook a short evaluation to seek key stakeholder feedback on the system to further improve outputs and recommend further enhancements. Lastly, I conducted an interrupted time series analysis to determine the impact of COVID-19 public health response in 2020-2022 on legionellosis cases in Australia. We measured how these impacts varied by the main reported species; Legionella longbeachae and Legionella pneumophila.

Additionally, I describe how I meet the minor competencies, such as teaching field epidemiology and briefly detail my experience in a two-month field epidemiology fellowship program based at the World Health Organization's Western Pacific Regional Office in Manila, Philippines.