A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Handle URI:
http://hdl.handle.net/10754/334566
Title:
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
Authors:
Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso; Glynn, Judith R.; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Pain, Arnab ( 0000-0002-1755-2819 ) ; Martin, Nigel; Clark, Taane G.
Abstract:
Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)
Citation:
Coll F, McNerney R, Guerra-Assunção JA, Glynn JR, Perdigão J, et al. (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 5: 4812. doi:10.1038/ncomms5812.
Publisher:
Nature Pub. Group
Journal:
Nature Communications
Issue Date:
1-Sep-2014
DOI:
10.1038/ncomms5812
PubMed ID:
25176035
PubMed Central ID:
PMC4166679
Type:
Article
ISSN:
20411723
Appears in Collections:
Articles; Bioscience Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorColl, Francescen
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorGuerra-Assunção, José Afonsoen
dc.contributor.authorGlynn, Judith R.en
dc.contributor.authorPerdigão, Joãoen
dc.contributor.authorViveiros, Miguelen
dc.contributor.authorPortugal, Isabelen
dc.contributor.authorPain, Arnaben
dc.contributor.authorMartin, Nigelen
dc.contributor.authorClark, Taane G.en
dc.date.accessioned2014-11-11T14:29:53Z-
dc.date.available2014-11-11T14:29:53Z-
dc.date.issued2014-09-01en
dc.identifier.citationColl F, McNerney R, Guerra-Assunção JA, Glynn JR, Perdigão J, et al. (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 5: 4812. doi:10.1038/ncomms5812.en
dc.identifier.issn20411723en
dc.identifier.pmid25176035en
dc.identifier.doi10.1038/ncomms5812en
dc.identifier.urihttp://hdl.handle.net/10754/334566en
dc.description.abstractStrain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.en
dc.language.isoenen
dc.publisherNature Pub. Groupen
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleA robust SNP barcode for typing Mycobacterium tuberculosis complex strainsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNature Communicationsen
dc.identifier.pmcidPMC4166679en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

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