Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade
Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and...
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| creator | Blouin, Yann Hauck, Yolande Soler, Charles Fabre, Michel Vong, Rithy Dehan, Céline Cazajous, Géraldine Massoure, Pierre-Laurent Kraemer, Philippe Jenkins, Akinbowale Garnotel, Eric Pourcel, Christine Vergnaud, Gilles |
| description | Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates. |
| doi_str_mv | 10.1371/journal.pone.0052841 |
| format | Article |
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The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0052841</identifier><identifier>PMID: 23300794</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Biochemistry, Molecular Biology ; Biology ; Cluster Analysis ; Clustering ; Djibouti ; Ecotypes ; Gene sequencing ; Genes, Bacterial ; Genetic diversity ; Genetic factors ; Genomes ; Genomics ; Genotype ; Host preferences ; Humans ; Hypotheses ; Kenya ; Life Sciences ; Microbiology and Parasitology ; Migration ; Minisatellite Repeats ; Models, Genetic ; Multilocus Sequence Typing ; Mutation ; Mycobacterium ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - genetics ; Mycobacterium tuberculosis - isolation & purification ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Population ; Somalia ; Spoligotyping ; Sudan ; Tuberculosis ; Tuberculosis - microbiology</subject><ispartof>PloS one, 2012-12, Vol.7 (12), p.e52841-e52841</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Blouin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>2012 Blouin et al 2012 Blouin et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c726t-bf5af338eae0028b0560227f452264792b1509d044040cc0c5c38377e85dface3</citedby><cites>FETCH-LOGICAL-c726t-bf5af338eae0028b0560227f452264792b1509d044040cc0c5c38377e85dface3</cites><orcidid>0000-0003-0913-194X ; 0000-0002-8951-466X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531362/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531362/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23300794$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00772379$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Mokrousov, Igor</contributor><creatorcontrib>Blouin, Yann</creatorcontrib><creatorcontrib>Hauck, Yolande</creatorcontrib><creatorcontrib>Soler, Charles</creatorcontrib><creatorcontrib>Fabre, Michel</creatorcontrib><creatorcontrib>Vong, Rithy</creatorcontrib><creatorcontrib>Dehan, Céline</creatorcontrib><creatorcontrib>Cazajous, Géraldine</creatorcontrib><creatorcontrib>Massoure, Pierre-Laurent</creatorcontrib><creatorcontrib>Kraemer, Philippe</creatorcontrib><creatorcontrib>Jenkins, Akinbowale</creatorcontrib><creatorcontrib>Garnotel, Eric</creatorcontrib><creatorcontrib>Pourcel, Christine</creatorcontrib><creatorcontrib>Vergnaud, Gilles</creatorcontrib><title>Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. 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Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</description><subject>Analysis</subject><subject>Animals</subject><subject>Biochemistry, Molecular Biology</subject><subject>Biology</subject><subject>Cluster Analysis</subject><subject>Clustering</subject><subject>Djibouti</subject><subject>Ecotypes</subject><subject>Gene sequencing</subject><subject>Genes, Bacterial</subject><subject>Genetic diversity</subject><subject>Genetic factors</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Host preferences</subject><subject>Humans</subject><subject>Hypotheses</subject><subject>Kenya</subject><subject>Life Sciences</subject><subject>Microbiology and Parasitology</subject><subject>Migration</subject><subject>Minisatellite Repeats</subject><subject>Models, Genetic</subject><subject>Multilocus 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One</addtitle><date>2012-12-27</date><risdate>2012</risdate><volume>7</volume><issue>12</issue><spage>e52841</spage><epage>e52841</epage><pages>e52841-e52841</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23300794</pmid><doi>10.1371/journal.pone.0052841</doi><tpages>e52841</tpages><orcidid>https://orcid.org/0000-0003-0913-194X</orcidid><orcidid>https://orcid.org/0000-0002-8951-466X</orcidid><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1327226351 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Biochemistry, Molecular Biology Biology Cluster Analysis Clustering Djibouti Ecotypes Gene sequencing Genes, Bacterial Genetic diversity Genetic factors Genomes Genomics Genotype Host preferences Humans Hypotheses Kenya Life Sciences Microbiology and Parasitology Migration Minisatellite Repeats Models, Genetic Multilocus Sequence Typing Mutation Mycobacterium Mycobacterium tuberculosis Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - isolation & purification Phylogeny Phylogeography Polymorphism, Single Nucleotide Population Somalia Spoligotyping Sudan Tuberculosis Tuberculosis - microbiology |
| title | Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-02T21%3A45%3A35IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Significance%20of%20the%20identification%20in%20the%20Horn%20of%20Africa%20of%20an%20exceptionally%20deep%20branching%20Mycobacterium%20tuberculosis%20clade&rft.jtitle=PloS%20one&rft.au=Blouin,%20Yann&rft.date=2012-12-27&rft.volume=7&rft.issue=12&rft.spage=e52841&rft.epage=e52841&rft.pages=e52841-e52841&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0052841&rft_dat=%3Cgale_plos_%3EA477033891%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1327226351&rft_id=info:pmid/23300794&rft_galeid=A477033891&rft_doaj_id=oai_doaj_org_article_8fe6911c62ca4abeaefbf6dee99da692&rfr_iscdi=true |