Prevention and control of sexually transmissible infections and other infectious diseases across multiple settings

This thesis summarises the results of five major projects completed from February 2017 to November 2018 to meet the requirements of the Master of Philosophy in Applied Epidemiology (MAE), the Australian Field Epidemiology Program. The majority of the work presented here was completed at the Kirby Institute for infection and immunity at the University of New South Wales, with two additional projects carried out at the Communicable Disease Control Branch, South Australia Department for Health and Wellbeing (SA Health). Chapter 1 provides an introduction to the primary field placement at the Kirby Institute and an overview of activities undertaken over the course of the MAE program. Chapter 2 presents an epidemiological research project investigating gaps in the adolescent vaccination program for human papillomavirus (HPV), a sexually transmissible infection, with a view to informing interventions to improve coverage. The study examined school-level correlates of low initiation and completion of the vaccination course in several school-based programs in three jurisdictions, using a dataset built from several data sources, including the Australian Bureau of Statistics, the Australian Curriculum, Assessment and Reporting Authority, and the National HPV Program Register. Univariable and multivariable logistic regression analyses were conducted to determine characteristics of schools and school populations associated with low vaccination initiation and completion. Chapter 3 has a methodological focus, describing the development of geographical maps at the small area level for the Kirby Institute's 2017 Annual Surveillance Report of HIV, viral hepatitis and sexually transmissible infections. This project involved an iterative process to define the most appropriate methodological approach to show differences in age-standardised notification rates that could be applied in future reports. The chapter documents the investigation of the effects of administrative areas of different size, different classification methods of notification rates, and several suppression methods using maps developed for HIV and chlamydia as two diseases with contrasting epidemiology. Chapter 4 presents a full evaluation of the operations of the South Australian surveillance system for Neisseria gonorrhoeae antimicrobial resistance in the years 2016-17, using the United States Centers for Disease Control and Prevention (US CDC) guidelines for the assessment of disease surveillance systems. Also within the US CDC framework, chapter 5 describes work undertaken to support the introduction of HIV subtype and resistance surveillance at the national level and discusses potential indicators and data sources for a future evaluation of the new surveillance system, once operational. Finally, chapter 6 outlines a descriptive case series investigation of a Salmonella Typhimurium phage type 44 cluster in South Australia which did not identify a common source of infection, but contributed evidence that Salmonella Typhimurium is an important cause of foodborne illness in the community. Collectively, the majority of projects within this thesis contribute to strengthening STI surveillance in Australia, and the identification of factors associated with low uptake of HPV vaccination has the potential to guide future research and public health programming to improve prevention