Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography

Genome Research

Volumn 15, Issue 10, 2005, Pages 1357-1364

  Mokrousov, Igor ^a   Ho, Minh Ly ^c   Otten, Tatiana ^b   Nguyen, Ngoc Lan ^d   Vyshnevskyi, Boris ^b   Hoffner, Sven ^e   Narvskaya, Olga ^a  

^a ST PETERSBURG PASTEUR INSTITUTE   (Russian Federation)

^b ST PETERSBURG RESEARCH INSTITUTE OF PHTHISIOPULMONOLOGY   (Russian Federation)

^c NATIONAL INSTITUTE OF HYGIENE AND EPIDEMIOLOGY   (Viet Nam)

^d Pham Ngoc Thach Hospital   (Viet Nam)

^e SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASIA; BACTERIAL GENOME; BACTERIAL STRAIN; CHINA; CLIMATE; CLUSTER ANALYSIS; CONTROLLED STUDY; DEMOGRAPHY; GENETIC LINE; HUMAN; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGEOGRAPHY; PRIORITY JOURNAL; SOUTH AFRICA; Y CHROMOSOME;

DNA FINGERPRINTING; GENOME, BACTERIAL; GENOTYPE; GEOGRAPHY; HUMANS; MINISATELLITE REPEATS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY;

BACTERIA (MICROORGANISMS); HOMO SAPIENS; MYCOBACTERIUM TUBERCULOSIS;

EID: 25844476096     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.3840605     Document Type: Article

References (51)

1. Avise, J.C., Arnold, J., Ball Jr., R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., and Saunders, J. 1987. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. System 18: 489-522.
2. Baker, L., Brown, T., Maiden, M.C., and Drobniewski, F. 2004. Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg. Infect. Dis. 10: 1568-1577.
3. Banu, S., Gordon, S.V., Palmer, S., Islam, M.R., Ahmed, S., Alam, K.M., Cole, S.T., and Brosch, R. 2004. Genotypic analysis of Mycobacterium tuberculosis in Bangladesh and prevalence of the Beijing strain. J. Clin. Microbiol. 42: 674-682.
4. Beggs, M.L., Eisenach, K.D., and Cave, M.D. 2000. Mapping of IS6110 insertion sites in two epidemic strains of Mycobacterium tuberculosis. J. Clin. Microbiol. 38: 2923-2928.
5. Bettinger, R.L., Barton, L., Elston, R.G., Madsen, D.B., Brantingham, P.J., Oviatt, C.G., Wang, H., and Choi, W. 2005. The transition to agriculture in northwestern China. In Food systems and power structures among intermediate scale societies (eds. I. Kuijt and W.C. Prentiss), University of Arizona Press, Tucson, AZ (in press).
6. Bifani, P.J., Mathema, B., Kurepina, N.E., and Kreiswirth, B.N. 2002. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol. 10: 45-52.
7. Cavalli-Sforza, L.L. 2001. Genes, peoples and languages. Penguin Books. London.
8. Cavalli-Sforza, L.L. and Feldman, M.W. 2003. The application of molecular genetic approaches to the study of human evolution. Nat. Genet. Suppl. 33: 266-275.
9. Christian, D. 1998. A history of Russia, Central Asia and Mongolia. Vol. 1: Inner Eurasia from prehistory to the Mongol empire. Blackwell Publishers, Oxford, UK.
10. Cohen, D.J. 1998. The origin of domesticated cereals and the Pleistocene-Holocene transition in east Asia. Rev. Archaeol. 19: 22-29.
11. Deng, W., Shi, B., He, X., Zhang, Z., Xu, J. Li, B., Yang, J., Ling, L., Dai, C., Qiang, B., et al. 2004. Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence. J. Hum. Genet. 49: 339-348.
12. Falush, D., Wirth, T., Linz, B., Pritchard, J.K., Stephens, M., Kidd, M., Blaser, M.J., Graham, D.Y., Vacher, S., Perez-Perez, G.I., et al. 2003. Traces of human migrations in Helicobacter pylori populations. Science 299: 1582-1585.
13. Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6b. Department of Genome Sciences, University of Washington, Seattle.
14. Foley, R. 1998. The context of human genetic evolution. Genome Res. 8: 339-347.
15. Glynn, J.R., Whiteley, J., Bifani, P.J., Kremer, K., and van Soolingen, D. 2002. Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: A systematic review. Emerg. Infect. Dis. 8: 843-849.
16. Heady, R.B. and Lucas, J.L. 1997. PERMAP: An interactive program for making perceptual maps. Behavior Res. Meth. Instruments Computers 29: 450-455.
17. Hunter, P.R. and Gaston, M.A. 1988. Numerical index of the discriminatory ability of typing systems: An application of Simpson's index of diversity. J. Clin. Microbiol. 26: 2465-2466.
18. Jansen, R., van Embden, J.D.A., Gaastra, W., and Schouls, L.M. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43: 1565-1575.
19. Kamerbeek, J., Schouls, L., Kolk, A., van Agterveld, M., van Soolingen, D., Kuijper, S., Bunschoten, A., Molhuizen, H., Shaw, R., Goyal, M., et al. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35: 907-914.
20. Kremer, K. 2005. "Genetic markers for Mycobacterium tuberculosis: Characterization and spread of the Beijing genotype." Ph.D. thesis. University of Amsterdam, Blaricum, The Netherlands.
21. Kurepina, N.E., Sreevatsan, S., Plikaytis, B.B., Bifani, P.J., Connell, N.D., Donnelly, R.J., van Soolingen, D., Musser, J.M., and Kreiswirth, B.N. 1998. Characterization of the phylogenetic distribution and chromosomal insertion sites of five IS6110 elements in Mycobacterium tuberculosis: Non-random integration in the dnaA-dnaN region. Tuber. Lung Dis. 79: 31-42.
22. Lewis, P.O. and Zaykin, D. 2001. Genetic Data Analysis: Computer program for the analysis of allelic data. Version 1.0 (d16c). http://lewis.eeb.uconn. edu/lewishome/software.html.
23. Lopez, B., Aguilar, D., Orozco, H., Burger, M., Espitia, C., Ritacco, V., Barrera, L., Kremer, K., Hernandez-Pando, R., Huygen, K., et al. 2003. A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes. Clin. Exp. Immunol. 133: 30-37.
24. McNeill, W.H. 1976. Plagues and peoples. Anchor Press. New York.
25. Milan, S.J., Hauge, K.A., Kurepina, N.E., Lofy, K.H., Goldberg, S.V., Narita, M., Nolan, C.M., McElroy, P.D., Kreiswirth, B.N., and Cangelosi, G.A. 2004. Expanded geographical distribution of the N family of Mycobacterium tuberculosis strains within the United States. J. Clin. Microbiol. 42: 1064-1068.
26. Mithen, S. 2004. After the ice: A global human history 20,000-5000 BC. Phoenix, London.
27. Mokrousov, I., Narvskaya, O., Otten, T., Vyazovaya, A., Limeschenko, E., Steklova, L., and Vyshnevskyi, B. 2002. Phylogenetic reconstruction within Mycobacterium tuberculosis Beijing genotype in northwestern Russia. Res. Microbiol. 153: 629-637.
28. Mokrousov, I., Narvskaya, O., Limeschenko, E., Vyazovaya, A., Otten, T., and Vyshnevskyi, B. 2004. Analysis of the allelic diversity of the mycobacterial interspersed repetitive units in Mycobacterium tuberculosis strains of the Beijing family: Practical implications and evolutionary considerations. J. Clin. Microbiol. 42: 2438-2444.
29. Mulligan, C.J., Hunley, K., Cole, S., and Long, J.C. Population genetics, history, and health patterns in Native Americans. Annu. Rev. Genomics Hum. Genet. 5: 295-315.
30. Pavesi, A. 2004. Detecting traces of prehistoric human migrations by geographic synthetic maps of polyomavirus JC. J. Mol. Evol. 58: 304-313.
31. Plikaytis, B.B., Marden, J.L., Crawford, J.T., Woodley, C.L., Butler, W.R., and Shinnick, T.M. 1994. Multiplex PCR assay specific for the multi-drug-resistant strain W of Mycobacterium tuberculosis. J. Clin. Microbiol. 32: 1542-1546.
32. Rad, M.E., Bifani, P., Martin, C., Kremer, K., Samper, S., Rauzier, J., Kreiswirth, B., Blazquez, J., Jouan, M., van Soolingen, D., et al. 2003. Mutations in putative mutator genes of Mycobacterium tuberculosis strains of the W-Beijing family. Emerg. Infect. Dis. 9: 838-845.
33. Shelach, G. 2000. The earliest Neolithic cultures of northeast Asia: Recent discoveries and new perspectives on the beginning of agriculture. J. World Prehistory 14: 363-413.
34. Sola, C., Filliol, I., Legrand, E., Mokrousov, I., and Rastogi, N. 2001. Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS1081, IS6110, VNTR, and DR-based spoligotyping suggests the existence of two new phylogeographical clades. J. Mol. Evol. 53: 680-689.
35. Su, B., Xiao, C., Deka, R., Seielstad, M.T., Kangwanpong, D., Xiao, J., Lu, D., Underhill, P., Cavalli-Sforza, L., Chakraborty, R., et al. 2000. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107: 582-590.
36. Sun, Y.J., Bellamy, R., Lee, A.S., Ng, S.T., Ravindran, S., Wong, S.Y., Locht, C., Supply, P., and Paton, N.I. 2004. Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore. J. Clin. Microbiol. 42: 1986-1993.
37. Supply, P., Mazars, E., Lesjean, S., Vincent, V., Gicquel, B., and Locht, C. 2000. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol. Microbiol. 36: 762-771.
38. Supply, P., Lesjean, S., Savine, E., Kremer, K., van Soolingen, D., and Locht, C. 2001. Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J. Clin. Microbiol. 39: 3563-3571.
39. Supply, P., Warren, R.M., Banuls, A.-L., Lesjean, S., van der Spuy, G.D., Lewis, L.A., Tibayrenc, M., Van Helden, P.D., and Locht, C. 2003. Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area. Mol. Microbiol. 47: 529-538.
40. Thomas, B.E. 2000. Tuberculosis in women. In Status of tuberculosis in India (eds. R. Nayak et al.), pp. 25-32. Society for Innovation and Development, Indian Institute of Science, Bangalore, India.
41. Underhill, P.A., Passarino, G., Lin, A.A., Shen, P., Mirazon Lahr, M., Foley, R.A., Oefner, P.J., and Cavalli-Sforza, L.L. 2001. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann. Hum. Genet. 65: 43-62.
42. Uplekar, M.W., Rangan, S., Weiss, M.G., Ogden, J., Borgdorff, M.W., and Hudelson, P. 2001. Attention to gender issues in tuberculosis control. Int. J. Tuberc. Lung Dis. 5: 220-224.
43. van Embden, J.D.A., Cave, M.D., Crawford, J.T., Dale, J.W., Eisenach, K.D., Gicquel, B., Hermans, P., Martin, C., McAdam, R., Shinnik, T.M., et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: Recommendations for a standardized methodology. J. Clin. Microbiol. 31: 406-409.
44. van Embden, J.D.A., van Gorkom, T., Kremer, K., Jansen, T., van der Zeijst, B.A.M., and Schouls, L.M. 2000. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J. Bacteriol. 182: 2393-2401.
45. van Helden, P.D., Warren, R.M., Victor, T.C., van der Spuy, G., Richardson, M., and Hoal-van Helden, E. 2002. Strain families of Mycobacterium tuberculosis. Trends Microbiol. 10: 167-168.
46. van Soolingen, D., Qian, L., de Haas, P.E.W., Douglas, J.T., Traore, H., Portaels, F., Quing, H.Z., Enkhasaikan, D., Nymadawa, P., and van Embden, J.D. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia. J. Clin. Microbiol. 33: 3234-3238.
47. Weir, B. 1990. Genetic data analysis: Methods for discrete population data. Sinauer Associates, Sunderland, MA.
48. Y Chromosome Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12: 339-348.
49. Zhang, M., Cong, J., Yang, Z., Samten, B., and Barnes, P.F. 1999. Enhanced capacity of a widespread strain of Mycobacterium tuberculosis to grow in human macrophages. J. Infect. Dis. 179: 1213-1217.
50. http://www.nationmaster.com/encyclopedia/South-Africa; Encyclopedia: South Africa
51. http://61.1911encyclopedia.org/S/SO/SOUTH_AFRICA.htm; South Africa