Community-acquired pneumonia in Malawian adults: Aetiology and predictors of mortality. Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor of Philosophy Stephen James Aston MBChB, BMedSc, MRCP, DTMH August 2016 Declaration I declare that this thesis was composed by me and that the work contained therein is my own, except where explicitly stated otherwise in the text. Any contribution of others is described briefly below and in detail at the beginning of relevant chapters. The work within this thesis has not been submitted in whole or in part for any other degree or professional qualification. My supervisors Professor Stephen Gordon (Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW), Malawi) Professor Robert Heyderman (University College London, UK) and Dr Henry Mwandumba (MLW) provided advice on all aspects of the design, conduct and analysis of the research presented here. Professor Paul Garner (Liverpool School of Tropical Medicine, UK) advised on the methodology and analysis of the systematic review presented in chapter 2. Professor Charles Feldman (University of Witwatersrand, South Africa) independently reviewed all titles and corroborated study selection. Victoria Lutje (search strategist) advised on the search strategy and performed the database searches. The Malawian adult lower respiratory tract infection severity, aetiology and outcome (MARISO) study presented in chapters 3, 4 and 5 was one of several concurrently recruiting adult respiratory infection projects based at MLW and Queen Elizabeth Central Hospital (QECH), Malawi. Recruitment to the MARISO study was nested within that of the Burden and Severity of HIV-associated Influenza (BASH-FLU) Study (Principal Investigator: Dr Antonia Ho) and integrated with that of the existing severe acute respiratory infection surveillance programme (Principal Investigators: Dr Dean Everett and Dr Ingrid Peterson). Some patients recruited to MARISO were also recruited to the Acute Infection of the Respiratory Tract (AIR) study (Principal Investigator: Dr Hannah Jary); a case-control study investigating the impact of exposure to indoor air pollution on the risk of developing pneumonia. Dr Antonia Ho, Dr Hannah Jary and myself jointly oversaw the integrated research team of clinical officers and nurses that performed study procedures. I designed the case record forms in conjunction with Dr Ho; we shared the tasks of data management and cleaning processes. The chest radiograph interpreting proforma was developed by Dr Sarah Heath (Liverpool School of Tropical Medicine, UK) under my supervision as part of Masters research project. Reading and grading of the radiographs was performed by two UK based radiologists, Dr Elizabeth Joekes and Dr Simon Greenwood (both Royal Liverpool University Hospital, UK), and myself. Professor Brian Faragher (Liverpool ii School of Tropical Medicine, UK) advised on statistical analysis of the MARISO study; I undertook all analyses myself. Dr Jacqueline Huwa (MLW) acted as study coordinator for the Addressing hypoxaemia in adult pneumonia (AHIP) study presented in chapter 6. She directly oversaw the clinical research team and completed the routine data management activities. In addition to my supervisors, Dr Jamie Rylance (Liverpool School of Tropical Medicine, UK), Dr Mulinda Nyirenda (QECH) and Dr Aylwin Chick (formerly QECH) provided useful comments in the development of the study protocol. For both the AHIP and MARISO studies clinical specimens were processed at the MLW Clinical Diagnostic Laboratory under the supervision of its managers, Brigitte Denis and George Selemani, the MLW Molecular Laboratory under the supervision of senior laboratory technician, Mavis Menyere and the College of Medicine Tuberculosis Research Laboratory under the supervision of its manager, Aaron Mdolo. iii For my father, Robert Aston 1946-2010 iv Acknowledgements Whilst it is my name alone on the cover, this work would not have been possible without the generous support of a large number of people. Firstly, I want to express my gratitude to the patients and their guardians who willingly took part in the studies and generously donated their time. Also special thanks to the Wellcome Trust for awarding my Clinical PhD Fellowship that funded this work and giving me the incredible opportunity of living and working in Malawi. It was a privilege to conduct my research at Queen Elizabeth Central Hospital and to work alongside many dedicated and talented clinicians in the Department of Medicine and the Adult Emergency and Trauma Centre. All were supportive and accommodating of my work. Particular thanks go to Dr Mulinda Nyirenda and Dr Jane Mallewa whose advice and assistance facilitated the smooth running of my studies. The Malawi-Liverpool-Wellcome Trust Clinical Research Programme provided a supportive and motivating environment in which to work. I enjoyed and greatly benefitted from the exchange of ideas with my piers in the ‘Junior Research Fellows Room’. My work was well supported by the operational, administrative and laboratory staff throughout the organisation. In particular I am grateful to Brigitte Denis, George Selemani, Aaron Mdolo, Neema Mtunthama and Vella Kdazu. I was fortunate to arrive at MLW at a time of expansion in respiratory infection research. I had the great pleasure of working closely with Dr Antonia Ho (Principal investigator of the BASH-FLU Study) and Dr Hannah Jary (Principal Investigator of the AIR Study). I could not wish for better colleagues, co-investigators and friends. Our studies were well supported by the existing Influenza Surveillance Programme led by Dr Dean Everett and Dr Ingrid Peterson who generously shared staff and resources. Special thanks go to my study team who grafted diligently and cheerfully on the frontline of clinical research for two years: Dan Chunda, Blessings Mkwaila, Collins Chilwawa, Rosaleen Ng’oma, Hannah Masangwi, Wezi Chimang’anga, Tiwonge Chinunda, Mike Magola and Chimwemwe Mtawali. It was my great pleasure to work with Dr Jacqueline Huwa who acted as a project coordinator for the AHIP study. She was meticulous and cheerful throughout, and a huge asset to the study team. Thanks to Professor Charles Feldman for putting in many hours of hard work on the systematic review of pneumonia in Africa. Professor Paul Garner also provided v valuable input to its design and conduct. I’m grateful to the team of radiologists - Dr Liz Joekes and Dr Simon Greenwood - for generously giving their time in reporting study chest radiographs. In Liverpool, Carolyn O’Leary and Matt Hanlon at the Wellcome Trust Tropical Centre provided invaluable logistical support. Professor Brian Faragher was consistently on hand to give clear and practical advice on statistical analysis. My advisory panel, Professor Bertie Squire and Dr Kevin Mortimer and my clinical supervisor Professor David Lalloo each gave timely encouragement during the long process of completing my research and compiling this thesis. I want to express my sincere gratitude to my supervisors Professor Stephen Gordon, Professor Rob Heyderman and Dr Henry Mwandbumba. From the inception of this project to the final completion of this thesis, they have patiently provided support, encouragement and sage advice. Finally, to my family - my loving and longsuffering wife, Ellen, and my wonderful boys, Noah and Reuben - my deepest love and gratitude. vi Publications related to work presented in this thesis Zar HJ, Madhi SA, Aston SJ, Gordon SB. Pneumonia in low- and middle- income countries: progress and challenges. Thorax 2013;68(11):1052-1056. Wootton DG, Aston SJ, Gordon SB. The pathophysiology of pneumococcal pneumonia. In: Chalmers, Pletz MW, Aliberti S (Eds.). European Respiratory Monograph: Community- acquired pneumonia (Vol. 63). Sheffield, United Kingdom: European Respiratory Society; 2014, pp. 42-63. Aston SJ. The role of rapid diagnostic tests in managing adults with pneumonia in low- resource settings. Pneumonia 2014;5:8-17. Aston SJ, Rylance J. Community-acquired pneumonia in sub-Saharan Africa. Semin Respir Crit Care Med (in press). vii Abstract Background Community-acquired pneumonia (CAP) is one of the commonest causes of adult hospitalisation in sub-Saharan Africa, but recent data describing its epidemiology, microbial aetiology and outcome are limited. Focusing particularly on Malawi, the overall aim of this thesis was to describe the aetiology and outcome of CAP in sub- Saharan African to determine the key predictors of mortality. Methods Firstly, a systematic review of studies of CAP in adults in sub-Saharan Africa was performed to describe CAP aetiology, estimate the mortality rate and identify risk factors associated with death. Secondly, a prospective observational study of adults hospitalised with clinically diagnosed CAP to Queen Elizabeth Central Hospital, Blantyre, Malawi was completed to describe microbial aetiology using modern diagnostic modalities, determine outcome and identify prognostics factors. Thirdly, having identified in preliminary analyses of the prospective cohort that hypoxaemia was an independent risk factor for mortality, a study of the effectiveness of supplemental oxygen delivery by oxygen concentrator to correct hypoxaemia in adults with suspected CAP was performed. Results In both the systematic review and the prospective cohort the predominant burden of hospitalised CAP was in young (average age 38 and 35, respectively) and HIV-positive (52% and 78%) patients with