Foundation for Innovative New Diagnostics (FIND), University of Cape Town (UCT), University of Cape Town (UCT), University of California, San Francisco (UCSF), University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Foundation for Innovative New Diagnostics (FIND), University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Liverpool, Foundation for Innovative New Diagnostics (FIND), Rutgers, The State University of New Jersey, Foundation for Innovative New Diagnostics (FIND), Rutgers, The State University of New Jersey, Foundation for Innovative New Diagnostics (FIND), University of Cape Town (UCT), University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa and Foundation for Innovative New Diagnostics (FIND)

University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Oswaldo Cruz Foundation (FIOCRUZ) - Gonçalo Moniz Institute (IGM), University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Oswaldo Cruz Foundation (FIOCRUZ) - Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ) - Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ) - Gonçalo Moniz Institute (IGM), Government of the United States of America - National Institute of Allergy and Infectious Diseases (NIAID), University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative and University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine

National Department of Health - Drug Resistant TB Directorate, McGill University - School of Population and Global Health, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Division of Clinical Pharmacology, Stellenbosch University, University of Cape Town (UCT), affiliation not provided to SSRN, Médecins Sans Frontières - Khayelitsha Project and Cape Town Mission, Northern Cape South Africa Centre for Tuberculosis, National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases, Amity Health Consortium, Klerksdorp-Tshepong Hospital Complex, University of the Witwatersrand - Reproductive Health and HIV Research Unit (RHRU), University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA)University of the Witwatersrand - South African Medical Research Council and McGill University

University of Liverpool - Institute of Infection and Global Health, Liverpool School of Tropical Medicine, Liverpool School of Tropical Medicine, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of California, San Francisco (UCSF), Liverpool School of Tropical Medicine, Vanderbilt University - School of Medicine, Queen Mary University of London, University of Zambia (UNZA), University of Zambia (UNZA), Institute of Infectious Diseases Emilio Ribas, Federal University of Espirito Santo, Dignitas International, Dignitas International, Doctors Without Borders (MSF), University of Otago, Rutgers, The State University of New Jersey - New Jersey Medical School, London School of Hygiene & Tropical Medicine, Max Planck Institute for Infection Biology, All India Institute of Medical Sciences (AIIMS), University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Division of Infectious Diseases & HIV Medicine, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Liverpool - Institute of Infection and Global Health, Dartmouth College - Dartmouth Medical School, Muhimbili University of Health and Allied Sciences, Johns Hopkins University - Center for Tuberculosis Research, Johns Hopkins University - Center for Tuberculosis Research, Johns Hopkins University - Center for Tuberculosis Research, Government of the United States of America - Centers for Disease Control and Prevention (CDC), Government of the United States of America - Centers for Disease Control and Prevention (CDC), Government of the United States of America - Centers for Disease Control and Prevention (CDC), National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis, Government of the United States of America - Food and Drug Administration (FDA), University of KwaZulu-Natal, Liverpool School of Tropical Medicine, University of Malawi - Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Liverpool - Institute of Infection and Global Health and University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa

University of Liverpool - Institute of Infection and Global Health, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, Stanford University - Department of Biology, University of California, Berkeley - Department of Chemistry, University of Cape Town (UCT) - SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, University of Cape Town (UCT) - SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Liverpool - Institute of Infection and Global Health, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, The University of Western Australia - Division of Infection and Immunity, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Liverpool - School of Tropical Medicine, University of Cape Town (UCT) - SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa and University of Liverpool - Institute of Infection and Global Health

University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town (UCT) - Wellcome Centre for Infectious Diseases Research in Africa, The University of Western Australia - Division of Infection and Immunity, Khayelitsha Hospital - Department of Medicine, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa and University of Liverpool - Institute of Infection and Global Health

University of Cape Town (UCT) - University of Cape Town Lung InstituteUniversity of Cape Town (UCT) - Centre for Lung Infection and Immunity, Stellenbosch University - Division of Pulmonology, University of Cape Town (UCT) - Groote Schuur Hospital, University of Cape Town (UCT) - University of Cape Town Lung Institute, University of Cape Town (UCT) - Department of Anaesthesia and Perioperative Medicine, University of Cape Town (UCT) - Division of Infectious Diseases & HIV Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - Department of Medicine, University of Cape Town (UCT) - University of Cape Town Lung Institute, University of Cape Town (UCT) - Department of Statistical Sciences, Stellenbosch University - Department of Medicine, Stellenbosch University - Department of Medicine, Stellenbosch University - Department of Medicine, Stellenbosch University - Department of Medicine, Stellenbosch University - Department of Medicine, Stellenbosch University - Division of Pulmonology, University of Cape Town (UCT) - Centre for Lung Infection and Immunity and Stellenbosch University - Department of Medicine