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

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dc.authorscopusid24400996700
dc.authorscopusid57197768178
dc.authorscopusid6603514411
dc.authorscopusid55856268500
dc.authorscopusid6701668658
dc.authorscopusid15050841700
dc.authorscopusid55114040800
dc.contributor.authorBrites D.
dc.contributor.authorZwyer M.
dc.contributor.authorÇavusoglu C.
dc.contributor.authorGhielmetti G.
dc.contributor.authorPacciarini M.L.
dc.contributor.authorScaltriti E.
dc.contributor.authorVan Soolingen D.
dc.date.accessioned2023-01-12T20:23:44Z
dc.date.available2023-01-12T20:23:44Z
dc.date.issued2021
dc.departmentN/A/Departmenten_US
dc.description.abstractBackground 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. © 2021 Zwyer M et al.en_US
dc.identifier.doi10.12688/openreseurope.14029.2
dc.identifier.issn27325121
dc.identifier.issn2732-5121en_US
dc.identifier.scopus2-s2.0-85133651941en_US
dc.identifier.scopusqualityN/Aen_US
dc.identifier.urihttps://doi.org/10.12688/openreseurope.14029.2
dc.identifier.urihttps://hdl.handle.net/11454/79759
dc.identifier.volume1en_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherF1000 Research Ltden_US
dc.relation.ispartofOpen Research Europeen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGenetic diversityen_US
dc.subjectMycobacterium tuberculosis complexen_US
dc.subjectPhylogeneticsen_US
dc.subjectWhole-genome sequencingen_US
dc.subjectZoonotic tuberculosisen_US
dc.titleA new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomicsen_US
dc.typeArticleen_US

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