Applied Epidemiology of Infectious Diseases in Western Australia

Applied Epidemiology of Infectious Diseases in Western Australia by Darren William Westphal B.A. (Psych, International Studies), MPH A bound volume submitted to the Australian National University to fulfil the requirements for the degree of Master of Philosophy in Applied Epidemiology (MAE) November 2016 Field Supervisors Professor Paul Effler Dr. Hannah Moore Clinical Associate Professor Deborah Lehmann Academic Supervisors Dr. Stephanie Williams Dr. Kerri Viney This page has been intentionally left blank ii Author’s Declaration I hereby declare that the work herein now submitted as a bound volume for the degree of Master of Philosophy in Applied Epidemiology (MAE) of the Australian National University is the result of my own investigations, and all references to the ideas and work of other researchers have been specifically acknowledged. I hereby certify that the work embodied in this bound volume has not already been accepted in substance for any degree, and is not being currently submitted in candidature for any other degree. Darren Westphal MPhilAppEpi Scholar Communicable Disease Control Directorate, Public Health Division, Western Australia Department of Health and Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute November 2016 iii A note about terminology I use the term ‘Aboriginal’ throughout this work to refer to the original inhabitants of Australia, that is all Aboriginal and Torres Strait Islander peoples. I use this term for conciseness and in preference to ‘Indigenous’. iv Abstract I commenced the Master of Philosophy in Applied Epidemiology (MAE) in February 2015. My field placements were shared between the Communicable Diseases Control Directorate, Public Health Division at the Western Australia Department of Health (CDCD) and the Telethon Kids Institute (TKI), both located in Perth. Two of the three projects that I completed at the CDCD involved a statewide protracted mumps outbreak that went on for the duration of my MAE and reached almost 900 cases. The epidemiology of this outbreak including a discussion about vaccination is presented in Chapter 1. This satisfies the outbreak investigation requirement of the MAE. Chapter 2 comprises a late draft manuscript that explores the vaccine effectiveness (VE) of the measles-mumps-rubella vaccine among paediatric cases during the mumps outbreak. I designed and carried out a matched case-control study using paediatric outbreak cases and controls from a population database. I measured VE using a conditional logistic regression model and compared it with the screening method. Both methods yielded a very low VE this population. This is likely due to a multitude of factors that are discussed in the chapter. My work at TKI involved a data analysis using linked-administrative data on a total population birth cohort involving all children born in Western Australia between 1996-2012. I explored the burden of hospital separations that resulted from otitis media (OM), the most common infectious disease in children, and a common related procedure, myringotomy with ventilation tube insertion (MVTI). I calculated the age-specific hospitalisation rates for OM and MVTI over the study years. The second part of this analysis involved investigating the maternal and infant risk factors and population attributable fractions for OM-related hospitalisation in early life. This work was important because of its implications for practice. All of this is presented in Chapter 3. v Chapter 4 is an evaluation of SmartVax, a novel, real-time Adverse Events Following Immunisation (AEFI) surveillance system using SMS text messages to communicate directly with vaccinees after their vaccination. This was the third project that I completed at the CDCD. The chapter begins with a peer-reviewed publication, Continuous active surveillance of adverse events following immunisation using SMS technology, that describes the system and analyses data outputs for children <5 years from 2011-2015. I have included the publication first to provide a brief system overview including summarised surveillance data, to give context to the evaluation since SmartVax is a relatively new and developing system. The publication is followed by the formal evaluation. Finally, I include a summary of the teaching exercises that I was involved in during my MAE. The first was a “lesson from the field” where I prepared an exercise for my fellow scholars. The exercise was useful for me and the feedback from my colleagues was positive. The second was a collaborative teaching exercise about confounding that we taught to the first year MAE scholars on their last day of courseblock. These combined activities at both placements have enriched my understanding of epidemiology while working in health and research environments. vi Acknowledgements Now all glory to God… Eph 3:20 Without my family I would not have been able to complete the MAE. My wife Asha Bowen has been very supportive and provided excellent feedback throughout the course. She did not hesitate to look over my work and give constructive feedback like ‘your sentences are too long” or “where did this denominator come from?” She was also a great sounding board for talking about infectious diseases and helping me to understand the concepts that were new to me. Mostly she has been there, filled in when I needed to write, given me time to do the work which meant not being able to do some of the work she needed to get done. Thank you. Also to my children who have given me perspective and laughter throughout the sometimes stressful times. I’m now looking forward to going on bike rides, reading books and going to the park! Also a shout out to my mother-in-law Narelle for not hesitating to make the flight from Sydney to help keep things going at home when I was away at courseblock. You are an important part of the family and we all appreciate and love you very much. I have had the opportunity to meet and work with a number of people over the two years of my MAE, all of whom have enriched my experience. My field supervisors Paul Effler and Hannah Moore. I have been very fortunate to work with Paul and be welcomed into the Prevention and Control team. I’ve learned more about epidemiology from him than I ever could have from a textbook. I gleaned from the conversations we had about the mumps outbreak and vaccine safety surveillance. His passion for his work is evident. My writing has improved greatly from his ‘editorial review’ and I will “use my words wisely” and never forget the difference between sensitivity and specificity. vii I have benefited from working under Hannah Moore’s leadership. She has carefully guided me through the process of linked data analysis while giving me opportunities to expand and hone my data analysis skills by challenging me. She was very easy to approach when I had a question and was prompt with feedback about my work. I have learned a lot from her. Thank you. And…we still need to do the Cox Regression! My supervisor at NCEPH, Stephanie Williams. To say I couldn't have done it without her would be an understatement. I was very fortunate to have Stephanie pushing me when I didn’t want to be pushed, challenging my thinking when I wanted to take the easy way out. She has also helped me improve my writing skills by asking questions and forcing me to come up with the answers. I have benefitted from her expertise and have appreciated every bit of it. Well, all but this comment when I thought I was almost finished, “all the elements of the chapter are here, I think it is about 35% finished.” Deborah Lehmann has been an amazing support at the Telethon Kids Institute. Her knowledge about otitis media and willingness to share that knowledge is one of the reasons I’ve succeeded. She was always happy to answer my questions and posed great thoughts to consider. And, there’s always a good reason for a party! I’d also like to acknowledge and thank Parveen Fathima, Janice Lim, Tasnim Abdulla on my team. Particularly Parveen and Janice for a lot of the data cleaning that took place before I started, that made my life a little easier! Of course for that laughs, laughs and more laughs…and chocolate. Kingsley Wong, Nick De Klerk and Peter Jacoby for being willing to help with my stats questions. Peter Richmond for your support through two years of SmartVax, mumps and otitis media. Chris Blyth who helped make my MAE field placements possible. He went out of his way to help organise my placements here in Perth and did so out of his kind generosity and for that I’m grateful. Without his connections and effort, I may not have had such an awesome experience. viii Japanese Poem Translation If you try, you may succeed If you don’t try you will not succeed. This is true for all things. Not succeeding is the result of not trying. ix Table of Contents Author’s Declaration iii Abstract v Acknowledgements vii Table of Contents x Summary of competencies xi Summary of MAE presentations xii Travel awards awarded xiv Chapter 1. The epidemiology of a protracted mumps outbreak in remote Western Australia, primarily among highly vaccinated Aboriginal people 1 Chapter 2. Vaccine effectiveness during a mumps outbreak: a matched case-control study 47 Chapter 3. The epidemiology of otitis media hospitalisations in Western Australia: a retrospective population cohort study (1996-2012) 81 Chapter 4. An evaluation of SmartVax®: an active vaccine safety monitoring tool for collection of adverse events following immunisation 159 Chapter 5. Teaching exercises 231 x Summary

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