Applied epidemiology of vaccine preventable diseases and nationally notifiable invasive bacterial infections in Australia

Abstract

In this thesis I present collected works under the theme of applied epidemiology and surveillance of vaccine preventable diseases and nationally notifiable invasive bacterial infections in Australia, which I conducted while placed at the National Centre for Immunisation Research and Surveillance (NCIRS) from February 2021 to October 2024. The thesis presents the four core competencies required in the Master of Philosophy (Applied Epidemiology) (MAE).

In my data analysis project I compared the short-term safety of pneumococcal vaccines in adults following a change to the National Immunisation Program schedule using data from AusVaxSafety collected between November 2016 to March 2022. AusVaxSafety is Australia's active surveillance system for self-reported adverse events following immunisation. I analysed counts, proportions and odds of reporting any event, solicited events and any medical attention (proxy for serious event). Using mixed-effect logistic regression, I demonstrate that half as many people reported adverse events after receiving the newer 13-valent pneumococcal conjugate vaccine compared to the vaccine that was on the schedule prior. Furthermore, I found Indigeneity did not predict the likelihood of reporting an event.

Population susceptibility is a key indicator of risk for measles outbreaks of, the avoidance of which is a crucial part of maintaining elimination status. In my epidemiological study I triangulated existing Australian data sources to identify age-specific measles susceptibility to inform immunisation policy and program measures to support maintenance of elimination. I estimated measles susceptibility by single year birth cohort for Australians born 1920-2019 using previously collected national vaccine coverage data from the Australian Immunisation Register (AIR) and national seroprevalence surveys. I found that nearly 1.7 million Australians (6.6%) were susceptible to measles in 2019. Australia's population level susceptibility was on the lower edge of the WHO recommended herd immunity threshold of 93-95% protection.

Case definition and review are essential components of maintaining surveillance for a nationally notifiable communicable disease. My surveillance project comprised developing a surveillance case definition for a newly nationally notifiable disease invasive Group A Streptococcus. Following thorough review of existing jurisdictional, national and international surveillance mechanisms for the surveillance of invasive bacterial infections I was able to directly apply the knowledge to contribute a crucial element of the national surveillance process.

I investigated an outbreak of SARS-CoV-2 (COVID-19) Delta sub-lineage in a childcare centre in the Western Sydney Local Health District (WSLHD), NSW between 22 July and 24 August 2021. The study described patterns of transmission and tracked staff and student transmission based on room location. The evidence from this outbreak investigation confirmed the high rate of transmission (attack rate: 16%) within the childcare centre was strongly influenced by multiple adult cases continuing to work while infectious and symptomatic.