A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved]
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 phylogenetic...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2021-12-01
|
| Series: | Open Research Europe |
| Subjects: | |
| Online Access: | https://open-research-europe.ec.europa.eu/articles/1-100/v2 |
| _version_ | 1811246685314088960 |
|---|---|
| author | Anna Dötsch Dick Van Soolingen Miriam Reinhard Michaela Zwyer Giovanni Ghielmetti Cengiz Çavusoglu Erika Scaltriti Sebastien Gagneux Maria Lodovica Pacciarini Daniela Brites |
| author_facet | Anna Dötsch Dick Van Soolingen Miriam Reinhard Michaela Zwyer Giovanni Ghielmetti Cengiz Çavusoglu Erika Scaltriti Sebastien Gagneux Maria Lodovica Pacciarini Daniela Brites |
| author_sort | Anna Dötsch |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T14:57:53Z |
| format | Article |
| id | doaj.art-4cdbaee743824621a43aad31c1fd3e6e |
| institution | Directory Open Access Journal |
| issn | 2732-5121 |
| language | English |
| last_indexed | 2024-04-12T14:57:53Z |
| publishDate | 2021-12-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | Open Research Europe |
| spelling | doaj.art-4cdbaee743824621a43aad31c1fd3e6e2022-12-22T03:28:11ZengF1000 Research LtdOpen Research Europe2732-51212021-12-01115458A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved]Anna Dötsch0Dick Van Soolingen1Miriam Reinhard2Michaela Zwyer3Giovanni Ghielmetti4https://orcid.org/0000-0002-3936-9687Cengiz Çavusoglu5https://orcid.org/0000-0001-7152-5216Erika Scaltriti6Sebastien Gagneux7https://orcid.org/0000-0001-7783-9048Maria Lodovica Pacciarini8Daniela Brites9https://orcid.org/0000-0002-8090-2287Swiss Tropical and Public Health Institute, Basel, SwitzerlandNational Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands AntillesSwiss Tropical and Public Health Institute, Basel, SwitzerlandSwiss Tropical and Public Health Institute, Basel, SwitzerlandInstitute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, SwitzerlandDepartment of Medical Microbiology, Ege University Faculty of Medicine, Izmir, TurkeyRisk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, ItalySwiss Tropical and Public Health Institute, Basel, SwitzerlandNational Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, ItalySwiss Tropical and Public Health Institute, Basel, SwitzerlandBackground 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.https://open-research-europe.ec.europa.eu/articles/1-100/v2zoonotic tuberculosis genetic diversity mycobacterium tuberculosis complex phylogenetics whole-genome sequencingeng |
| spellingShingle | Anna Dötsch Dick Van Soolingen Miriam Reinhard Michaela Zwyer Giovanni Ghielmetti Cengiz Çavusoglu Erika Scaltriti Sebastien Gagneux Maria Lodovica Pacciarini Daniela Brites A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] Open Research Europe zoonotic tuberculosis genetic diversity mycobacterium tuberculosis complex phylogenetics whole-genome sequencing eng |
| title | A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] |
| title_full | A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] |
| title_fullStr | A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] |
| title_full_unstemmed | A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] |
| title_short | A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] |
| title_sort | new nomenclature for the livestock associated mycobacterium tuberculosis complex based on phylogenomics version 2 peer review 2 approved |
| topic | zoonotic tuberculosis genetic diversity mycobacterium tuberculosis complex phylogenetics whole-genome sequencing eng |
| url | https://open-research-europe.ec.europa.eu/articles/1-100/v2 |
| work_keys_str_mv | AT annadotsch anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT dickvansoolingen anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT miriamreinhard anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT michaelazwyer anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT giovannighielmetti anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT cengizcavusoglu anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT erikascaltriti anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT sebastiengagneux anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT marialodovicapacciarini anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT danielabrites anewnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT annadotsch newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT dickvansoolingen newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT miriamreinhard newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT michaelazwyer newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT giovannighielmetti newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT cengizcavusoglu newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT erikascaltriti newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT sebastiengagneux newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT marialodovicapacciarini newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved AT danielabrites newnomenclatureforthelivestockassociatedmycobacteriumtuberculosiscomplexbasedonphylogenomicsversion2peerreview2approved |