One Health -One City; the extent of Shiga- toxin producing Escherichia coli in Cape Town. By University of Cape Town John Bosco Kalule Submitted to the University of Cape Town for the degree of Doctor of Philosophy in Medical Microbiology June 2017 The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Declaration I, John Bosco Kalule, hereby declare that the work on which this thesis is based is my original work and that neither the whole work nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. Signature: signature removed Date: 7th 08 2017 Supervisor: Professor Mark Patrick Nicol (MBBCh, M.Med (Med Microbiol), SA FCPath (Microbiol),PhD)1, 2, 3 1Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. 2Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. 3National Health Laboratory Service of South Africa, Groote Schuur Hospital, Cape Town, South Africa Co-supervisors: Dr Karen. H. Keddy (BSc (Med), MBBCh, MMed (Microbiol), FCPath SA (Microbiol), DTM&H, PhD)4, 5 4Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa. 5Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Acknowledgements I thank God Almighty for allowing and enabling the execution of this research work. I acknowledge the help and support received from my family, friends, colleagues, supervisors, collaborators at the City of Cape Town Water and Sanitation Services, the clinical field study team, the laboratory scientists at the National Health Laboratory Services at the Groote Schuur Hospital, the scientists at the National Institute of Communicable Disease, and the staff at the Nyanga Community Health Centre. Support and tolerance from my family have been invaluable to the successful completion of this research. I particularly thank my wife Dorothy for the emotional support. I thank my supervisors Prof. Mark Nicol and Dr Karen H. Keddy for the guidance and encouragement during the study period. Without your guidance, this research would never have been possible. I thank Dr Lourens Robberts for the guidance and help he rendered during the initial stages of this research work. I have also received tremendous assistance and guidance from friends and colleagues at the Division of Medical Microbiology, Faculty of Health Sciences. Without the help of the team from the City of Cape Town Water and Sanitation Services, it would not have been possible to collect and process samples from the Lotus River. They generously provided logistics for the collection of the water samples and allowed me to use their water filtration units and water laboratories for the processing of the samples. During the collection of samples from Nyanga Township, the clinical research and ethics team of the Division of Medical Microbiology helped by providing a clinical research worker, as well as planning transportation and reception of samples from Nyanga to the clinical microbiology laboratory at the Division of Medical Microbiology, Faculty of Health Sciences. Special thanks to Ms Shireen Surtie, Ms Gaironesa Omar, and Ms Pam Jordan. iii I thank the team at the Groote Schuur Hospital (especially Dr. Colleen Bamford and Mr. Pascal Musoni) for allowing the use of the VITEK® 2 automated identification system and for the guidance throughout this research. I thank the team at the National Institute for Communicable Diseases, Sandringham, Johannesburg for serotyping of strains and provision of logistics to help transportation of isolates to their Laboratory in Johannesburg. I appreciate the tremendous effort from Dr Karen Keddy, Dr Arvinda Sooka, and Dr Anthony Smith. The nurses and doctors at the Nyanga Community Health Centre were a tremendous help and assisted in the organisation and execution of the research activities at the clinic. I also thank the patients that were recruited in this study for consenting to the study and offering time to fill out the questionnaires. The Jonathan Blackburn Laboratory at the Institute of Infectious Disease and Molecular Medicine facilitated the quantitative proteomics work. I specifically wish to thank Dr Nelson Soares, Dr Suereta Fortuin, and Prof. Jonathan Blackburn for the time they invested in this research. Finally, I wish to thank the ARISE-ACP scholarship, the NRF-South Africa, the Division of Medical Microbiology, the ADB-HEST scholarship, and the Jonathan Blackburn Proteomics Laboratory, for the funding that was used for this study. iv Table of Contents Acknowledgements ................................................................................................................................ iii Table of Contents ...................................................................................................................................... v List of Figures ......................................................................................................................................... xii List of abbreviations and acronyms .................................................................................................... xv Abstract .................................................................................................................................................... xxi Chapter One ............................................................................................................................................. 25 1 General Introduction and Thesis Outline .............................................................................. 25 1.1 General Introduction ............................................................................................................... 26 1.2 Aims of the study ..................................................................................................................... 28 1.3 Study design and population ................................................................................................. 29 1.3.1 Study design ............................................................................................................................. 29 1.3.2 Study population ...................................................................................................................... 29 1.4 Ethics consideration ................................................................................................................. 31 1.5 Overview of the laboratory work flow ................................................................................. 31 1.5.1 Laboratory work flow for stool samples from the Groote Schuur Hospital .................... 31 1.5.2 Laboratory work flow for stool, meat, and surface water samples collected in Nyanga. …………………………………………………………………………………………………..32 1.6 Outline of the thesis ................................................................................................................. 33 1.7 References ................................................................................................................................. 34 Chapter Two ............................................................................................................................................. 36 2 One Health- an integrated approach to surveillance of foodborne bacterial pathogens and Foodborne antimicrobial resistance: A Review of the Literature .......................................... 36 2.1 The Global Foodborne Disease Burden ................................................................................ 37 2.2 Surveillance for foodborne disease ........................................................................................ 38 2.2.1 The One- Health approach...................................................................................................... 38 2.3 Foodborne Antimicrobial Resistance .................................................................................... 39 2.3.1 A general overview .................................................................................................................. 39 2.3.2 Informal abattoirs and storm water as reservoirs of antibiotic resistant pathogens ...... 40 2.3.3 The South African situation analysis, strategy, and challenges ........................................ 41 2.4 Source Attribution for STEC and other foodborne bacterial pathogens .......................... 42 2.5 Diarrheagenic Escherichia coli .................................................................................................. 44 v 2.5.1 Enteropathogenic E. coli .......................................................................................................... 46 2.5.2 Enteroinvasive E. coli ............................................................................................................... 47 2.5.3 Enteroaggregative E. coli and the enteroaggregative haemorrhagic E. coli ..................... 47 2.5.4 Adherent-Invasive E. coli (AIEC) ........................................................................................... 47 2.5.5 Diffusely Adherent E. coli ......................................................................................................