Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method

Autores
Abadia, Edgar; Zhang, Jian; dos Vultos, Tiago; Ritacco, Gloria Viviana; Kremer, Kristin; Aktas, Elif; Matsumoto, Tomoshige; Refregier, Guislaine; van Soolingen , Dick; Gicquel, Brigitte; Sola, Christophe
Año de publicación
2010
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We developed a new multiplexed-PCR assay to accurately classify Mycobacterium tuberculosis complex (MTC) isolates at the sublineage level by single nucleotide polymorphisms (SNPs). This method relies on 7 SNPs located in different genes of the MTC strains (recC, rec0, recR, ligB, ligC, alkA, and mgtC). Most of these genes are involved in replication, repair and recombination (3R) functions of M. tuberculosis strains, four of the mutations are synonymous, and thus neutral. Genes were chosen as a first empirical approach to assess the congruence between spoligotyping-based phylogeographical classification and SNP typing.This scheme efficiently classifies most of MTC phylogeographical groups: (1) confirming and identifying new sublineage-specific SNPs, (2) unraveling phylogenetical relationships between spoligotyping-defined MTC sublineages, (3) appropriately assigning sublineages to some spoligotypes and reassigning sublineages to other mis-labeled spoligotype signatures. This study opens the way to a more meaningful taxonomic, evolutionary and epidemiological classification. It also allows evaluation of spoligotype-signature significance towards a more comprehensive understanding of the evolutionary mechanisms of the clustered regularly interspaced short palindromic repeat (CRISPR) locus in MTC.
Fil: Abadia, Edgar. Université de Paris XI; Francia
Fil: Zhang, Jian. Université de Paris XI; Francia
Fil: dos Vultos, Tiago. Instituto Pasteur; Francia
Fil: Ritacco, Gloria Viviana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Kremer, Kristin. National Institute Of Public Health And The Environment; Países Bajos
Fil: Aktas, Elif. Inonu University Medical Faculty; Turquía
Fil: Matsumoto, Tomoshige. onguldak Karaelmas University Hospital; Japón
Fil: Refregier, Guislaine. Université de Paris XI; Francia
Fil: van Soolingen , Dick. National Institute Of Public Health And The Environment; Países Bajos
Fil: Gicquel, Brigitte. Instituto Pasteur; Francia
Fil: Sola, Christophe. Université de Paris XI; Francia
Materia
CRISPR
EVOLUTION
HIGH-THROUGHPUT
MULTIPLEX
MYCOBACTERIUM TUBERCULOSIS COMPLEX
PHYLOGENY
POPULATION STUDIES
SNPS
SPOLIGOTYPING
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/189442
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/189442
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based methodAbadia, EdgarZhang, Jiandos Vultos, TiagoRitacco, Gloria VivianaKremer, KristinAktas, ElifMatsumoto, TomoshigeRefregier, Guislainevan Soolingen , DickGicquel, BrigitteSola, ChristopheCRISPREVOLUTIONHIGH-THROUGHPUTMULTIPLEXMYCOBACTERIUM TUBERCULOSIS COMPLEXPHYLOGENYPOPULATION STUDIESSNPSSPOLIGOTYPINGhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3We developed a new multiplexed-PCR assay to accurately classify Mycobacterium tuberculosis complex (MTC) isolates at the sublineage level by single nucleotide polymorphisms (SNPs). This method relies on 7 SNPs located in different genes of the MTC strains (recC, rec0, recR, ligB, ligC, alkA, and mgtC). Most of these genes are involved in replication, repair and recombination (3R) functions of M. tuberculosis strains, four of the mutations are synonymous, and thus neutral. Genes were chosen as a first empirical approach to assess the congruence between spoligotyping-based phylogeographical classification and SNP typing.This scheme efficiently classifies most of MTC phylogeographical groups: (1) confirming and identifying new sublineage-specific SNPs, (2) unraveling phylogenetical relationships between spoligotyping-defined MTC sublineages, (3) appropriately assigning sublineages to some spoligotypes and reassigning sublineages to other mis-labeled spoligotype signatures. This study opens the way to a more meaningful taxonomic, evolutionary and epidemiological classification. It also allows evaluation of spoligotype-signature significance towards a more comprehensive understanding of the evolutionary mechanisms of the clustered regularly interspaced short palindromic repeat (CRISPR) locus in MTC.Fil: Abadia, Edgar. Université de Paris XI; FranciaFil: Zhang, Jian. Université de Paris XI; FranciaFil: dos Vultos, Tiago. Instituto Pasteur; FranciaFil: Ritacco, Gloria Viviana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kremer, Kristin. National Institute Of Public Health And The Environment; Países BajosFil: Aktas, Elif. Inonu University Medical Faculty; TurquíaFil: Matsumoto, Tomoshige. onguldak Karaelmas University Hospital; JapónFil: Refregier, Guislaine. Université de Paris XI; FranciaFil: van Soolingen , Dick. National Institute Of Public Health And The Environment; Países BajosFil: Gicquel, Brigitte. Instituto Pasteur; FranciaFil: Sola, Christophe. Université de Paris XI; FranciaElsevier Science2010-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/189442Abadia, Edgar; Zhang, Jian; dos Vultos, Tiago; Ritacco, Gloria Viviana; Kremer, Kristin; et al.; Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method; Elsevier Science; Infection, Genetics and Evolution; 10; 7; 7-2010; 1066-10741567-1348CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S1567134810001942info:eu-repo/semantics/altIdentifier/doi/10.1016/j.meegid.2010.07.006info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:33:03Zoai:ri.conicet.gov.ar:11336/189442instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:33:04.182CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
title Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
spellingShingle Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
Abadia, Edgar
CRISPR
EVOLUTION
HIGH-THROUGHPUT
MULTIPLEX
MYCOBACTERIUM TUBERCULOSIS COMPLEX
PHYLOGENY
POPULATION STUDIES
SNPS
SPOLIGOTYPING
title_short Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
title_full Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
title_fullStr Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
title_full_unstemmed Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
title_sort Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
dc.creator.none.fl_str_mv Abadia, Edgar
Zhang, Jian
dos Vultos, Tiago
Ritacco, Gloria Viviana
Kremer, Kristin
Aktas, Elif
Matsumoto, Tomoshige
Refregier, Guislaine
van Soolingen , Dick
Gicquel, Brigitte
Sola, Christophe
author Abadia, Edgar
author_facet Abadia, Edgar
Zhang, Jian
dos Vultos, Tiago
Ritacco, Gloria Viviana
Kremer, Kristin
Aktas, Elif
Matsumoto, Tomoshige
Refregier, Guislaine
van Soolingen , Dick
Gicquel, Brigitte
Sola, Christophe
author_role author
author2 Zhang, Jian
dos Vultos, Tiago
Ritacco, Gloria Viviana
Kremer, Kristin
Aktas, Elif
Matsumoto, Tomoshige
Refregier, Guislaine
van Soolingen , Dick
Gicquel, Brigitte
Sola, Christophe
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CRISPR
EVOLUTION
HIGH-THROUGHPUT
MULTIPLEX
MYCOBACTERIUM TUBERCULOSIS COMPLEX
PHYLOGENY
POPULATION STUDIES
SNPS
SPOLIGOTYPING
topic CRISPR
EVOLUTION
HIGH-THROUGHPUT
MULTIPLEX
MYCOBACTERIUM TUBERCULOSIS COMPLEX
PHYLOGENY
POPULATION STUDIES
SNPS
SPOLIGOTYPING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv We developed a new multiplexed-PCR assay to accurately classify Mycobacterium tuberculosis complex (MTC) isolates at the sublineage level by single nucleotide polymorphisms (SNPs). This method relies on 7 SNPs located in different genes of the MTC strains (recC, rec0, recR, ligB, ligC, alkA, and mgtC). Most of these genes are involved in replication, repair and recombination (3R) functions of M. tuberculosis strains, four of the mutations are synonymous, and thus neutral. Genes were chosen as a first empirical approach to assess the congruence between spoligotyping-based phylogeographical classification and SNP typing.This scheme efficiently classifies most of MTC phylogeographical groups: (1) confirming and identifying new sublineage-specific SNPs, (2) unraveling phylogenetical relationships between spoligotyping-defined MTC sublineages, (3) appropriately assigning sublineages to some spoligotypes and reassigning sublineages to other mis-labeled spoligotype signatures. This study opens the way to a more meaningful taxonomic, evolutionary and epidemiological classification. It also allows evaluation of spoligotype-signature significance towards a more comprehensive understanding of the evolutionary mechanisms of the clustered regularly interspaced short palindromic repeat (CRISPR) locus in MTC.
Fil: Abadia, Edgar. Université de Paris XI; Francia
Fil: Zhang, Jian. Université de Paris XI; Francia
Fil: dos Vultos, Tiago. Instituto Pasteur; Francia
Fil: Ritacco, Gloria Viviana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Kremer, Kristin. National Institute Of Public Health And The Environment; Países Bajos
Fil: Aktas, Elif. Inonu University Medical Faculty; Turquía
Fil: Matsumoto, Tomoshige. onguldak Karaelmas University Hospital; Japón
Fil: Refregier, Guislaine. Université de Paris XI; Francia
Fil: van Soolingen , Dick. National Institute Of Public Health And The Environment; Países Bajos
Fil: Gicquel, Brigitte. Instituto Pasteur; Francia
Fil: Sola, Christophe. Université de Paris XI; Francia
description We developed a new multiplexed-PCR assay to accurately classify Mycobacterium tuberculosis complex (MTC) isolates at the sublineage level by single nucleotide polymorphisms (SNPs). This method relies on 7 SNPs located in different genes of the MTC strains (recC, rec0, recR, ligB, ligC, alkA, and mgtC). Most of these genes are involved in replication, repair and recombination (3R) functions of M. tuberculosis strains, four of the mutations are synonymous, and thus neutral. Genes were chosen as a first empirical approach to assess the congruence between spoligotyping-based phylogeographical classification and SNP typing.This scheme efficiently classifies most of MTC phylogeographical groups: (1) confirming and identifying new sublineage-specific SNPs, (2) unraveling phylogenetical relationships between spoligotyping-defined MTC sublineages, (3) appropriately assigning sublineages to some spoligotypes and reassigning sublineages to other mis-labeled spoligotype signatures. This study opens the way to a more meaningful taxonomic, evolutionary and epidemiological classification. It also allows evaluation of spoligotype-signature significance towards a more comprehensive understanding of the evolutionary mechanisms of the clustered regularly interspaced short palindromic repeat (CRISPR) locus in MTC.
publishDate 2010
dc.date.none.fl_str_mv 2010-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/189442
Abadia, Edgar; Zhang, Jian; dos Vultos, Tiago; Ritacco, Gloria Viviana; Kremer, Kristin; et al.; Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method; Elsevier Science; Infection, Genetics and Evolution; 10; 7; 7-2010; 1066-1074
1567-1348
CONICET Digital
CONICET
url http://hdl.handle.net/11336/189442
identifier_str_mv Abadia, Edgar; Zhang, Jian; dos Vultos, Tiago; Ritacco, Gloria Viviana; Kremer, Kristin; et al.; Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method; Elsevier Science; Infection, Genetics and Evolution; 10; 7; 7-2010; 1066-1074
1567-1348
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S1567134810001942
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.meegid.2010.07.006
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier Science
publisher.none.fl_str_mv Elsevier Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844613013139619840
score 13.070432

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