A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Francesc Coll, Ruth McNerney, José Afonso Guerra-Assunção, Judith R. Glynn, João Perdigão, Miguel Viveiros, Isabel Portugal, Arnab Pain, Nigel Martin, Taane G. Clark
<span title="2014-09-01">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
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 B92k SNP across a global collection of
more &raquo; ... 601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the B7k 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.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms5812">doi:10.1038/ncomms5812</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25176035">pmid:25176035</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4166679/">pmcid:PMC4166679</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m4eqgignjrbv7ngv7c4gmwwora">fatcat:m4eqgignjrbv7ngv7c4gmwwora</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171116040918/https://core.ac.uk/download/pdf/20665066.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e9/54/e95457ed28d08ab0e2d3e63a0e861fc8a40a5fa9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms5812"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166679" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>