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Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: Insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set

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dc.creatorFilliol, Ingrid
dc.creatorMotiwala, Alifiya S.
dc.creatorCavatore, Magali
dc.creatorQi, Weihong
dc.creatorHazbón, Manzour Hernando
dc.creatorBobadilla del Valle, Miriam
dc.creatorFyfe, Janet
dc.creatorGarcía-García, Lourdes
dc.creatorRastogi, Nalin
dc.creatorSola, Christophe
dc.creatorZozio, Thierry
dc.creatorGuerrero, Marta Inírida
dc.creatorLeón, Clara Inés
dc.creatorCrabtree, Jonathan
dc.creatorAngiuoli, Sam
dc.creatorEisenach, Kathleen D.
dc.creatorDurmaz, Riza
dc.creatorJoloba, Moses L.
dc.creatorRendón, Adrian
dc.creatorSifuentes-Osornio, José
dc.creatorPonce de León, Alfredo
dc.creatorCave, M. Donald
dc.creatorFleischmann, Robert
dc.creatorWhittam, Thomas S.
dc.creatorAlland, David
dc.creator.googleFilliol, Ingridspa
dc.creator.googleMotiwala, Alifiya S.spa
dc.creator.googleCavatore, Magalispa
dc.creator.googleQi, Weihongspa
dc.creator.googleHazbón, Manzour Hernandospa
dc.creator.googleBobadilla Del Valle, Miriamspa
dc.creator.googleFyfe, Janetspa
dc.creator.googleGarcía-García, Lourdesspa
dc.creator.googleRastogi, Nalinspa
dc.creator.googleSola, Christophespa
dc.creator.googleZozio, TThierryspa
dc.creator.googleGuerrero, Marta Iníridaspa
dc.creator.googleLeón, Clara Inésspa
dc.creator.googleCrabtree, Jonathanspa
dc.creator.googleAngiuoli, Samspa
dc.creator.googleEisenach, Kathleen D.spa
dc.creator.googleDurmaz, Rizaspa
dc.creator.googleJoloba, Moses L.spa
dc.creator.googleRendón, Adrianspa
dc.creator.googleSifuentes-Osornio, Joséspa
dc.creator.googlePonce de Leon, Alfredospa
dc.creator.googleCave, M. Donaldspa
dc.creator.googleFleischmann, Robertspa
dc.creator.googleWhittam, Thomas S.spa
dc.creator.googleAlland, Davidspa
dc.date.accessioned2020-05-10T05:10:41Z
dc.date.available2020-05-10T05:10:41Z
dc.date.created2006
dc.date.issued2006
dc.description.abstractWe analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis. Copyright © 2006, American Society for Microbiology. All Rights Reserved.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1128/JB.188.2.759-772.2006
dc.identifier.issn0021-9193
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/21927
dc.language.isoengspa
dc.relation.citationEndPage772
dc.relation.citationIssueNo. 2
dc.relation.citationStartPage759
dc.relation.citationTitleJournal of Bacteriology
dc.relation.citationVolumeVol. 188
dc.relation.ispartofJournal of Bacteriology, ISSN: 0021-9193 Vol. 188, No. 2 (2006) pp. 759-772spa
dc.relation.urihttps://jb.asm.org/content/188/2/759.shortspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosario
dc.source.reponamereponame:Repositorio Institucional EdocUR
dc.subject.ddcEnfermedadesspa
dc.subject.ddcEvolución & genéticaspa
dc.subject.ddcMicrobiologíaspa
dc.subject.keywordControlled studyspa
dc.subject.keywordGenetic variabilityspa
dc.subject.keywordHumansspa
dc.subject.keywordMycobacterium tuberculosisspa
dc.subject.keywordBacteria (microorganisms)spa
dc.subject.keywordMycobacterium tuberculosisspa
dc.subject.keywordDNA fingerprintingspa
dc.subject.keywordDNA sequencespa
dc.titleGlobal phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: Insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP setspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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