Author(s): Coll, Francesc ; McNerney, Ruth ; Guerra-Assunção, José Afonso ; Glynn, Judith R. ; Perdigão, João ; Viveiros, Miguel ; Portugal, Isabel ; Pain, Arnab ; Martin, Nigel ; Clark, Taane G.
Date: 2014
Persistent ID: http://hdl.handle.net/10362/116795
Origin: Repositório Institucional da UNL
Subject(s): Biochemistry, Genetics and Molecular Biology(all); Chemistry(all); Physics and Astronomy(all); SDG 3 - Good Health and Well-being
PMID:25176035 WOS:000342929000002
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.
