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Pulmonary Tuberculosis: Towards Improved Adjunctive Therapies

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Pulmonary Tuberculosis: Towards Improved Adjunctive Therapies Pulmonary Tuberculosis: towards improved adjunctive therapies Anna Ralph July 2010 A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy of The Australian National University Front section: Author’s statement Author’s statement This thesis describes the development, implementation and preliminary results of the Arginine and Vitamin D Adjunctive Therapy in Pulmonary Tuberculosis (AVDAPT) randomised controlled trial. I had a central role in developing and implementing the study protocol collaboratively with my PhD supervisors Associate Professor Paul Kelly (Australian National University, Canberra) and Professor Nicholas Anstey (Menzies School of Health Research, Darwin), and with additional input from the investigators listed in Appendix 1. I wrote the initial draft of the study protocol for submission to the relevant ethics committees and for trial registration purposes (http://clinicaltrials.gov/show/ NCT00677339). I supervised and participated in the collection of data, performed the data analyses, wrote the thesis, and wrote all published and submitted manuscripts arising from the thesis. The named co-authors made intellectual and writing contributions to the final manuscripts. One section of data analysis was not performed by me: the interim safety analysis described in Chapter 10 was conducted by an independent biostatistician (Mr Joseph McDonnell, Menzies School of Health Research) in his role as a member of the AVDAPT study Data and Safety Monitoring Committee. I am a named Chief Investigator on the successful National Health and Medical Research Council Project Grant Application 605806 entitled ―L-Arginine and Vitamin D Adjunctive Therapies in Pulmonary Tuberculosis‖. _________________________ Anna Ralph BMedSci, MBBS(Hons), MPH, DTM&H, FRACP July 2010 i Front section: Acknowledgements Acknowledgements I would like to acknowledge a number of people and organisations who have played significant roles in this research project. I am very grateful to the National Health and Medical Research Council for providing a Postgraduate scholarship and a 2009 research grant, and the Australian Respiratory Council and the Royal Australasian College of Physicians (Covance award) which generously provided funds for the project. At the field research site in Timika, my very great thanks go to the research assistants Bapak Govert Waramori and Dr Gysje Pontororing, and director of the Timika Translational Research Facility Dr Enny Kenangalem, for their enthusiasm and commitment to the project, and for making the work so enjoyable. Profound thanks also to all Timika Translational Research Facility staff who make the project possible: Ferryanto Chalfein, Prayoga, Daud Rumere, Frans Wabiser, Yeni, Henwi Pieris and Baspak Gobay (laboratory staff); Natalia Dwi Haryanti and Sri Hasunik (data management), Sri Rahayu (administration), and Gertruida Bellatrix and Hendrix Antonius (research assistants). Thanks also to Dr Daniel Lampah for medical and logistical help, and Maikel Zonggonau for driving, errands, and making sense of my limited Bahasa Indonesia. At RSMM, I sincerely thank Dr Paulus Sugiarto for his support and for chairing the Data and Safety Monitoring Committee, and Dr Enny Malonda, for helpful discussions about TB management in Timika. Dr Rini Poespoprodjo and Drs Franciscus Thio have also offered very valuable assistance for which I thank them very much. Special thanks also to TB clinic staff Dr Andri Wiguna for medical support, Bapak Djonny Lempoy for frequent general assistance, and to Bapak Erstanto, Head, Timika TB laboratory, for diligently processing, recording and storing sputum slides for the study. I also greatly thank Drs Pasi Pennitien, Michael Bangs, and Michael Stone (Public Health / Malaria Control, Timika), for their vital support across many tasks, including facilitating access to consumables and transporting specimens to Jakarta. Finally in Timika, I am indebted to all the study participants, healthy volunteers and their families for their involvement in the study. ii Front section: Acknowledgements In Jakarta, I extend my thanks to colleagues at the Ministry of Health‘s National Institute of Health Research and Development who allowed this study to proceed. In particular, I thank Dr Sandjaja for his assistance in facilitating the project, and his intellectual and practical input to the project; Dr Dina Bisara Lolong for contributing to the development of the study protocol and visiting the field site, Ibu Merryani Girsang for contributing to laboratory quality control checks, and Dr Emiliana Tjitra for providing a co-ordinating role. Major thanks to Dr Retno Soemanto and Mbak Yuni Rukminiati at the University of Indonesia Faculty of Microbiology for taking on the large task of processing all specimens collected for this project (culture / DST), and for being readily available for frequent discussions about results. In Darwin at Menzies School of Health Research (MSHR), I wish to convey deep thanks to my supervisor Professor Nicholas Anstey who has been a greatly valued mentor, and whose intellectual rigor is a constant inspiration. His attention to detail and boundless reserves of optimism, tenacity and diplomacy mitigated many potential problems, solved the seemingly insoluble, and kept the project afloat. He also provided greatly-appreciated contributions to the development of this thesis and the publications arising from it. I greatly thank Dr Ric Price (PhD co-supervisor) for trying to impart to me some of his knowledge regarding statistics, data management and data analysis; the databases created for this thesis relied heavily on his assistance, and his detailed statistical advice was greatly appreciated. Great thanks to Kim Piera for her meticulous approach to managing logistics and supplies, providing laboratory expertise, packaging medications, and helping with data entry, as well as providing good company in Timika. Other laboratory personnel including Drs Tonia Woodberry, Gabriella Minigo and Jutta Marfurt have been extremely helpful in educating both myself and the Timika staff in laboratory methods, and striving to maintain good laboratory standards. Administrative staff at MSHR essential to the operation of this project include Tania Paul, Ella Curry, Robi Cohalan, Asriana Kebon and Joanne Bex, to all of whom I am very grateful. Also at MSHR, thanks to Associate Professor Peter Morris (PhD Advisor) for his major contributions to development of the study protocol, advice regarding the analytical plan, and input to devising a composite clinical outcome score; to Dr Nick Douglas for greatly- appreciated help and company in Timika; to Dr Tsin Yeo for statistical advice and for making available his data and knowledge on exhaled nitric oxide measurement; to Dr iii Front section: Acknowledgements Joshua Davis for friendly and comprehensible statistical advice; to Dr Louise Maple- Brown and Joseph McDonnell for their roles in the Data and Safety Monitoring Committee. At ANU, immense thanks to Associate Professor Paul Kelly who chaired my PhD supervisory panel. It was through enthusiastic discussions with him in 2006 that I was inspired to embark on this research. His earlier tuberculosis work in Timika and in other international settings provided a strong basis for the current project, and his contributions to discussions with collaborators in Timika and Jakarta have been vital for the project‘s operation. I also sincerely thank Paul for making available to me the TB data that he and others had previously obtained in Timika, for providing templates on which I could model the study protocol and data collection forms, and for providing essential feedback on manuscripts, including this thesis. My thanks also go to Professor Niels Becker (PhD co-supervisor) for providing patient and detailed statistical help, especially in relation to the x-ray analyses and the exhaled nitric oxide correction factors, and to Dr Mark Clemens for his major assistance in the complicated factorial study sample size calculation. To all other ANU staff who provided help (including Dr Robyn Lucas for vitamin D advice, and Sarah Geddes and Barbara Bowen for administrative help), to many fellow ANU PhD students who provided much-appreciated camaraderie and support, I convey my great thanks also. I also wish to sincerely thank Associate Professor Graeme Maguire, James Cook University (PhD Advisor), for support with supplies, logistics, lung function testing, data analyses, and occasional accommodation (snakes notwithstanding). I am very grateful for the important mycobacteriological advice and expertise provided by Mr Richard Lumb at the Institute for Medical & Veterinary Science, including his visits to the Jakarta laboratory. Many thanks also to Dr Cheryl Salome, Woolcock Institute of Medical Research, for valuable exhaled nitric oxide advice and kind provision of materials. Thanks also to Dr Mairwen Jones for proof reading sections of this thesis. Deepest thanks finally go to my partner Deborah for tolerating my absences and other difficulties this project has brought, and for supporting me unconditionally in every way. iv Front section: Figure FIGURE 1: NIHRD-MSHR Timika research staff outside the research buidling L to R: Front row Maikel Zonggonau, Enny Kenangalem, Sri Rahayu, Basbak Gobay, Hendrix Antonius Back row: Yani Reyaan, Wendelina Fobia, Anna Ralph, Frans Wabiser, Gysje Pontororing, Adol Fobia, Sri Hasunik. Photo: Nick Anstey. v Front section: Abstract Abstract The potential to
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