Discordance between mycobacterial interspersed repetitive-unit-variable- number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis

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dc.contributor.authorHanekom M.
dc.contributor.authorVan Der Spuy G.D.
dc.contributor.authorGey Van Pittius N.C.
dc.contributor.authorMcEvoy C.R.E.
dc.contributor.authorHoek K.G.P.
dc.contributor.authorNdabambi S.L.
dc.contributor.authorJordaan A.M.
dc.contributor.authorVictor T.C.
dc.contributor.authorVan Helden P.D.
dc.contributor.authorWarren R.M.
dc.date.accessioned2011-05-15T15:56:54Z
dc.date.available2011-05-15T15:56:54Z
dc.date.issued2008
dc.description.abstractIS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP 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 IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains 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 IS6110 RFLP 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 IS6110 RFLP 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. Copyright © 2008, American Society for Microbiology. All Rights Reserved.
dc.description.versionArticle
dc.identifier.citationJournal of Clinical Microbiology
dc.identifier.citation46
dc.identifier.citation10
dc.identifier.issn951137
dc.identifier.other10.1128/JCM.00770-08
dc.identifier.urihttp://hdl.handle.net/10019.1/10107
dc.subjectethambutol
dc.subjectisoniazid
dc.subjectrifampicin
dc.subjectstreptomycin
dc.subjectantibiotic resistance
dc.subjectarticle
dc.subjectChina
dc.subjectcontrolled study
dc.subjectconvergent evolution
dc.subjectgene locus
dc.subjectgenetic distance
dc.subjectgenetic variability
dc.subjectgenotype
dc.subjectinterspersed repeat
dc.subjectmorbidity
dc.subjectMycobacterium tuberculosis
dc.subjectnonhuman
dc.subjectphylogenetic tree
dc.subjectpriority journal
dc.subjectrestriction fragment length polymorphism
dc.subjectsensitivity and specificity
dc.subjecttandem repeat
dc.subjecttuberculosis
dc.subjectBacterial Typing Techniques
dc.subjectCluster Analysis
dc.subjectDNA Fingerprinting
dc.subjectDNA Transposable Elements
dc.subjectDNA, Bacterial
dc.subjectEpidemiology, Molecular
dc.subjectEvolution, Molecular
dc.subjectGenotype
dc.subjectHumans
dc.subjectInterspersed Repetitive Sequences
dc.subjectMycobacterium tuberculosis
dc.subjectPolymorphism, Restriction Fragment Length
dc.subjectSensitivity and Specificity
dc.subjectTuberculosis
dc.subjectMycobacterium tuberculosis
dc.titleDiscordance between mycobacterial interspersed repetitive-unit-variable- number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis
dc.typeArticle
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