Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

• Keira A. Cohen ,

  Contributed equally to this work with: Keira A. Cohen, Thomas Abeel

  Affiliations Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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• Thomas Abeel ,

  Contributed equally to this work with: Keira A. Cohen, Thomas Abeel

  Affiliations Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands

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• Abigail Manson McGuire,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Christopher A. Desjardins,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Vanisha Munsamy,

  Affiliation KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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• Terrance P. Shea,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Bruce J. Walker,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Nonkqubela Bantubani,

  Affiliation Medical Research Council, Durban, South Africa

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• Deepak V. Almeida,

  Affiliations KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa, Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America

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• Lucia Alvarado,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Sinéad B. Chapman,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Nomonde R. Mvelase,

  Affiliations School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa, National Health Laboratory Service, Durban, South Africa

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• Eamon Y. Duffy,

  Affiliation KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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• Michael G. Fitzgerald,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Pamla Govender,

  Affiliation KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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• Sharvari Gujja,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Susanna Hamilton,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Clinton Howarth,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Jeffrey D. Larimer,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Kashmeel Maharaj,

  Affiliation KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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• Matthew D. Pearson,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Margaret E. Priest,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Qiandong Zeng,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Nesri Padayatchi,

  Affiliation Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa

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• Jacques Grosset,

  Affiliations KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa, Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America

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• Sarah K. Young,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Jennifer Wortman,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Koleka P. Mlisana,

  Affiliations School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa, National Health Laboratory Service, Durban, South Africa

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• Max R. O'Donnell,

  Affiliations Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa, Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, United States of America, Department of Epidemiology, Columbia Mailman School of Public Health, New York, United States of America

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• Bruce W. Birren,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• William R. Bishai,

  Affiliation Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America

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• Alexander S. Pym ,

  * E-mail: alex.pym@k-rith.org (ASP); aearl@broadinstitute.org (AME)

  ¶‡ These authors also contributed equally to this work.

  Affiliation KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa

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•  [ ... ],
• Ashlee M. Earl

  * E-mail: alex.pym@k-rith.org (ASP); aearl@broadinstitute.org (AME)

  ¶‡ These authors also contributed equally to this work.

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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