Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

David Stucki; Daniela Brites; Leïla Jeljeli; Mireia Coscolla; Qingyun Liu; Andrej Trauner; Lukas Fenner; Liliana Rutaihwa; Sonia Borrell; Tao Luo; Qian Gao; Midori Kato-Maeda; Marie Ballif; Matthias Egger; Rita Macedo; Helmi Mardassi; Milagros Moreno; Griselda Tudo Vilanova; Janet Fyfe; Maria Globan; Jackson Thomas; Frances Jamieson; Jennifer L. Guthrie; Adwoa Asante-Poku; Dorothy Yeboah-Manu; Eddie Wampande; Willy Ssengooba; Moses Joloba; W. Henry Boom; Indira Basu; James Bower; Margarida Saraiva; Sidra E.G. Vasconcellos; Philip Suffys; Anastasia Koch; Robert Wilkinson; Linda Gail-Bekker; Bijaya Malla; Serej D. Ley; Hans Peter Beck; Bouke C. De Jong; Kadri Toit; Elisabeth Sanchez-Padilla; Maryline Bonnet; Ana Gil-Brusola; Matthias Frank; Veronique N. Penlap Beng; Kathleen Eisenach; Issam Alani; Perpetual Wangui Ndung'U; Gunturu Revathi; Florian Gehre; Suriya Akter; Francine Ntoumi; Lynsey Stewart-Isherwood; Nyanda E. Ntinginya; Andrea Rachow; Michael Hoelscher; Daniela Maria Cirillo; Girts Skenders; Sven Hoffner; Daiva Bakonyte; Petras Stakenas; Roland Diel; Valeriu Crudu; Olga Moldovan; Sahal Al-Hajoj; Larissa Otero; Francesca Barletta; E. Jane Carter; Lameck Diero; Philip Supply; Iñaki Comas; Stefan Niemann; Sebastien Gagneux

doi:10.1038/ng.3704

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

David Stucki
, Daniela Brites
, Leïla Jeljeli
, Mireia Coscolla
, Qingyun Liu
, Andrej Trauner
, Lukas Fenner
, Liliana Rutaihwa
, Sonia Borrell
, Tao Luo
, Qian Gao
, Midori Kato-Maeda
, Marie Ballif
, Matthias Egger
, Rita Macedo
, Helmi Mardassi
, Milagros Moreno
, Griselda Tudo Vilanova
, Janet Fyfe
, Maria Globan

Jackson Thomas, Frances Jamieson, Jennifer L. Guthrie, Adwoa Asante-Poku, Dorothy Yeboah-Manu, Eddie Wampande, Willy Ssengooba, Moses Joloba, W. Henry Boom, Indira Basu, James Bower, Margarida Saraiva, Sidra E.G. Vasconcellos, Philip Suffys, Anastasia Koch, Robert Wilkinson, Linda Gail-Bekker, Bijaya Malla, Serej D. Ley, Hans Peter Beck, Bouke C. De Jong, Kadri Toit, Elisabeth Sanchez-Padilla, Maryline Bonnet, Ana Gil-Brusola, Matthias Frank, Veronique N. Penlap Beng, Kathleen Eisenach, Issam Alani, Perpetual Wangui Ndung'U, Gunturu Revathi, Florian Gehre, Suriya Akter, Francine Ntoumi, Lynsey Stewart-Isherwood, Nyanda E. Ntinginya, Andrea Rachow, Michael Hoelscher, Daniela Maria Cirillo, Girts Skenders, Sven Hoffner, Daiva Bakonyte, Petras Stakenas, Roland Diel, Valeriu Crudu, Olga Moldovan, Sahal Al-Hajoj, Larissa Otero, Francesca Barletta, E. Jane Carter, Lameck Diero, Philip Supply, Iñaki Comas, Stefan Niemann, Sebastien Gagneux

Swiss Tropical and Public Health Institute Swiss TPH
University of Basel
Research Center Borstel - Leibniz Lung Center
Université de Tunis El Manar
Fudan University
Institute of Social and Preventive Medicine
Sichuan University
University of California at San Francisco
Laboratório de Saúde Pública
Hospital Nossa Senhora da Paz
Hospital Clínic-ISGlobal
Victorian Infectious Diseases Reference Laboratory
Ifakara Health Institute
Public Health Ontario
University of Ghana
Makerere University
University of Amsterdam
Case Western Reserve University
LabPLUS
University of Minho
Fundação Oswaldo Cruz
University of Cape Town
Imperial College London
Francis Crick Institute
Papua New Guinea Institute of Medical Research
Institute of Tropical Medicine Antwerp
Tartu University Hospital United Laboratories
Epicentre
University Hospital la Fe
University of Tübingen
Université de Yaoundé I
University of Arkansas for Medical Sciences
Middle Technical University
Jomo Kenyatta University of Agriculture and Technology
Aga Khan University
Medical Research Council Unit at the LSTHM
Université Marien Gouabi
University of the Witwatersrand, Johannesburg
National Institute for Medical Research Tanzania
Ludwig Maximilian University of Munich
IRCCS San Raffaele Scientific Institute
Riga East University Hospital
Public Health Agency of Sweden
Vilnius University
University of Schleswig-Holstein
Phthysiopneumology Institute
Marius Nasta Pneumophtisiology Institute
King Faisal Specialist Hospital and Research Centre
Universidad Peruana Cayetano Heredia, Instituto de Medicina Tropical Alexander von Humboldt
Brown University
Moi University
University of Lille
Institute of Biomedicine of Valencia (IBV-CSIC)
CIBER Epidemiología y Salud Pública (CIBERESP)
Borstel Site

Research output: Contribution to journal › Article › peer-review

327 Citations (Scopus)

Abstract

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.

Original language	English
Pages (from-to)	1535-1543
Number of pages	9
Journal	Nature Genetics
Volume	48
Issue number	12
DOIs	https://doi.org/10.1038/ng.3704
Publication status	Published - 1 Dec 2016
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1038/ng.3704

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Stucki, D., Brites, D., Jeljeli, L., Coscolla, M., Liu, Q., Trauner, A., Fenner, L., Rutaihwa, L., Borrell, S., Luo, T., Gao, Q., Kato-Maeda, M., Ballif, M., Egger, M., Macedo, R., Mardassi, H., Moreno, M., Vilanova, G. T., Fyfe, J., ... Gagneux, S. (2016). Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genetics, 48(12), 1535-1543. https://doi.org/10.1038/ng.3704

@article{ced6406e0df040d982a4e0fe6e33d5b4,

title = "Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages",

abstract = "Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.",

author = "David Stucki and Daniela Brites and Le{\"i}la Jeljeli and Mireia Coscolla and Qingyun Liu and Andrej Trauner and Lukas Fenner and Liliana Rutaihwa and Sonia Borrell and Tao Luo and Qian Gao and Midori Kato-Maeda and Marie Ballif and Matthias Egger and Rita Macedo and Helmi Mardassi and Milagros Moreno and Vilanova, \{Griselda Tudo\} and Janet Fyfe and Maria Globan and Jackson Thomas and Frances Jamieson and Guthrie, \{Jennifer L.\} and Adwoa Asante-Poku and Dorothy Yeboah-Manu and Eddie Wampande and Willy Ssengooba and Moses Joloba and Boom, \{W. Henry\} and Indira Basu and James Bower and Margarida Saraiva and Vasconcellos, \{Sidra E.G.\} and Philip Suffys and Anastasia Koch and Robert Wilkinson and Linda Gail-Bekker and Bijaya Malla and Ley, \{Serej D.\} and Beck, \{Hans Peter\} and \{De Jong\}, \{Bouke C.\} and Kadri Toit and Elisabeth Sanchez-Padilla and Maryline Bonnet and Ana Gil-Brusola and Matthias Frank and \{Penlap Beng\}, \{Veronique N.\} and Kathleen Eisenach and Issam Alani and Ndung'U, \{Perpetual Wangui\} and Gunturu Revathi and Florian Gehre and Suriya Akter and Francine Ntoumi and Lynsey Stewart-Isherwood and Ntinginya, \{Nyanda E.\} and Andrea Rachow and Michael Hoelscher and Cirillo, \{Daniela Maria\} and Girts Skenders and Sven Hoffner and Daiva Bakonyte and Petras Stakenas and Roland Diel and Valeriu Crudu and Olga Moldovan and Sahal Al-Hajoj and Larissa Otero and Francesca Barletta and Carter, \{E. Jane\} and Lameck Diero and Philip Supply and I{\~n}aki Comas and Stefan Niemann and Sebastien Gagneux",

year = "2016",

month = dec,

day = "1",

doi = "10.1038/ng.3704",

language = "English",

volume = "48",

pages = "1535--1543",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "12",

}

Stucki, D, Brites, D, Jeljeli, L, Coscolla, M, Liu, Q, Trauner, A, Fenner, L, Rutaihwa, L, Borrell, S, Luo, T, Gao, Q, Kato-Maeda, M, Ballif, M, Egger, M, Macedo, R, Mardassi, H, Moreno, M, Vilanova, GT, Fyfe, J, Globan, M, Thomas, J, Jamieson, F, Guthrie, JL, Asante-Poku, A, Yeboah-Manu, D, Wampande, E, Ssengooba, W, Joloba, M, Boom, WH, Basu, I, Bower, J, Saraiva, M, Vasconcellos, SEG, Suffys, P, Koch, A, Wilkinson, R, Gail-Bekker, L, Malla, B, Ley, SD, Beck, HP, De Jong, BC, Toit, K, Sanchez-Padilla, E, Bonnet, M, Gil-Brusola, A, Frank, M, Penlap Beng, VN, Eisenach, K, Alani, I, Ndung'U, PW, Revathi, G, Gehre, F, Akter, S, Ntoumi, F, Stewart-Isherwood, L, Ntinginya, NE, Rachow, A, Hoelscher, M, Cirillo, DM, Skenders, G, Hoffner, S, Bakonyte, D, Stakenas, P, Diel, R, Crudu, V, Moldovan, O, Al-Hajoj, S, Otero, L, Barletta, F, Carter, EJ, Diero, L, Supply, P, Comas, I, Niemann, S & Gagneux, S 2016, 'Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages', Nature Genetics, vol. 48, no. 12, pp. 1535-1543. https://doi.org/10.1038/ng.3704

TY - JOUR

T1 - Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

AU - Stucki, David

AU - Brites, Daniela

AU - Jeljeli, Leïla

AU - Coscolla, Mireia

AU - Liu, Qingyun

AU - Trauner, Andrej

AU - Fenner, Lukas

AU - Rutaihwa, Liliana

AU - Borrell, Sonia

AU - Luo, Tao

AU - Gao, Qian

AU - Kato-Maeda, Midori

AU - Ballif, Marie

AU - Egger, Matthias

AU - Macedo, Rita

AU - Mardassi, Helmi

AU - Moreno, Milagros

AU - Vilanova, Griselda Tudo

AU - Fyfe, Janet

AU - Globan, Maria

AU - Thomas, Jackson

AU - Jamieson, Frances

AU - Guthrie, Jennifer L.

AU - Asante-Poku, Adwoa

AU - Yeboah-Manu, Dorothy

AU - Wampande, Eddie

AU - Ssengooba, Willy

AU - Joloba, Moses

AU - Boom, W. Henry

AU - Basu, Indira

AU - Bower, James

AU - Saraiva, Margarida

AU - Vasconcellos, Sidra E.G.

AU - Suffys, Philip

AU - Koch, Anastasia

AU - Wilkinson, Robert

AU - Gail-Bekker, Linda

AU - Malla, Bijaya

AU - Ley, Serej D.

AU - Beck, Hans Peter

AU - De Jong, Bouke C.

AU - Toit, Kadri

AU - Sanchez-Padilla, Elisabeth

AU - Bonnet, Maryline

AU - Gil-Brusola, Ana

AU - Frank, Matthias

AU - Penlap Beng, Veronique N.

AU - Eisenach, Kathleen

AU - Alani, Issam

AU - Ndung'U, Perpetual Wangui

AU - Revathi, Gunturu

AU - Gehre, Florian

AU - Akter, Suriya

AU - Ntoumi, Francine

AU - Stewart-Isherwood, Lynsey

AU - Ntinginya, Nyanda E.

AU - Rachow, Andrea

AU - Hoelscher, Michael

AU - Cirillo, Daniela Maria

AU - Skenders, Girts

AU - Hoffner, Sven

AU - Bakonyte, Daiva

AU - Stakenas, Petras

AU - Diel, Roland

AU - Crudu, Valeriu

AU - Moldovan, Olga

AU - Al-Hajoj, Sahal

AU - Otero, Larissa

AU - Barletta, Francesca

AU - Carter, E. Jane

AU - Diero, Lameck

AU - Supply, Philip

AU - Comas, Iñaki

AU - Niemann, Stefan

AU - Gagneux, Sebastien

PY - 2016/12/1

Y1 - 2016/12/1

N2 - Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.

AB - Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.

UR - https://www.scopus.com/pages/publications/84992759009

U2 - 10.1038/ng.3704

DO - 10.1038/ng.3704

M3 - Article

C2 - 27798628

AN - SCOPUS:84992759009

SN - 1061-4036

VL - 48

SP - 1535

EP - 1543

JO - Nature Genetics

JF - Nature Genetics

IS - 12

ER -

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Abstract

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