Phylogenomic perspective on a unique mycobacterium bovis clade dominating bovine tuberculosis infections among cattle and buffalos in Northern Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES), Instituto Evandro Chagas/MS/SVS and Fundação para o desenvolvimento científco e tecnológico em saúde [PRES-012-FIO-16]; CAPES – Finance Code 001, [194–88881.187587/2018–01, 2018].; German Center for Infection Research (DZIF). European Society of Clinical Microbiology and Infectious Diseases, for which we would like to would like to acknowledge the Study Group for Mycobacterial Infections and Fundação para a Ciência e Tecnologia (UID/DTP/04138/2019). CEECIND/00394/2017.State University of Pará. Belém, PA, Brazil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade de Lisboa. Faculty of Pharmacy. Research Institute for Medicines. Lisbon, Portugal.Federal University of Rio de Janeiro. Rio de Janeiro, RJ, Brazil / Oswald Cruz Foundation. Rio de Janeiro, RJ, Brazil.State University of Pará. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.State University of Pará. Belém, PA, Brazil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade de Lisboa. Faculty of Pharmacy. Research Institute for Medicines. Lisbon, Portugal.French Agency for Food, Environmental and Occupational Health and Safety. Maisons-Alfort, France.French Agency for Food, Environmental and Occupational Health and Safety. Maisons-Alfort, France.Leibniz Research Center Borstel. Borstel, Germany / German Center for Infection Research. Heidelberg, Germany.Research Center Borstel Leibniz Lung Center. National Reference Center for Mycobacteria. Borstel, Germany / London School of Hygiene and Tropical Medicine. London, UK / London School of Hygiene and Tropical Medicine. Clinical Research Department. London, UK.Federal Rural University of Amazon. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade de Lisboa. Faculty of Pharmacy. Research Institute for Medicines. Lisbon, Portugal.Universidade de Lisboa. Faculty of Pharmacy. Research Institute for Medicines. Lisbon, Portugal.State University of Pará. Belém, PA, Brazil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Lack of routine surveillance in countries endemic for bovine tuberculosis (TB) and limited laboratory support contributes to the inability to differentiate the Mycobacterium tuberculosis Complex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing of Mycobacterium bovis isolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission of M. bovis is ongoing at distinct sites. Moreover, the M. bovis epidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from other M. bovis clades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for the M. bovis Marajó strain. In conclusion, this study contributes with data regarding the identification of a novel M. bovis phylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB