Genotyping of the Mycobacterium tuberculosis complex using MIRUs: Association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics

Infection, Genetics and Evolution

Volumn 3, Issue 2, 2003, Pages 125-133

  Sola, Christophe ^a   Filliol, Ingrid ^a   Legrand, Eric ^a   Lesjean, Sarah ^b   Locht, Camille ^b   Supply, Philippe ^b   Rastogi, Nalin ^a  

^a Institut Pasteur de Guadeloupe   (Guadeloupe)

^b INSTITUT PASTEUR DE LILLE   (France)

Author keywords

Bacterial typing techniques; Epidemiology; Genetics; MIRU; Mycobacterium tuberculosis complex; Spoligotyping

Indexed keywords

ALLELE; ARTICLE; ASIAN; BACTERIAL GENE; BACTERIUM ISOLATION; CALCULATION; CHINA; CONTROLLED STUDY; GENE CLUSTER; GENE LOCUS; GENETIC EPIDEMIOLOGY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHY; MOLECULAR EVOLUTION; MOLECULAR TYPING; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOUTH AND CENTRAL AMERICA; SOUTHERN EUROPE; STRAIN DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

ALLELES; BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENOTYPE; HUMANS; MINISATELLITE REPEATS; MYCOBACTERIUM TUBERCULOSIS; SPECIES SPECIFICITY; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM CANETTII; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS COMPLEX;

EID: 0037503639     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1567-1348(03)00011-X     Document Type: Article

References (35)

1. Bifani P.J. Mathema B. Kurepina N.E. Kreiswirth B.N. Global dissemination of the Mycobacterium tuberculosis W/Beijing family strains Trends Microbiol. 10 2002 45-52
2. Bonora S. Gutierrez M.C. Perri G.D. Brunello F. Allegranzi B. Ligozzi M. Fontana R. Concia E. Vincent V. Comparative evaluation of ligation-mediated PCR and spoligotyping as screening methods for genotyping of Mycobacterium tuberculosis strains J. Clin. Microbiol. 37 1999 3118-3123
3. Brosch R. Gordon S.V. Marmiesse M. Brodin P. Buchrieser C. Eiglmeier K. Garnier T. Gutierrez C. Hewinson G. Kremer K. Parsons L.M. Pym A.S. Samper S. van Soolingen D. Cole S.T. A new evolutionary scenario for the Mycobacterium tuberculosis complex Proc. Natl. Acad. Sci. U.S.A. 99 2002 3684-3689
4. Cowan L.S. Mosher L. Diem L. Massey J.P. Crawford J.T. Variable number tandem repeat typing of Mycobacterium tuberculosis isolates with low-copy numbers of IS 6110 by using mycobacterial interspersed repetitive units J. Clin. Microbiol. 40 2002 1592-1602
5. Filliol I. Ferdinand S. Negroni L. Sola C. Rastogi N. Molecular typing of Mycobacterium tuberculosis based on variable number of tandem DNA repeats (VNTRs) used alone, and in association with spoligotyping J. Clin. Microbiol. 38 2000 2520-2524
6. Filliol I. Driscoll J.R. van Soolingen D. Kreiswirth B.N. Kremer K. Valétudie G. Anh D.D. Barlow R. Banerjee D. Bifani P.J. Brudey K. Cataldi A. Cooksey R.C. Cousins D.V. Dale J.W. Dellagostin O.A. Drobniewski F. Engelmann G. Ferdinand S. Gascoyne-Binzi D. Gordon M. Gutierrez M.C. Haas W.H. Heersma H. Källenius G. Kassa-Kelembho E. Koivula T. Ly H.M. Makristathis A. Mammina C. Martin G. Moström P. Mokrousov I. Narbonne V. Narvskaya O. Nastasi A. Eyangoh S.N.N. Pape J.W. Rasolofo-Razanamparany V. Ridell M. Rossetti M.L. Stauffer F. Suffys P.N. Takiff H. Texier-Maugein J. Vincent V. de Waard J. Sola C. Rastogi N. Global distribution of Mycobacterium tuberculosis spoligotypes Emerg. Infect. Dis. 8 2002 1347-1349
7. Frothingham R. Meeker-O'Connell W.A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats Microbiology 144 1998 1189-1196
8. Goguet de la Salmonière Y.-O. Li H.M. Torrea G. Bunschoten A. van Embden J.D.A. Gicquel B. Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis J. Clin. Microbiol. 35 1997 2210-2214
9. Gutacker M.M. Smoot J.C. Migliaccio C.A. Ricklefs S.M. Hua S. Cousins D.V. Graviss E.A. Shashkina E. Kreiswirth B.N. Musser J.M. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms. Resolution of genetic relationships among closely related microbial strains Genetics 162 2002 1533-1543
10. Hunter P.R. Gaston M.A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity J. Clin. Microbiol. 26 1988 2465-2466
11. Jaccard P. Nouvelles recherches sur la distribution florale Bull. Soc. Vaud. Sci. Nat. 44 1908 223-270
12. Kamerbeek J. Schouls L. Kolk A. van Agterveld M. van Soolingen D. Kuijper S. Bunschoten A. Molhuizen H. Shaw R. Goyal M. van Embden J.D.A. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology J. Clin. Microbiol. 35 1997 907-914
13. Kremer K. van Soolingen D. Frothingham R. Haas W.H. Hermans P.W.M. Martin C. Palittapongarnpim P. Plikaytis B.B. Riley L.W. Yakrus M.A. Musser J.M. van Embden J.D.A. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis strains: interlaboratory study of discriminatory power and reproducibility J. Clin. Microbiol. 37 1999 2607-2618
14. Lee A.S. Tang L.L. Lim I.H. Bellamy R. Wong S.Y. Discrimination of single-copy IS 6110 DNA fingerprints of Mycobacterium tuberculosis isolates by high-resolution minisatellite-based typing J. Clin. Microbiol. 40 2002 657-659
15. Mazars E. Lesjean S. Banuls A.L. Gilbert M. Vincent V. Gicquel B. Tibayrenc M. Locht C. Supply P.High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology Proc. Natl. Acad. Sci. U.S.A. 98 2001 1901-1906
16. Radhakrishnan I. Manju Y.K. Kumar R.A. Mundayoor S. Implications of low frequency of IS 6110 in fingerprinting field isolates of Mycobacterium tuberculosis from Kerala, India J. Clin. Microbiol. 39 2001 1683
17. Roring S. Scott A. Brittain D. Walker I. Hewinson G. Neill S. Skuce R. Development of variable number tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping J. Clin. Microbiol. 40 2002 2126-2133
18. Savine E. Warren R. van der Spuy G.D. Beyers N. van Helden P.D. Locht C. Supply P.Stability of variable number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis J. Clin. Microbiol. 40 2002 4561-4566
19. Sebban M. Mokrousov I. Rastogi N. Sola C. A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis Bioinformatics 18 2002 235-243
20. Skuce R.A. McCorry T.P. McCarroll J.F. Roring S.M. Scott A.N. Brittain D. Hughes S.L. Hewinson R.G. Neill S.D. Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets Microbiology 148 2002 519-528
21. Smittipat N. Palittapongarnpim P. Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis Tuber. Lung Dis. 80 2000 69-74
22. Sneath, P.H.A., Sokal, R., 1973. Numerical Taxonomy: The Principles and Practices of Classification. Freeman, San Francisco, USA.
23. Sola C. Horgen L. Maïsetti J. Devallois A. Goh K.S. Rastogi N. Spoligotyping followed by double-repetitive element PCR is a rapid alternative methodology to IS 6110-fingerprinting for epidemiological studies of tuberculosis J. Clin. Microbiol. 36 1998 1122-1124
24. Sola C. Filliol I. Guttierez C. Mokrousov I. Vincent V. Rastogi N. Spoligotype database of Mycobacterium tuberculosis: biogeographical distribution of shared types and epidemiological and phylogenetic perspectives Emerg. Infect. Dis. 7 2001a 390-396
25. Sola C. Filliol I. Legrand E. Mokrousov I. Rastogi N. Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS 1081, IS 6110, VNTR and DR-based spoligotyping suggests the existence of two new phylogeographical clades J. Mol. Evol. 53 2001b 680-689
26. Sreevatsan S. Pan X. Stockbauer K.E. Connell N.D. Kreiswirth B.N. Whittam T.S. Musser J.M. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionary recent global dissemination Proc. Natl. Acad. Sci. U.S.A. 94 1997 9869-9874
27. Supply P. Magdalena J. Himpens S. Locht C. Identification of novel intergenic repetitive units in a mycobacterial two-component system operon Mol. Microbiol. 26 1997 991-1003
28. Supply P. Mazars E. Lesjean S. Vincent V. Gicquel B. Locht C. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome Mol. Microbiol. 36 2000 762-771
29. Supply P. Lesjean S. Savine E. Kremer K. van Soolingen D. Locht C. Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units J. Clin. Microbiol. 39 2001 3563-3571
30. 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. Shinnick T.M. Small P.M.Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology J. Clin. Microbiol. 31 1993 406-409
31. van Embden J.D.A. van Gorkom T. Kremer K. Jansen R.van der Zeijst B.A.M. Schouls L.M. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria J. Bacteriol. 182 2000 2393-2401
32. van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements J. Intern. Med. 249 2001 1-26
33. van Soolingen D. Hermans P.W.M. de Haas P.E.W. Sool D.R. van Embden J.D.A. The occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis J. Clin. Microbiol. 29 1991 2578-2586
34. van Soolingen D. Qian L. de Haas P.E.W. Douglas J.T. Traore H. Portaels F. Qing H.Z. Enkhsaikan D. Nymadawa P. van Embden J.D.A. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia J. Clin. Microbiol. 33 1995 3234-3238
35. World Health Organization, 2002. Global Tuberculosis Control: Surveillance, Planning, Financing. WHO/CDS/TB/2002.295. WHO, Geneva, Switzerland.