Coll, F. and McNerney, R. and Guerra-Assunção, J.A. and Glynn, J.R. and Perdigão, J. and Viveiros, M. and Portugal, I. and Pain, A. and Martin, Nigel and Clark, T.G. (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 5 , p. 4812. ISSN 2041-1723.
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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.
Metadata
| Item Type: | Article |
|---|---|
| School: | Birkbeck Faculties and Schools > Faculty of Science > School of Computing and Mathematical Sciences |
| Research Centres and Institutes: | Structural Molecular Biology, Institute of (ISMB), Birkbeck Knowledge Lab |
| Depositing User: | Administrator |
| Date Deposited: | 04 Sep 2014 12:50 |
| Last Modified: | 09 Aug 2023 12:35 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/10453 |
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