IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes

Autores
Reyes, Alejandro; Sandoval, Andrea; Cubillos Ruiz, Andrés; Varley, Katherine E; Hernández Neuta, Ivan; Samper, Sofía; Martín, Carlos; García, María J.; Ritacco, Gloria Viviana; López, Lucelly; Robledo, Jaime; Zambrano, María M.; Mitra, Robi D; Del Portillo, Patricia
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
Fil: Reyes, Alejandro. University of Washington. School of Medicine; Estados Unidos
Fil: Sandoval, Andrea. No especifíca;
Fil: Cubillos Ruiz, Andrés. No especifíca;
Fil: Varley, Katherine E. University of Washington. School of Medicine; Estados Unidos
Fil: Hernández Neuta, Ivan. No especifíca;
Fil: Samper, Sofía. Hospital Universitario Miguel Servet; España
Fil: Martín, Carlos. Universidad de Zaragoza; España
Fil: García, María J.. Universidad Autónoma de Madrid; España
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: López, Lucelly. Universidad de Antioquia; Colombia
Fil: Robledo, Jaime. Corporación Para Investigaciones Biológicas; Colombia
Fil: Zambrano, María M.. No especifíca;
Fil: Mitra, Robi D. University of Washington. School of Medicine; Estados Unidos
Fil: Del Portillo, Patricia. No especifíca;
Materia
Mycobacterium tuberculosis
IS6110
high-throughput sequencing
flanking regions
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/192101
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/192101
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomesReyes, AlejandroSandoval, AndreaCubillos Ruiz, AndrésVarley, Katherine EHernández Neuta, IvanSamper, SofíaMartín, CarlosGarcía, María J.Ritacco, Gloria VivianaLópez, LucellyRobledo, JaimeZambrano, María M.Mitra, Robi DDel Portillo, PatriciaMycobacterium tuberculosisIS6110high-throughput sequencingflanking regionshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.Fil: Reyes, Alejandro. University of Washington. School of Medicine; Estados UnidosFil: Sandoval, Andrea. No especifíca;Fil: Cubillos Ruiz, Andrés. No especifíca;Fil: Varley, Katherine E. University of Washington. School of Medicine; Estados UnidosFil: Hernández Neuta, Ivan. No especifíca;Fil: Samper, Sofía. Hospital Universitario Miguel Servet; EspañaFil: Martín, Carlos. Universidad de Zaragoza; EspañaFil: García, María J.. Universidad Autónoma de Madrid; EspañaFil: 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: López, Lucelly. Universidad de Antioquia; ColombiaFil: Robledo, Jaime. Corporación Para Investigaciones Biológicas; ColombiaFil: Zambrano, María M.. No especifíca;Fil: Mitra, Robi D. University of Washington. School of Medicine; Estados UnidosFil: Del Portillo, Patricia. No especifíca;BioMed Central2012-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/192101Reyes, Alejandro; Sandoval, Andrea; Cubillos Ruiz, Andrés; Varley, Katherine E; Hernández Neuta, Ivan; et al.; IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes; BioMed Central; BMC Genomics; 13; 1; 6-2012; 1-151471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.biomedcentral.com/1471-2164/13/249info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-13-249info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:42:56Zoai:ri.conicet.gov.ar:11336/192101instacron: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 09:42:56.305CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
title IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
spellingShingle IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
Reyes, Alejandro
Mycobacterium tuberculosis
IS6110
high-throughput sequencing
flanking regions
title_short IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
title_full IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
title_fullStr IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
title_full_unstemmed IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
title_sort IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
dc.creator.none.fl_str_mv Reyes, Alejandro
Sandoval, Andrea
Cubillos Ruiz, Andrés
Varley, Katherine E
Hernández Neuta, Ivan
Samper, Sofía
Martín, Carlos
García, María J.
Ritacco, Gloria Viviana
López, Lucelly
Robledo, Jaime
Zambrano, María M.
Mitra, Robi D
Del Portillo, Patricia
author Reyes, Alejandro
author_facet Reyes, Alejandro
Sandoval, Andrea
Cubillos Ruiz, Andrés
Varley, Katherine E
Hernández Neuta, Ivan
Samper, Sofía
Martín, Carlos
García, María J.
Ritacco, Gloria Viviana
López, Lucelly
Robledo, Jaime
Zambrano, María M.
Mitra, Robi D
Del Portillo, Patricia
author_role author
author2 Sandoval, Andrea
Cubillos Ruiz, Andrés
Varley, Katherine E
Hernández Neuta, Ivan
Samper, Sofía
Martín, Carlos
García, María J.
Ritacco, Gloria Viviana
López, Lucelly
Robledo, Jaime
Zambrano, María M.
Mitra, Robi D
Del Portillo, Patricia
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Mycobacterium tuberculosis
IS6110
high-throughput sequencing
flanking regions
topic Mycobacterium tuberculosis
IS6110
high-throughput sequencing
flanking regions
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
Fil: Reyes, Alejandro. University of Washington. School of Medicine; Estados Unidos
Fil: Sandoval, Andrea. No especifíca;
Fil: Cubillos Ruiz, Andrés. No especifíca;
Fil: Varley, Katherine E. University of Washington. School of Medicine; Estados Unidos
Fil: Hernández Neuta, Ivan. No especifíca;
Fil: Samper, Sofía. Hospital Universitario Miguel Servet; España
Fil: Martín, Carlos. Universidad de Zaragoza; España
Fil: García, María J.. Universidad Autónoma de Madrid; España
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: López, Lucelly. Universidad de Antioquia; Colombia
Fil: Robledo, Jaime. Corporación Para Investigaciones Biológicas; Colombia
Fil: Zambrano, María M.. No especifíca;
Fil: Mitra, Robi D. University of Washington. School of Medicine; Estados Unidos
Fil: Del Portillo, Patricia. No especifíca;
description Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
publishDate 2012
dc.date.none.fl_str_mv 2012-06
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/11336/192101
Reyes, Alejandro; Sandoval, Andrea; Cubillos Ruiz, Andrés; Varley, Katherine E; Hernández Neuta, Ivan; et al.; IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes; BioMed Central; BMC Genomics; 13; 1; 6-2012; 1-15
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/192101
identifier_str_mv Reyes, Alejandro; Sandoval, Andrea; Cubillos Ruiz, Andrés; Varley, Katherine E; Hernández Neuta, Ivan; et al.; IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes; BioMed Central; BMC Genomics; 13; 1; 6-2012; 1-15
1471-2164
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.biomedcentral.com/1471-2164/13/249
info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-13-249
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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
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score 13.070432

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