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 GlobanJackson 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

IRCCS Ospedale San Raffaele

Research output: Contribution to journal › Article

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
Journal	Nature Genetics
DOIs	https://doi.org/10.1038/ng.3704
Publication status	Accepted/In press - Oct 31 2016

ASJC Scopus subject areas

Genetics

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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. (Accepted/In press). Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genetics. https://doi.org/10.1038/ng.3704

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. / Stucki, David; Brites, Daniela; Jeljeli, Leïla; Coscolla, Mireia; Liu, Qingyun; Trauner, Andrej; Fenner, Lukas; Rutaihwa, Liliana; Borrell, Sonia; Luo, Tao; Gao, Qian; Kato-Maeda, Midori; Ballif, Marie; Egger, Matthias; Macedo, Rita; Mardassi, Helmi; Moreno, Milagros; Vilanova, Griselda Tudo; Fyfe, Janet; Globan, Maria; Thomas, Jackson; Jamieson, Frances; Guthrie, Jennifer L.; Asante-Poku, Adwoa; Yeboah-Manu, Dorothy; Wampande, Eddie; Ssengooba, Willy; Joloba, Moses; Boom, W. Henry; Basu, Indira; Bower, James; Saraiva, Margarida; Vasconcellos, Sidra E G; Suffys, Philip; Koch, Anastasia; Wilkinson, Robert; Gail-Bekker, Linda; Malla, Bijaya; Ley, Serej D.; Beck, Hans Peter; de Jong, Bouke C.; Toit, Kadri; Sanchez-Padilla, Elisabeth; Bonnet, Maryline; Gil-Brusola, Ana; Frank, Matthias; Penlap Beng, Veronique N.; Eisenach, Kathleen; Alani, Issam; Ndung'u, Perpetual Wangui; Revathi, Gunturu; Gehre, Florian; Akter, Suriya; Ntoumi, Francine; Stewart-Isherwood, Lynsey; Ntinginya, Nyanda E.; Rachow, Andrea; Hoelscher, Michael; Cirillo, Daniela Maria; Skenders, Girts; Hoffner, Sven; Bakonyte, Daiva; Stakenas, Petras; Diel, Roland; Crudu, Valeriu; Moldovan, Olga; Al-Hajoj, Sahal; Otero, Larissa; Barletta, Francesca; Carter, E. Jane; Diero, Lameck; Supply, Philip; Comas, Iñaki; Niemann, Stefan; Gagneux, Sebastien.

In: Nature Genetics, 31.10.2016.

Research output: Contribution to journal › Article

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. https://doi.org/10.1038/ng.3704

Stucki, David ; Brites, Daniela ; Jeljeli, Leïla ; Coscolla, Mireia ; Liu, Qingyun ; Trauner, Andrej ; Fenner, Lukas ; Rutaihwa, Liliana ; Borrell, Sonia ; Luo, Tao ; Gao, Qian ; Kato-Maeda, Midori ; Ballif, Marie ; Egger, Matthias ; Macedo, Rita ; Mardassi, Helmi ; Moreno, Milagros ; Vilanova, Griselda Tudo ; Fyfe, Janet ; Globan, Maria ; Thomas, Jackson ; Jamieson, Frances ; Guthrie, Jennifer L. ; Asante-Poku, Adwoa ; Yeboah-Manu, Dorothy ; Wampande, Eddie ; Ssengooba, Willy ; Joloba, Moses ; Boom, W. Henry ; Basu, Indira ; Bower, James ; Saraiva, Margarida ; Vasconcellos, Sidra E G ; Suffys, Philip ; Koch, Anastasia ; Wilkinson, Robert ; Gail-Bekker, Linda ; Malla, Bijaya ; Ley, Serej D. ; Beck, Hans Peter ; de Jong, Bouke C. ; Toit, Kadri ; Sanchez-Padilla, Elisabeth ; Bonnet, Maryline ; Gil-Brusola, Ana ; Frank, Matthias ; Penlap Beng, Veronique N. ; Eisenach, Kathleen ; Alani, Issam ; Ndung'u, Perpetual Wangui ; Revathi, Gunturu ; Gehre, Florian ; Akter, Suriya ; Ntoumi, Francine ; Stewart-Isherwood, Lynsey ; Ntinginya, Nyanda E. ; Rachow, Andrea ; Hoelscher, Michael ; Cirillo, Daniela Maria ; Skenders, Girts ; Hoffner, Sven ; Bakonyte, Daiva ; Stakenas, Petras ; Diel, Roland ; Crudu, Valeriu ; Moldovan, Olga ; Al-Hajoj, Sahal ; Otero, Larissa ; Barletta, Francesca ; Carter, E. Jane ; Diero, Lameck ; Supply, Philip ; Comas, Iñaki ; Niemann, Stefan ; Gagneux, Sebastien. / Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. In: Nature Genetics. 2016.

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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.",

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