Optimizing and accelerating the assignation of lineages in Mycobacterium tuberculosis using novel alternative single-tube assays

PloS One
María CarcelénD García-de-Viedma

Abstract

The assignation of lineages in Mycobacterium tuberculosis (MTB) provides valuable information for evolutionary and phylogeographic studies and makes for more accurate knowledge of the distribution of this pathogen worldwide. Differences in virulence have also been found for certain lineages. MTB isolates were initially assigned to lineages based on data obtained from genotyping techniques, such as spoligotyping or MIRU-VNTR analysis, some of which are more suitable for molecular epidemiology studies. However, since these methods are subject to a certain degree of homoplasy, other criteria have been chosen to assign lineages. These are based on targeting robust and specific SNPs for each lineage. Here, we propose two newly designed multiplex targeting methods-both of which are single-tube tests-to optimize the assignation of the six main lineages in MTB. The first method is based on ASO-PCR and offers an inexpensive and easy-to-implement assay for laboratories with limited resources. The other, which is based on SNaPshot, enables more refined standardized assignation of lineages for laboratories with better resources. Both methods performed well when assigning lineages from cultured isolates from a control panel, a test panel, a...Continue Reading

References

Oct 24, 2001·American Journal of Respiratory and Critical Care Medicine·J A CamineroC Martin
May 1, 1963·The American Review of Respiratory Disease·G P KUBICAG MIDDLEBROOK
Apr 24, 2007·The Lancet Infectious Diseases·Sebastien Gagneux, Peter M Small
Mar 1, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Christophe DemayNalin Rastogi
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Sep 6, 2014·Cold Spring Harbor Perspectives in Medicine·Stefan Niemann, Philip Supply
Dec 3, 2014·Seminars in Immunology·Mireia Coscolla, Sebastien Gagneux

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Citations

Jan 31, 2019·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Estefanía AbascalDarío García-de-Viedma

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Methods Mentioned

BETA
genotyping
PCR
electrophoresis

Software Mentioned

Geospiza
ASO
PCR
TBminer
FinchTV
SNaPshot

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