Discordance between Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Typing and IS6110Restriction Fragment Length Polymorphism Genotyping for Analysis ofMycobacterium tuberculosisBeijing Strains in a Setting of High Incidence of Tuberculosis

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Abstract
IS6110restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology ofMycobacterium tuberculosis. However, due to the complexity of the IS6110RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110RFLP genotyping, using a collection of Beijing genotypeM. tuberculosisstrains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.

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