A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
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Guerra-Assunção, José Afonso
Glynn, Judith R.
Clark, Taane G.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Pathogen Genomics Laboratory
Online Publication Date2014-09-01
Print Publication Date2014-12
Permanent link to this recordhttp://hdl.handle.net/10754/334566
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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.
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.
PubMed Central IDPMC4166679
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