A Modern Treatise concerning the Plague and the Pox: Applied Epidemiology of Infectious Diseases in New South Wales

Abstract

In this thesis I present the body of work I have completed to fulfil the requirements of the Master of Philosophy (Applied Epidemiology) (MAE) at the Australian National University, conducted during my field placement at Health Protection NSW. I present my research projects, teaching activities, and additional field placement activities that together document my experiences as an MAE Scholar and demonstrate the competencies required of the MAE. I conducted an eight year retrospective cohort study using routine surveillance data to investigate syphilis reinfections in NSW. Using survival analysis I was able to quantify syphilis reinfections over this period, determine a reinfection incidence rate, and identify factors that predict syphilis reinfection. I evaluated the NSW multidrug resistant organism (MRO) surveillance system, identifying shortcomings in the acceptability and timeliness of the system, and making recommendations for improvement. I worked on the NSW public health response to the global mpox outbreak in 2022, monitoring the epidemiology of the outbreak in NSW, developing resources including contact factsheets and guidance, and planning for the vaccination rollout. To support the COVID-19 response I conducted data analyses to characterise the arrival of the SARS-CoV-2 Omicron variant in NSW, its spread among the population, and the differences in disease severity between Delta variant and Omicron variant cases. In November 2022 I investigated a foodborne illness outbreak linked to a high tea event at a hotel in the Blue Mountains. I presented my research on syphilis reinfection and mpox at three national and international conferences in 2022 and 2023, and I prepared a manuscript on the NSW response to the global mpox outbreak for submission to a scientific journal. As part of the MAE teaching requirements, I prepared a lesson from the field for my cohort on neglected tropical diseases, and I co-designed and delivered a group teaching session for the 2022 MAE cohort on antimicrobial resistance and multidrug resistant organism surveillance. In addition to these projects, I contributed to a range of other activities in Health Protection NSW, including extensive work in the COVID-19 response in 2021 and coordinating and chairing the seminar series Epi Grand Rounds in 2022 for the NSW Infectious Disease Network.