A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
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Type
ArticleAuthors
Coll, Francesc
McNerney, Ruth

Guerra-Assunção, José Afonso
Glynn, Judith R.

Perdigão, João

Viveiros, Miguel

Portugal, Isabel
Pain, Arnab

Martin, Nigel
Clark, Taane G.

KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Computational Bioscience Research Center (CBRC)
Pathogen Genomics Laboratory
Date
2014-09-01Online Publication Date
2014-09-01Print Publication Date
2014-12Permanent link to this record
http://hdl.handle.net/10754/334566
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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.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
Springer NatureJournal
Nature CommunicationsPubMed ID
25176035PubMed Central ID
PMC4166679ae974a485f413a2113503eed53cd6c53
10.1038/ncomms5812
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