Concordance of variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses of Mycobacterium tuberculosis strains |
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| Authors: | Eiji Yokoyama Yushi Hachisu Ruiko Hashimoto Kazunori Kishida |
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| Institution: | 1. Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, Chiba, 260-8715, Japan;2. Laboratory of Animal Health, Department of Animal Science, Tokyo University of Agriculture, 1737, Funako, Atsugi, Kanagawa, 243-0034, Japan;3. Division of Pathology and Bacteriology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39, Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan;4. Genome Research Center, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya, Tokyo, 256-0054, Japan;5. Department of Microbiology, Yamanashi Institute of Public Health and Environments, 1-7-31, Fujimi, Kofu, Yamanashi, 400-0027, Japan;1. Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile;2. GAIA Antártica – Universidad de Magallanes, Bulnes 01890, Punta Arenas, XII Región de Magallanes y de la Antártica Chilena, Chile;3. Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile;1. Northern State Medical University, Archangelsk, Russia;2. Regional Clinical Antituberculosis Dispensary, Archangelsk, Russia;3. Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden;4. Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Göteborg, Sweden;5. Department of Medicine, Division of Respiratory Medicine, Karolinska University Hospital, Stockholm, Sweden;1. Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation;2. Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany;3. St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation;4. German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany;1. Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia;2. WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes Cedex, Guadeloupe, France;3. Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan;4. The Stephan Angeloff Institute of Microbiology BAS, Sofia, Bulgaria;1. Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan;2. Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Japan;3. Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Japan;4. Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Japan |
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| Abstract: | Variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses were compared to determine whether VNTR analysis was effective for population genetic analysis of Mycobacterium tuberculosis strains. A total of 682 strains, 510 Beijing genotype and 172 non-Beijing genotype strains, were studied.The number of repeats was investigated for 24 VNTR loci: the 15 loci of “optimized miru”, the 8 loci of “Beijing option”, and 1 locus for “JATA12”. Six loci (miru31, Mtub4, QUB4156c, QUB3232, VNTR3820, and VNTR4120) showed significantly different median numbers of repeats in strains belonging to different lineages defined by LSP (P < 0.01, Mann–Whitney U test). When a minimum-spanning tree (MST) was reconstructed using these 6 loci, most strains clustered in the expected branches in the MST branches. However, topology of the MST was not congruent with the evolutional hypothesis of M. tuberculosis, indicating that MST analysis using VNTR data should not use for phylogeny of the organism.When the standardized index of association (sIA) was calculated using data for the 6 VNTR loci, the value of sIA was significantly different from zero (Monte Carlo simulation with 10,000 resamplings) in every lineage, indicating the linkage disequilibrium in different lineage strains of M. tuberculosis. These results were consistent with the hypothesis that clonal evolution of lineages of the organism has occurred.Therefore, the 6 loci identified in this study would be effective for M. tuberculosis population genetic analysis due to their significantly different median numbers of repeat and linkage disequilibrium though VNTR data was not effective for phylogeny of the organism. |
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