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Volume 7, Number 3—June 2001
Synopsis

Spoligotype Database of Mycobacterium tuberculosis: Biogeographic Distribution of Shared Types and Epidemiologic and Phylogenetic Perspectives

Christophe Sola*Comments to Author , Ingrid Filliol*, Maria Cristina Gutierrez†, Igor Mokrousov*, Véronique Vincent†, and Nalin Rastogi*Comments to Author 
Author affiliations: *Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe; †Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France

Main Article

Figure A1

Description of the 259 shared types of Mycobacterium tuberculosis with their nomenclatures (for data source, see Table 1). First column (type): number attribution for each spoligotype in our database. Second column (HN): numbers for some patterns described recently in Houston, Texas (12). Third column (spoligotype description): patterns obtained (8). Fourth column (geographic distribution): origin of isolates according to the original publication as ISO-code 3166. Fifth column (total): total num

Figure A1. . Description of the 259 shared types of Mycobacterium tuberculosis with their nomenclatures (for data source, see Table 1). First column (type): number attribution for each spoligotype in our database. Second column (HN): numbers for some patterns described recently in Houston, Texas (12). Third column (spoligotype description): patterns obtained (8). Fourth column (geographic distribution): origin of isolates according to the original publication as ISO-code 3166. Fifth column (total): total number of isolates for each of the shared types. Sixth column (carib): number of shared-type isolates found in the Caribbean by our team. Seventh column (other): number of shared-type isolates found elsewhere than the Caribbean. Note that number of isolates in fifth column for types 69 and 104 to 106 was not available (mentioned as 0). The ISO-codes 3166 are as follows: ARG, Argentina; AUT, Austria; BRB, Barbados; BOL, Bolivia; BRA, Brazil; BDI, Burundi; CAN, Canada; CHL, Chile; CHN, China; COM, Comoros; CIV, Côte d'Ivoire; CUB, Cuba; CZE, Czech Republic; DNK, Denmark; ECU, Ecuador; ETH, Ethiopia; FXX, metropolitan France; GUF, French Guiana; PYF, French Polynesia; GRL, Greenland; GLP, Guadeloupe; GNB, Guinea-Bissau; HND, Honduras; IND, India; ITA, Italy; KOR, Republic of Korea; MTQ, Martinique; MNG, Mongolia; NLD, Netherlands; PER, Peru; PHL, Philippines; ROM, Romania; RUS, Russian Federation; RWA, Rwanda; SAU, Saudi Arabia; SEN, Senegal; SOM, Somalia; ESP, Spain; LKA, Sri Lanka; SUR, Surinam ; TZA, Tanzania; THA, Thaïland; TUN, Tunisia; UGA, Uganda; GBR, United Kingdom; VNM, Vietnam; ZWE, Zimbabwe. Investigators wishing to obtain further information about an upgraded full version of this database may contact the author at csola@pasteur.gp

Main Article

References
  1. World Health Organization. Global tuberculosis control. WHO report 1999. Geneva: The Organization; 1999.
  2. Slutkin  G. Global AIDS 1981-1999: the response. Int J Tuberc Lung Dis. 2000;4:S24–33.PubMedGoogle Scholar
  3. Snider  DE, Castro  KG. The global threat of drug resistant tuberculosis. N Engl J Med. 1998;338:1689–90. DOIPubMedGoogle Scholar
  4. Long  R, Nobert  E, Chomyc  S, van Embden  J, McNamee  C, Duran  RR, Transcontinental spread of multidrug-resistant Mycobacterium bovis. Am J Respir Crit Care Med. 1999;159:2014–7.PubMedGoogle Scholar
  5. Bifani  PJ, Mathema  B, Liu  Z, Moghazeh  SL, Shopsin  B, Tempalski  B, Identification of a W variant outbreak of Mycobacterium tuberculosis via population-based molecular epidemiology. JAMA. 1999;282:2321–7. DOIPubMedGoogle Scholar
  6. Sola  C, Devallois  A, Horgen  L, Maïsetti  J, Filliol  I, Legrand  E, Tuberculosis in the Carribean: using spacer oligonucleotide typing to understand strain origin and transmission. Emerg Infect Dis. 1999;5:404–14. DOIPubMedGoogle Scholar
  7. Kamerbeek  J, Schouls  L, Kolk  A, van Agterveld  M, van Soolingen  D, Kuijper  S, Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35:907–14.PubMedGoogle Scholar
  8. Frothingham  R, Meeker-O'Connell  WA. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology. 1998;144:1189–96. DOIPubMedGoogle Scholar
  9. Grimont  PAD. TAXOTRON instruction manual. Paris: Taxolab, Institut Pasteur; 1996.
  10. Jaccard  P. Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat. 1908;44:223–70.
  11. Saitou  N, Nei  M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
  12. Soini  H, Pan  X, Amin  A, Graviss  EA, Siddiqui  A, Musser  JM. Characterization of Mycobacterium tuberculosis isolates from patients in Houston, Texas, by spoligotyping. J Clin Microbiol. 2000;38:669–76.PubMedGoogle Scholar
  13. Groenen  PMA, Bunschoten  AE, van Soolingen  D, van Embden  JDA. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol. 1993;10:1057–65. DOIPubMedGoogle Scholar
  14. Hancock  JM. The contribution of slippage-like processes to genome evolution. J Mol Evol. 1995;41:1038–47. DOIPubMedGoogle Scholar
  15. Kremer  K, van Soolingen  D, Frothingham  R, Haas  WH, Hermans  PWM, Martin  C, Comparison of methods based on different molecular epidemiologial markers for typing of Mycobacterium tuberculosis strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol. 1999;37:2607–18.PubMedGoogle Scholar
  16. Fang  Z, Doig  C, Kenna  DT, Smittipat  N, Palittapongarnpim  P, Watt  B, IS6110-mediated deletions of wild-type chromosomes of Mycobacterium tuberculosis. J Bacteriol. 1999;181:1014–20.PubMedGoogle Scholar
  17. Fang  Z, Morrison  N, Watt  B, Doig  C, Forbes  KJ. IS6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains. J Bacteriol. 1998;180:2102–9.PubMedGoogle Scholar
  18. Filliol  I, Sola  C, Rastogi  N. Detection of a previously unamplified spacer within the DR locus of Mycobacterium tuberculosis: Epidemiological implications. J Clin Microbiol. 2000;38:1231–4.PubMedGoogle Scholar
  19. van Embden  JDA, van Gorkom  T, Kremer  K, Jansen  R, Van der Zeijst  BAM, Schouls  LM. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J Bacteriol. 2000;182:2393–01. DOIPubMedGoogle Scholar
  20. Buikstra  JE. Paleoepidemiology of tuberculosis in the Americas. In: Palfi G, Dutour O, Deak J, Hutas I, editors: Tuberculosis: past and present. Szeged, Hungary: Golden Book Publisher Ltd.; 1999. p. 479-94.
  21. Ortner  DJ. Paleopathology: implications for the history and evolution of tuberculosis. In: Palfi G, Dutour O, Deak J, Hutas I, editors. Tuberculosis: past and present. Szeged, Hungary: Golden Book Publisher Ltd; 1999. p. 255-61.
  22. Kurepina  NE, Sreevatsan  S, Plikaytis  BB, Bifani  PB, Connell  ND, Donneelly  RJ, 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. 1998;79:31–42. DOIPubMedGoogle Scholar
  23. Nei  M. Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet. 1996;30:371–403. DOIPubMedGoogle Scholar
  24. Saitou  N, Nei  M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
  25. Källenius  G, Koivula  T, Ghebremichael  S, Hoffner  SE, Norberg  R, Svensson  E, Evolution and clonal traits of Mycobacterium tuberculosis in Guinea-Bissau. J Clin Microbiol. 1999;37:3872–8.PubMedGoogle Scholar
  26. Sreevatsan  S, Pan  X, Stockbauer  K, Connell  N, Kreiswirth  B, Whittam  T, Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A. 1997;97:9869–74. DOIPubMedGoogle Scholar
  27. Castets  M, Boisvert  H, Grumbach  F, Brunel  M, Rist  N. Les bacilles tuberculeux de type africain: note préliminaire. Rev Tuberc Pneumol (Paris). 1968;32:179–84.PubMedGoogle Scholar
  28. Frothingham  R, Strickland  PL, Bretzel  G, Ramaswamy  S, Musser  JM, Williams  DL. Phenotypic and genotypic characterization of Mycobacterium africanum isolates from West Africa. J Clin Microbiol. 1999;37:1921–6.PubMedGoogle Scholar
  29. Warren  GM, Richardson  M, Sampson  S, Bourn  W, van der Spuy  G, Hide  W, RFLP analysis of M. tuberculosis demonstrates strain-dependent evolution. Int J Tuberc Lung Dis. 1999;3(Suppl. I):S38.
  30. Tanaka  MM, Small  PM, Salamon  H, Feldman  MW. The dynamics of repeated elements: applications to the epidemiology of tuberculosis. Proc Natl Acad Sci U S A. 2000;97:3532–7. DOIPubMedGoogle Scholar
  31. Bauer  J, Andersen  AB, Kremer  K, Miörner  H. Usefulness of spoligotyping to discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultures in Denmark. J Clin Microbiol. 1999;37:2602–6.PubMedGoogle Scholar
  32. Bonora  S, Gutierrez  MC, Perri  GD, Brunello  F, Allegranzi  B, Ligozzi  M, Comparative evaluation of Ligation-mediated PCR and spoligotyping as screening methods for genotyping of Mycobacterium tuberculosis strains. J Clin Microbiol. 1999;37:3118–23.PubMedGoogle Scholar
  33. Diaz  R, Kremer  K, de Haas  PEW, Gomez  RI, Marrero  A, Valdivia  JA, Molecular epidemiology of tuberculosis in Cuba outside of Havana, July 1994-June 1995: utility of spoligotyping versus IS6110 restriction fragment length polymorphism. Int J Tuberc Lung Dis. 1998;2:743–50.PubMedGoogle Scholar
  34. Douglas  JT, Qian  L, Montoya  JC, Sreevatsan  S, Musser  J, van Soolingen  D, Detection of a novel family of tuberculosis isolates in the Philippines. 97th general meeting of the American Society for Microbiology. Washington: ASM Press; 1997. p.572.
  35. Escalante  P, Ramaswamy  S, Sanabria  H, Soini  H, Pan  X, Valiente-Castillo  O, Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru. Tuber Lung Dis. 1998;79:111–8. DOIPubMedGoogle Scholar
  36. Goguet dela Salmonière  YO, Li  HM, Torrea  G, Bunschoten  A, van Embden  JDA, Gicquel  B. Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis. J Clin Microbiol. 1997;35:2210–4.PubMedGoogle Scholar
  37. Goyal  M, Saunders  NA, van Embden  JDA, Young  DB, Shaw  RJ. Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism. J Clin Microbiol. 1997;35:647–51.PubMedGoogle Scholar
  38. Heyderman  RS, Goyal  M, Roberts  P, Ushewokunze  S, Zishou  S, Marshall  BG, Pulmonary tuberculosis in Harare, Zimbabwe: analysis by spoligotyping. Thorax. 1998;53:346–50. DOIPubMedGoogle Scholar
  39. Niang  MN, Goguet de la Salmonière  YO, Samb  A, Hane  AA, Cisse  MF, Gicquel  B, Characterization of M. tuberculosis strains from West-African patients by spoligotyping. Microbes Infect. 1999;1:1189–92. DOIPubMedGoogle Scholar
  40. Popa  MI, Goguet de la Salmonière  YO, Teodor  I, Popa  L, Stefan  M, Banica  D, Genomic profile of Romanian M. tuberculosis strains appreciated by spoligotyping. Roum Arch Microbiol Immunol. 1997;56:63–75.PubMedGoogle Scholar
  41. de C. Ramos M. Soini H, Roscanni GC, Jaques M, Villares MC, Musser JM. Extensive cross-contamination of specimens with Mycobacterium tuberculosis in a reference laboratory. J Clin Microbiol. 1999;37:916–9.PubMedGoogle Scholar
  42. Taylor  GM, Goyal  M, Legge  AJ, Shaw  RJ, Young  D. Genotypic analysis of Mycobacterium tuberculosis from medieval human remains. Microbiology. 1999;145:899–904. DOIPubMedGoogle Scholar
  43. van der Zanden  AG, Hoentgen  AH, Heilmann  FG, Weltvreden  EF, Schouls  LM, van Embden  JD. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded tissues and in stained microscopic preparations. Mol Pathol. 1998;51:209–14. DOIPubMedGoogle Scholar
  44. van Soolingen  D, Qian  L, de Haas  PEW, Douglas  JT, Traore  H, Portaels  F, Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J Clin Microbiol. 1995;33:3234–8.PubMedGoogle Scholar

Main Article

1For this purpose, the independent sampling sizes for Europe and the USA were taken as n1 and n2, the number of individuals within a given shared-type "x" was k1 and k2, and in this case, the representativeness of the two samples was p1=k1/n1 and P2=k2/n2, respectively. To assess if the divergence observed between p1 and p2 was due to sampling bias or the existence of two distinct populations, the percentage of individuals (p0) harboring shared-type "x" in the population studied was estimated by the equation p0= k1+k2/n1+n2=n1p1+n2p2/n1+n2. The distribution of the percentage of shared-type "x" in the sample sizes n1 and n2 follows a normal distribution with a mean p0 and a standard deviation of formula imageand formula imagerespectively, and the difference d=p1-p2 follows a normal distribution of mean p0-p0=0 and of variance σd2=σp12+σp22 = p0q0/n1+p0q0/n2 or σd2=p0q0 (1/n1+1/n2). The two samples being independent, the two variances were additive; the standard deviation σd= was calculated, and the homogeneity of the samples tested was assessed using the quotient d/σd=p1-p2/formula image. If the absolute value of the quotient d/σd<2, the two samples were considered to belong to a same population (CI 95%) and the variation observed in the distribution of isolates for given shared types could be due to a sampling bias. Inversely, if d/σd>2, then the differences observed in the distribution of isolates for given shared types were statistically significant and not due to potential sample bias.

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