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Zwyer M, Çavusoglu C, Ghielmetti G, Pacciarini ML, Scaltriti E, Van Soolingen D, Dötsch A, Reinhard M, Gagneux S, Brites D. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. Open Res Eur 2021; 1:100. [PMID: 37645186 PMCID: PMC10445919 DOI: 10.12688/openreseurope.14029.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 08/31/2023]
Abstract
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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Affiliation(s)
- Michaela Zwyer
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cengiz Çavusoglu
- Department of Medical Microbiology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Dick Van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands Antilles
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Anna Dötsch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Miriam Reinhard
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Sebastien Gagneux
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Daniela Brites
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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Rufai SB, McIntosh F, Poojary I, Chothe S, Sebastian A, Albert I, Praul C, Venkatesan M, Mahata G, Maity H, Dandapat P, Michael JS, Katani R, Kapur V, Behr MA. Complete Genome Sequence of Mycobacterium orygis Strain 51145. Microbiol Resour Announc 2021; 10:e01279-20. [PMID: 33414309 PMCID: PMC8407732 DOI: 10.1128/mra.01279-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
We report the complete 4,352,172-bp genome sequence of Mycobacterium orygis strain 51145 assembled into a single circular chromosome. Comparative genomic analyses with other lineages of the Mycobacterium tuberculosis complex can provide insights into the biology, evolution, and epidemiology of this important group of pathogenic mycobacteria.
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Affiliation(s)
- Syed Beenish Rufai
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Fiona McIntosh
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Indira Poojary
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shubhada Chothe
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Craig Praul
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Gibarni Mahata
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Hindol Maity
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Cisgen Biotech Discoveries, Chennai, India
| | - Premanshu Dandapat
- Indian Veterinary Research Institute, Eastern Region Station, Kolkata, West Bengal, India
| | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Robab Katani
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
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