{"corpus_id":1597629,"paper_sha":"05cdc01ac09ee45a2ee17015af2402683de839a2","doi":"10.1038/ng.3704","arxiv_id":null,"pmid":27798628,"pmcid":"5238942","mag_id":2544696205,"dblp_id":null,"acl_id":null,"title":"Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages","year":2016,"publication_date":"2016-10-04","venue":"Nature Genetics","journal":{"name":"Nature genetics","pages":"1535 - 1543","volume":"48"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, N.I.H., Extramural","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine","Environmental Science"],"reference_count":97,"citation_count":354,"influential_citation_count":23,"is_open_access":false,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"DNA, Bacterial","mj":false,"qs":[{"q":"analysis","mj":true,"ui":"Q000032"}],"ui":"D004269"},{"d":"Genomics","mj":false,"qs":[{"q":"methods","mj":true,"ui":"Q000379"}],"ui":"D023281"},{"d":"Genotype","mj":false,"ui":"D005838"},{"d":"Global Health","mj":false,"ui":"D014943"},{"d":"Humans","mj":false,"ui":"D006801"},{"d":"Mycobacterium tuberculosis","mj":false,"qs":[{"q":"classification","mj":true,"ui":"Q000145"},{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"isolation & purification","mj":false,"ui":"Q000302"}],"ui":"D009169"},{"d":"Phylogeography","mj":false,"ui":"D058974"},{"d":"Polymorphism, Genetic","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"}],"ui":"D011110"},{"d":"Tuberculosis","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"microbiology","mj":true,"ui":"Q000382"}],"ui":"D014376"}],"chemicals":[{"n":"DNA, Bacterial","ui":"D004269","reg":"0"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":null,"s2_open_access_landing_url":null,"s2_open_access_license":null,"s2_open_access_status":null,"pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.","claims":[{"public_id":"cl_045f7ebf42a41bd65dff14273dcbe983","status":"active","text":"Lineage 4 comprises both globally distributed and geographically restricted sublineages.","confidence":0.99,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_045f7ebf42a41bd65dff14273dcbe983"},{"public_id":"cl_65386e795b564715435bd4855345c1eb","status":"active","text":"Most human T cell epitopes are conserved across all sublineages, but variable epitopes are more common in generalists.","confidence":0.96,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_65386e795b564715435bd4855345c1eb"},{"public_id":"cl_321753c5e855062cd6ef51cab458f3dd","status":"active","text":"The distinction between globally distributed and geographically restricted sublineages suggests a generalist-versus-specialist split within lineage 4.","confidence":0.92,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_321753c5e855062cd6ef51cab458f3dd"},{"public_id":"cl_4a9dfb84d76b4b5d1166f45a46348e09","status":"active","text":"The global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.","confidence":0.93,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_4a9dfb84d76b4b5d1166f45a46348e09"},{"public_id":"cl_a2275bc704785e58f9fe1c8a690db7a7","status":"active","text":"The most common generalist sublineage has a European origin.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_a2275bc704785e58f9fe1c8a690db7a7"}],"concepts":[{"public_id":"co_013ab59d9bf1a9de92ba323d5e668a08","status":"active","name":"European origin","description":"An inferred geographic source region for the most common generalist sublineage.","types":["origin"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous 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sublineages.","types":["process"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_89de6abf431c306b42388f6637997dea"},{"public_id":"co_d09d5f40610305f1f1a2613f46af0a93","status":"active","name":"human T cell epitopes","description":"Peptide regions recognized by human T cells in the pathogen genome.","types":["immunological feature"],"aliases":["T cell epitopes"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_d09d5f40610305f1f1a2613f46af0a93"},{"public_id":"co_dd5f434c12ef297dc88ac738a6c68c10","status":"active","name":"globally distributed and geographically restricted sublineages","description":"Sublineages within lineage 4 that differ in whether they occur worldwide or in limited 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