A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics

Background:  The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenet...

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Autores principales: Zwyer, Michaela, Çavusoglu, Cengiz, Ghielmetti, Giovanni, Pacciarini, Maria Lodovica, Scaltriti, Erika, Van Soolingen, Dick, Dötsch, Anna, Reinhard, Miriam, Gagneux, Sebastien, Brites, Daniela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10445919/
https://www.ncbi.nlm.nih.gov/pubmed/37645186
http://dx.doi.org/10.12688/openreseurope.14029.2
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author Zwyer, Michaela
Çavusoglu, Cengiz
Ghielmetti, Giovanni
Pacciarini, Maria Lodovica
Scaltriti, Erika
Van Soolingen, Dick
Dötsch, Anna
Reinhard, Miriam
Gagneux, Sebastien
Brites, Daniela
author_facet Zwyer, Michaela
Çavusoglu, Cengiz
Ghielmetti, Giovanni
Pacciarini, Maria Lodovica
Scaltriti, Erika
Van Soolingen, Dick
Dötsch, Anna
Reinhard, Miriam
Gagneux, Sebastien
Brites, Daniela
author_sort Zwyer, Michaela
collection PubMed
description Background:  The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods:  We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results:  We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions:  Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.
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spelling pubmed-104459192023-08-29 A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics Zwyer, Michaela Çavusoglu, Cengiz Ghielmetti, Giovanni Pacciarini, Maria Lodovica Scaltriti, Erika Van Soolingen, Dick Dötsch, Anna Reinhard, Miriam Gagneux, Sebastien Brites, Daniela Open Res Eur Research Article Background:  The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods:  We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results:  We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions:  Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies. F1000 Research Limited 2021-12-01 /pmc/articles/PMC10445919/ /pubmed/37645186 http://dx.doi.org/10.12688/openreseurope.14029.2 Text en Copyright: © 2021 Zwyer M et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zwyer, Michaela
Çavusoglu, Cengiz
Ghielmetti, Giovanni
Pacciarini, Maria Lodovica
Scaltriti, Erika
Van Soolingen, Dick
Dötsch, Anna
Reinhard, Miriam
Gagneux, Sebastien
Brites, Daniela
A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title_full A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title_fullStr A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title_full_unstemmed A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title_short A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
title_sort new nomenclature for the livestock-associated mycobacterium tuberculosis complex based on phylogenomics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10445919/
https://www.ncbi.nlm.nih.gov/pubmed/37645186
http://dx.doi.org/10.12688/openreseurope.14029.2
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