A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.


Coll, F; McNerney, R; Guerra-Assunção, JA; Glynn, JR; Perdigão, J; Viveiros, M; Portugal, I; Pain, A; Martin, N; Clark, TG; (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun, 5. p. 4812. ISSN 2041-1723 DOI: 10.1038/ncomms5812

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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.

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Clinical Research
Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Faculty of Epidemiology and Population Health > Dept of Non-Communicable Disease Epidemiology
Research Centre: MEIRU
TB Centre
PubMed ID: 25176035
Web of Science ID: 342929000002
URI: http://researchonline.lshtm.ac.uk/id/eprint/1911930

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