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IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
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 site...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443423/ https://www.ncbi.nlm.nih.gov/pubmed/22703188 http://dx.doi.org/10.1186/1471-2164-13-249 |
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author | Reyes, Alejandro Sandoval, Andrea Cubillos-Ruiz, Andrés Varley, Katherine E Hernández-Neuta, Ivan Samper, Sofía Martín, Carlos García, María Jesús Ritacco, Viviana López, Lucelly Robledo, Jaime Zambrano, María Mercedes Mitra, Robi D Del Portillo, Patricia |
author_facet | Reyes, Alejandro Sandoval, Andrea Cubillos-Ruiz, Andrés Varley, Katherine E Hernández-Neuta, Ivan Samper, Sofía Martín, Carlos García, María Jesús Ritacco, Viviana López, Lucelly Robledo, Jaime Zambrano, María Mercedes Mitra, Robi D Del Portillo, Patricia |
author_sort | Reyes, Alejandro |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-3443423 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34434232012-09-18 IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes Reyes, Alejandro Sandoval, Andrea Cubillos-Ruiz, Andrés Varley, Katherine E Hernández-Neuta, Ivan Samper, Sofía Martín, Carlos García, María Jesús Ritacco, Viviana López, Lucelly Robledo, Jaime Zambrano, María Mercedes Mitra, Robi D Del Portillo, Patricia BMC Genomics Research Article 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. BioMed Central 2012-06-15 /pmc/articles/PMC3443423/ /pubmed/22703188 http://dx.doi.org/10.1186/1471-2164-13-249 Text en Copyright ©1900 Reyes et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Reyes, Alejandro Sandoval, Andrea Cubillos-Ruiz, Andrés Varley, Katherine E Hernández-Neuta, Ivan Samper, Sofía Martín, Carlos García, María Jesús Ritacco, Viviana López, Lucelly Robledo, Jaime Zambrano, María Mercedes Mitra, Robi D Del Portillo, Patricia 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 |
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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443423/ https://www.ncbi.nlm.nih.gov/pubmed/22703188 http://dx.doi.org/10.1186/1471-2164-13-249 |
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