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J Med Microbiol 56 (2007), 1052-1057; DOI: 10.1099/jmm.0.46990-0
© 2007 Society for General Microbiology
ISSN 1473-5644

Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan

Takayuki Wada1, Shinji Maeda2, Atsushi Hase1 and Kazuo Kobayashi3

1 Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan

2 Molecular Epidemiology and Genetic Identification, Mycobacterium Reference Center, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan

3 Department of Immunology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan

Correspondence
Takayuki Wada
taka-wada{at}city.osaka.lg.jp

Received 6 October 2006
Accepted 16 March 2007

Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter–Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.

Abbreviations: ETR, exact tandem repeat; HGDI, Hunter–Gaston discriminatory index; MIRU, mycobacterial interspersed repetitive unit; QUB, Queen's University Belfast; TB, tuberculosis; VNTR, variable numbers of tandem repeat.

A table of VNTR profiles for the strains is available as supplementary material with the online version of this paper.




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