IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
Entity
UAM. Departamento de Medicina Preventiva y Salud Pública y MicrobiologíaPublisher
BioMed CentralDate
2012-06-15Citation
10.1186/1471-2164-13-249
BMC Genomics 13 (2012): 249
ISSN
1471-2164DOI
10.1186/1471-2164-13-249Funded by
This work was supported by Colciencias project No. 657040820410, grant No. 431–2004 for the Colombian Center for Excellence in Tuberculosis Research, CCITB, the StopLATENT-TB network (Collaborative Project) supported by the EC under the Health Cooperation Work Programme of the 7th Framework Programme (G.A. no. 200999) (http://cordis.europa.eu/fp7/dc/index.cfm), the Children’s Discovery Institute grant MC-II-2006-1, and the NIH Epigenetics Roadmap grant (1R01DA025744-01 and 3R01DA025744-02 S1). Part of this work was developed in the context of the Network of multidrug resistant tuberculosis in Latin America supported by Latin-American Science & Technology Development Programme (CYTED). Reyes A. is the recipient of an International Fulbright Science and Technology Program award.Project
info:eu-repo/grantAgreement/EC/FP7/200999Editor's Version
http://dx.doi.org/10.1186/1471-2164-13-249Subjects
IS6110; Mycobacterium tuberculosis; IS-seq; MedicinaRights
Reyes et al.Abstract
Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium
tuberculosis, the etiological agent of human tuberculosis. Although IS6110 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
Files in this item
Google Scholar:Reyes, Alejandro C.
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Sandoval, Andrea
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Cubillos-Ruiz, Andrés
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Varley, Katherine Elena
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Hernández-Neuta, Iván
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Samper, Sofía
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Martín, Carlos G.
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García García, María Jesús
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Ritacco, Viviana
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López, Lucelly
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Robledo, Jaime A.
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Zambrano, María Mercedes
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Mitra, Robi David
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Del Portillo, Patricia
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