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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
Nature Communications, Volume 5, Article 4812, Year 2014
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Description
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.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC4166679/bin/ncomms5812-s1.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC4166679/bin/ncomms5812-s2.xlsx
Authors & Co-Authors
Coll, Francesc
Unknown Affiliation
McNerney, R.
Unknown Affiliation
Guerra-Assunção, José Afonso
Unknown Affiliation
Glynn, Judith R.
Unknown Affiliation
Perdigão, João
Unknown Affiliation
Viveiros, Miguel
Unknown Affiliation
Portugal, Isabel
Unknown Affiliation
Pain, Arnab P.
Unknown Affiliation
Martin, Nigel
Unknown Affiliation
Clark, Taane Gregory
Unknown Affiliation
Statistics
Citations: 506
Authors: 10
Affiliations: 6
Identifiers
Doi:
10.1038/ncomms5812
e-ISSN:
20411723
Research Areas
Genetics And Genomics