Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria

Journal of Bacteriology

Volumn 182, Issue 9, 2000, Pages 2393-2401

  Van Embden, J D A ^a   Van Gorkom, T ^a   Kremer, K ^a   Jansen, R ^b   Van Der Zeijst, B A M ^b   Schouls, L M ^a  

^a NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; GENE DELETION; GENE LOCUS; GENE REARRANGEMENT; GENETIC ORGANIZATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRAIN DIFFERENCE;

ANIMALS; BASE SEQUENCE; CATTLE; DNA, BACTERIAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENES, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM CANETTII; MYCOBACTERIUM TUBERCULOSIS; UNCULTURED ACTINOMYCETE;

EID: 0034000319     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.9.2393-2401.2000     Document Type: Article

References (41)

1. Bachellier, S., E. Gilson, M. Hofnung, and C. W. Hill. 1996. Repeated sequences, p. 2012-2040. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, Jr., B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: American Society for cellular and molecular biology, 2nd ed. Microbiology, Washingington, D.C.
2. Beggs, M. L., M. D. Cave, C. Marlowe, L. Cloney, P. Duck, and K. D. Eisenach. 1996. Characterization of Mycobacterium tuberculosis complex direct repeat sequence for use in cycling probe reaction. J. Clin Microbiol. 34: 2985-2989.
3. Blazquez, J., L. E. Espinoza de Los Monteros, S. Samper, C. Martin, A. Guerrero, J. Cobo, J. van Embden, F. Baquero, and E. Gomez-Mampaso. 1997. Genetic characterization of multidrug-resistant Mycobacterium bovis from a hospital outbreak involving human immunodeficiency virus-positive patients. J. Clin. Microbiol. 35:1390-1393.
4. Bult, C. J., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. FitzGerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodek, J. D. Scott, N. S. Geoghagen, J. F. Weidman, J. L. Fuhrmann, D. T. Nguyen, T. Utterback, J. M. Kelley, J. D. Peterson, P. W. Sadow, M. C. Hanna, M. D. Cotton, M. A. Hurst, K. M. Roberts, B. B. Kaine, M. Borodovsky, H. P. Klenk, C. M. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073.
5. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwtll, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, S. Oliver, J. Osborne, M. A. Quail, M. A. Rajandream, J. Rogers, S. Rutter, K. Seeger, S. Skelton, S. Squares, R. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
6. Cousins, D., S. Williams, E. Liebana, A. Aranaz, A. Bunschoten, J. D. A. van Embden, and T. Ellis. 1998. Evaluation of four DNA typing techniques in epidemiological investigations of bovine tuberculosis. J. Clin. Microbiol. 36: 168-178.
7. DelSolar, G., R. Giraldo, M. J. RuizEchevarria, M. Espinosa, and R. DiazOrejas. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62:434-464.
8. Diaz, R., K. Kremer, P. de Haas, R. I. Gomez, A. Marrero, J. A. Valdivia, J. D. A. van Embden, and D. van Soolingen. 1998. 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. 2:743-750.
9. Driscoll, J. R., M. A. McGarry, and H. W. Taber. 1998. DNA typing of a nonviable culture of Mycobacterium tuberculosis in a homeless shelter outbreak. J. Clin. Microbiol. 37:274-275.
10. Fang, Z., N. Morrison, B. Watt, C. Doig, and K. J. Forbes. 1998. IS6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains. J. Bacteriol. 180:2102-2109.
11. Frottingham, R., and W. A. Meeker-O'Connell. 1998. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144:1189-1196.
12. Gordon, S. V., R. Brosch, A. Billault, T. Garnier, K. Eiglmeijer, and S. T. Cole. 1999. Identification of variable regions in the genome of tubercle bacilli using artificial chromosome arrays. Mol. Microbiol. 32:643-655.
13. Goyal, M., N. A. Saunders, J. D. A. van Embden, D. B. Young, and R. J. Shaw. 1997. Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism. J. Clin. Microbiol. 35:647-651.
14. Groenen, P. M. A., A. E. Bunschoten, D. van Soolingen, and J. D. A. van Embden. 1993. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis: application for strain differentiation by a novel typing method. Mol. Microbiol. 10:1057-1085.
15. Gutiérrez, M., S. Samper, M. S. Jiménez, J. D. A. Embden, J. F. García-Marín, and C. Martin. 1997. Identification by spoligotyping of a caprine genotype in Mycobacterium bovis strains causing human tuberculosis. J. Clin. Microbiol. 35:3328-3330.
16. Hermans, P. W. M., D. van Soolingen, E. M. Bik, P. E. W. de Haas, J. W. Dale, and J. D. A. van Embden. 1991. The insertion element IS987 from Mycobacterium bovis BCG is located in a hot spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect. Immun. 59:2695-2705.
17. Hoe, N., K. Nakashima, D. Grigsby, X. Pan, S. J. Dou, S. Naidich, M. Garcia, E. Kahn, D. Bergmire-Sweat, and J. M. Musser. 1999. Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg. Infect. Dis. 5:254-263.
18. Kamerbeek, J., L. M. Schouls, A. Kolk, M. van Agterveld, D. van Soolingen, S. Kuijrper, J. E. Bunschnten, H. Molhuizen, R. Shaw, M. Goyal, and J. D. A. van Embden. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914.
19. Kapur, V., T. S. Whittam, and J. M. Musser. 1994. Is Mycobacterium tuberculosis 15,000 years old? J. Infect. Dis. 170:1348-1349.
20. Kawarabayasi, Y., M. Sawada, H. Horikawa, Y. Haikawa, Y. Hino, S. Yamamoto, M. Sekine, S. Baba, H. Kosugi, A. Hosoyama, Y. Nagai, M. Sakai, K. Ogura, R. Otuka, H. Nakazawa, M. Takamiya, Y. Ohfuku, T. Funahashi, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, K. Aoki, Y. Nakamura, T. F. Robb, K. Horikoshi, Y. Masuchi, H. Shizuya, and H. Kikuchi. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:55-76.
21. Klenk, H. P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Kelchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson, D. L. Richardson, A. R. Kerlavage, D. E. Graham, B. A. Kyrpides, R. D. Fleischmann, J. Quackenbush, N. H. Lee, G. G. Sutton, S. Gill, E. F. Kirkness, B. A. Dougherty, K. McKenney, M. D. Adams, B. Loftus, S. Peterson, C. I. Reich, L. K. McNeil, J. H. Badger, A. Glodek, L. X. Zhou, R. Overbeek, J. D. Gocayne, J. F. Weidman, L. McDonald, T. Utterback, M. D. Cotton, T. Spriggs, P. Artiach, B. P. Kaine, S. M. Sykes, P. W. Sadow, K. P. Dandrea, C. Bowman, C. Fujii, S. A. Garland, T. M. Mason, G. J. Olsen, C. M. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archacon Archaeoglo-bus. fulggidus. Nature 390:364-370.
22. Kremer, K., D. van Soolingen, R. Frothingham, W. H. Haas, P. W. M. Hermans, C. Martin, P. Palittapongarnpim, B. B. Plikaytis, L. Riley, M. A. Yakrus, J. M. Musser, and J. D. A. van Embden. 1999. Comparison of methods for typing of Mycobacterium tuberculosis complex strains for use in the epidemiology: an interlaboratory study on strain discriminatory power and reproducibility. J. Clin. Microbiol. 37:2607-2618.
23. Long, R., E. Nobert, S. Chomyc, J. D. A. van Embden, C. McNamee, R. R. Duran, J. Talbot, and A. Fanning. 1999. Transcontinental spread of multidrug-resistant Mycobacterium bovis. Am. J. Respir. Crit. Care Med. 159: 2014-2017.
24. Masepohl, B., K. Gorlitz, and H. Bohme. 1996. Long tandemly repeated repetitive (LTRR) sequences in the filamentous cyanobacterium Anabaena sp. PCC 7120 Biochim. Biophys. Acta Gene Struct. Expr. 1307:26-30.
25. McAdam, R. A., T. R. Weisbrod, J. Martin, J. D. Scuderi, A. M. Brown, J. D. Cirillo, B. R. Bloom, and W. R. Jacobs, Jr. 1995. In vivo growth characteristics of leucine and methionine auxotrophic mutants of Mycobacterium bovis BCG generated by transposon mutagenesis. Infect. Immun. 63:1004-1012.
26. Moijica, F. J. M., G. Ferrer, and F. Rodriguez-Valera. 1995. Long stretches of short tandem repeats are present in the largest replicons of the archea Haloferax mediterranci and Huloferax volcanii and could be involved in replicon partitioning, Mol. Microbiol. 17:85-93.
27. Nakata, A., M. Amemura, and K. Makino. 1989. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171:3553-3356.
28. Pfyffer, G., E. R. Auckenthaler, J. D. A. van Embden, and D. van Soolingen. 1998. Mycobacterium canettii, the smooth variant of M. tuberculosis, isolated from a Swiss patient exposed in Africa. Emerg. Infect. Dis. 4:631-634.
29. Poulet, S., and S. T. Cole. 1995. Repeated DNA sequences in mycobacteria. Arch. Microbiol. 163:79-86.
30. Qian, L., J. T. Douglas, A. van der Zanden, H. Duanmu, and J. D. A. van Embden. 1999. Retrospective analysis of M. tuberculosis DNA types in preserved lung tissues, J. Clin. Microbiol. 37:471-474.
31. Shreevatsan, S., P. Escalante, X. Pan, K. E. Stockbauer, N. D. Conell, B. N. Kreiwirth, T. S. Whittam, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionary recent global dissemination. Proc. Natl. Acad. Sci. USA 94:9869-9874.
32. Small, P. M., and J. D. A. van Embden. 1994. Molecular epidemiology of tuberculosis, p. 569-582. In B. Bloom (ed.), Tuberculosis: pathogenesis, protection, and control. ASM Press, Washington, D.C.
33. Smith, D. R., L. A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert, D. Harrison, L. Hoang, P. Keagle, W. Lumm, B. Pothier, D. Qiu, R. Spadafora, R. Vicaire, Y. Wang, J. Wierzbowski, R. Gibson, N. Jiwani, A. Caruso, D. Bush, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179:7135-7155.
34. Sola, C., A. Devallois, L. Horgen, J. Maïsetti, I. Filliol, E. Legrand, and N. Rastogi. 1999. Tuberculosis in the Caribbean: using spacer oligonucleotide typing to understand strain origin and transmission. Emerg. Infect. Dis. 5: 404-414.
35. Taylor, G. M., M. Goyal, A. J. Legge, R. J. Shaw, and D. Young. 1999. Genotypic analysis of Mycobacterium tuberculosis from medieval human remains. Microbiology 145:899-904.
36. van der Zanden, A. G. M., A. H. Hoentjen, F. G. C. Heilmann, E. F. Weltevreden, L. M. Schouls, and J. D. A. van Embden. 1998. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded tissues and in stained microscopic preparations. Mol. Pathol. 51:209-214.
37. van Soolingen, D., T. Hoogenboezem, P. E. W. de Haas, P. W. M. Hermans, M. A. Koedam, K. S. Teppema, P. J. Brennan, G. S. Besra, F. Portaels, J. Top, L. M. Schouls, and J. D. A. van Embden. 1997. A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int. J. Syst. Bacteriol. 47:1236-1245.
38. van Soolingen, D., L. Qian, P. E. W. de Haas, J. T. Douglas, H. Traore, F. Portaels, H. Z. Qing, D. Enkhasaikan, P. Nymadawa, and J. D. A. van Embden. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries at East Asia. J. Clin. Microbiol. 33:3234-3238.
39. van Soolingen, D., P. de Haas, P. W. M. Hermans, P. Groenen, and J. D. A. van Embden. 1993. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of M. tuberculosis. J. Clin. Microbiol. 31:1987-1995.
40. van Soolingen, D., A. G. M. van der Zanden, P. E. W. de Haas, G. T. Noordhoek, A. Kiers, N. A. Foudraine, F. Portaels, A. H. J. Kolk, K. Kremer, and J. D. A. van Embden. 1998. Diagnosis off Mycobacterium microti infections among humans by using novel genetic markers. J. Clin. Microbiol. 36: 1840-1845.
41. van Soolingen, D., and P. W. M. Hermans. 1995. Epidemiology of tuberculosis by DNA fingerprinting. Eur. Respir. J. 8:S649-S656.