Abstract
BackgroundIn comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard in typing of Mycobacterium tuberculosis. However, some reports indicated that VNTR typing may be less suitable for Beijing genotype isolates. We therefore compared the performance of internationally standardized RFLP and 24 loci VNTR typing to discriminate among 100 Beijing genotype isolates from the Southern Vietnam.MethodsHundred Beijing genotype strains defined by spoligotyping were randomly selected and typed by RFLP and VNTR typing. The discriminatory power of VNTR and RFLP typing was compared using the Bionumerics software.ResultsAmong 95 Beijing strains available for analysis, 14 clusters were identified comprising 34 strains and 61 unique profiles in 24 loci VNTR typing ((Hunter Gaston Discrimination Index (HGDI = 0.994)). 13 clusters containing 31 strains and 64 unique patterns in RFLP typing (HGDI = 0.994) were found. Nine RFLP clusters were subdivided by VNTR typing and 12 VNTR clusters were split by RFLP. Five isolates (5%) revealing double alleles or no signal in two or more loci in VNTR typing could not be analyzed.ConclusionsOverall, 24 loci VNTR typing and RFLP typing had similar high-level of discrimination among 95 Beijing strains from Southern Vietnam. However, loci VNTR 154, VNTR 2461 and VNTR 3171 had hardly added any value to the level of discrimination.
Highlights
In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format
As in Vietnam about 40% of the M. tuberculosis isolates are of this genotype, we in this study compared the performance of RFLP and internationally standardized 24 loci VNTR typing to discriminate among one hundred Beijing genotype isolates from the South of Vietnam
In recent years VNTR typing has increasingly been explored in the molecular epidemiology worldwide and with the proposal on international standardization of this technique in 2006 it has become the new gold standard [2]
Summary
In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. This technique has gained recognition as the new international gold standard in typing of Mycobacterium tuberculosis. We compared the performance of internationally standardized RFLP and 24 loci VNTR typing to discriminate among 100 Beijing genotype isolates from the Southern Vietnam. The IS6110 restriction fragment length polymorphism (RFLP) typing was previously considered the gold standard in the molecular epidemiology of tuberculosis [1] This typing technique generally revealed a high level of discrimination among Mycobacterium tuberculosis isolates, it was considered complicated, technically. Vietnam about 40% of the M. tuberculosis isolates are of this genotype, we in this study compared the performance of RFLP and internationally standardized 24 loci VNTR typing to discriminate among one hundred Beijing genotype isolates from the South of Vietnam
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