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, 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
Fil: Abadia, Edgar. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: Zhang, Jian. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: dos Vultos, Tiago. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.
Fil: Ritacco, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.
Fil: Kremer, Kristin. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.
Fil: Aktas, Elif. Departamento de Microbiología Clínica, Hospital Universitario Zonguldak Karaelmas, Zonguldak; Turquía.
Fil: Matsumoto, Tomoshige. Organización del Hospital de la Prefectura de Osaka Centro Médico de la Prefectura de Osaka para Enfermedades Alérgicas y Respiratorias; Japón.
Fil: Refregier, Guislaine. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: van Soolingen, Dick. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.
Fil: Gicquel, Brigitte. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.
Fil: Sola, Christophe. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
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.
Fuente
Infection, Genetics and Evolution 2010; 10 (7): 1066-74.
Materia
Mycobacterium tuberculosis
Filogenia
Polimorfismo de Nucleótido Simple
Nivel de accesibilidad
acceso abierto
Condiciones de uso
none
Repositorio
Sistema de Gestión del Conocimiento ANLIS MALBRÁN
Institución
Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
OAI Identificador
oai:sgc.anlis.gob.ar:123456789/2046
Acceder
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oai_identifier_str oai:sgc.anlis.gob.ar:123456789/2046
network_acronym_str SGCANLIS
repository_id_str a
network_name_str Sistema de Gestión del Conocimiento ANLIS MALBRÁN
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, VivianaKremer, KristinAktas, ElifMatsumoto, TomoshigeRefregier, Guislainevan Soolingen, DickGicquel, BrigitteSola, ChristopheMycobacterium tuberculosisFilogeniaPolimorfismo de Nucleótido SimpleFil: Abadia, Edgar. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.Fil: Zhang, Jian. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.Fil: dos Vultos, Tiago. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.Fil: Ritacco, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Kremer, Kristin. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.Fil: Aktas, Elif. Departamento de Microbiología Clínica, Hospital Universitario Zonguldak Karaelmas, Zonguldak; Turquía.Fil: Matsumoto, Tomoshige. Organización del Hospital de la Prefectura de Osaka Centro Médico de la Prefectura de Osaka para Enfermedades Alérgicas y Respiratorias; Japón.Fil: Refregier, Guislaine. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.Fil: van Soolingen, Dick. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.Fil: Gicquel, Brigitte. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.Fil: Sola, Christophe. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.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.Elsevier2010-10info:ar-repo/semantics/articuloinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdf1567-1348https://www.sciencedirect.com/science/article/abs/pii/S1567134810001942?via%3Dihubhttp://sgc.anlis.gob.ar/handle/123456789/204610.1016/j.meegid.2010.07.006Infection, Genetics and Evolution 2010; 10 (7): 1066-74.reponame:Sistema de Gestión del Conocimiento ANLIS MALBRÁNinstname:Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"instacron:ANLISInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseasesnoneinfo:eu-repo/semantics/openAccesseng2025-09-04T11:18:07Zoai:sgc.anlis.gob.ar:123456789/2046Institucionalhttp://sgc.anlis.gob.ar/Organismo científico-tecnológicoNo correspondehttp://sgc.anlis.gob.ar/oai/biblioteca@anlis.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:a2025-09-04 11:18:08.278Sistema de Gestión del Conocimiento ANLIS MALBRÁN - Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"false
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
Mycobacterium tuberculosis
Filogenia
Polimorfismo de Nucleótido Simple
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, 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, 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, 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 Mycobacterium tuberculosis
Filogenia
Polimorfismo de Nucleótido Simple
topic Mycobacterium tuberculosis
Filogenia
Polimorfismo de Nucleótido Simple
dc.description.none.fl_txt_mv Fil: Abadia, Edgar. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: Zhang, Jian. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: dos Vultos, Tiago. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.
Fil: Ritacco, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.
Fil: Kremer, Kristin. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.
Fil: Aktas, Elif. Departamento de Microbiología Clínica, Hospital Universitario Zonguldak Karaelmas, Zonguldak; Turquía.
Fil: Matsumoto, Tomoshige. Organización del Hospital de la Prefectura de Osaka Centro Médico de la Prefectura de Osaka para Enfermedades Alérgicas y Respiratorias; Japón.
Fil: Refregier, Guislaine. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
Fil: van Soolingen, Dick. Instituto Nacional de Salud Pública y Medio Ambiente, Bilthoven; Países Bajos.
Fil: Gicquel, Brigitte. Unité de Génétique Mycobactérienne, Institut Pasteur, París; Francia.
Fil: Sola, Christophe. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
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.
description Fil: Abadia, Edgar. Instituto de Genética y Microbiología, UMR8621, Equipo IGEPE, Universud, CNRS Université; Francia.
publishDate 2010
dc.date.none.fl_str_mv 2010-10
dc.type.none.fl_str_mv info:ar-repo/semantics/articulo
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv 1567-1348
https://www.sciencedirect.com/science/article/abs/pii/S1567134810001942?via%3Dihub
http://sgc.anlis.gob.ar/handle/123456789/2046
10.1016/j.meegid.2010.07.006
identifier_str_mv 1567-1348
10.1016/j.meegid.2010.07.006
url https://www.sciencedirect.com/science/article/abs/pii/S1567134810001942?via%3Dihub
http://sgc.anlis.gob.ar/handle/123456789/2046
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
dc.rights.none.fl_str_mv none
info:eu-repo/semantics/openAccess
rights_invalid_str_mv none
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Infection, Genetics and Evolution 2010; 10 (7): 1066-74.
reponame:Sistema de Gestión del Conocimiento ANLIS MALBRÁN
instname:Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
instacron:ANLIS
reponame_str Sistema de Gestión del Conocimiento ANLIS MALBRÁN
collection Sistema de Gestión del Conocimiento ANLIS MALBRÁN
instname_str Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
instacron_str ANLIS
institution ANLIS
repository.name.fl_str_mv Sistema de Gestión del Conocimiento ANLIS MALBRÁN - Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
repository.mail.fl_str_mv biblioteca@anlis.gov.ar
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score 12.623145

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