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Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing

Mai NT Huyen1*, Kristin Kremer23, Nguyen TN Lan1, Tran N Buu1, Frank GJ Cobelens4, Edine W Tiemersma45, Petra de Haas3 and Dick van Soolingen36

Author affiliations

1 Phạm Ngọc Thạch hospital, 120 Hung Vuong, district 5, Ho Chi Minh City, Viet Nam

2 World Health Organization, Regional Office for Europe, Copenhagen, Denmark

3 Tuberculosis Reference Laboratory, RIVM, PO Box 1, Bilthoven, 3720 BA, The Netherlands

4 Centre for Infection and Immunity Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands

5 KNCV Tuberculosis Foundation, PO Box 146, The Hague, 2501 CC, The Netherlands

6 Departments of Pulmonary Diseases and Medical Microbiology, Radboud University, PO box 9101, Nijmegen, 6500 HB, The Netherlands

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Citation and License

BMC Infectious Diseases 2013, 13:63  doi:10.1186/1471-2334-13-63

Published: 2 February 2013



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. 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.


Hundred 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.


Among 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.


Overall, 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.