Molecular tools for Mycobacterium tuberculosis genotyping;Herramientas moleculares empleadas en genotipificación de Mycobacterium tuberculosis

Revista de Salud Publica

Volumn 12, Issue 3, 2010, Pages 510-521

  Rozo Anaya, Juan C ^a,b   Ribón, Wellman ^a,c  

^a INSTITUTO NACIONAL DE SALUD   (Colombia)

^b UNIVERSIDAD DE PAMPLONA   (Colombia)

^c UNIVERSIDAD INDUSTRIAL DE SANTANDER   (Colombia)

Author keywords

DNA; Genotype; Molecular epidemiology; Mycobacterium tuberculosis; Polymorphism; Restriction fragment length; Tuberculosis

Indexed keywords

EID: 79751501179     PISSN: 01240064     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (64)

1. Organización mundial de la salud OMS. Plan mundial para detener la tuberculosis 2006-2015. Actuar para salvar vidas. Hacia un mundo sin tuberculosis. Ginebra: Organización Mundial de la Salud; 2006. p. 35.
2. Musser JM. Antimicrobial agent resistance in mycobacteria: molecular genetic insights. Clin Microbiol Rev 1995;8:496-514.
3. Feizabadi MM, Robertson ID, Cousins DV, Hampson DJ. Genomic analysis of Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex by isoenzyme analysis and pulsed-field gel electrophoresis. J Clin Microbiol 1996;34:1136-42.
4. Kalantri S, Pai M, Pascopella L, Riley L, Reingold A. Bacteriophage- based tests for the detection of Mycobacterium tuberculosis in clinical specimens: a systematic review and metaanalysis. BMC Infect Dis 2005;5:59.
5. Kato-Maeda M, Small PM. How molecular epidemiology has changed what we know about tuberculosis. West J Med 2000;172:256-9.
6. van Soolingen D, De Haas, Kremer K. Restriction fragment length polymorphism (RFLP) typing of mycobacteria. National Institute of Public Health and Environment. Bilthoven. The Netherlands; 2002.
7. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993;31:406-9.
8. Aranaz A, Liebana E, Gomez-Mampaso E, Galan JC, Cousins D, Ortega A, et al. Mycobacterium tuberculosis subsp. caprae subsp. nov.: a taxonomic study of a new member of the Mycobacterium tuberculosis complex isolated from goats in Spain. Int J Syst Bacteriol 1999;493:1263-73.
9. Gutacker MM, Smoot JC, Migliaccio CA, Ricklefs SM, Hua S, Cousins DV, et al. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 2002;162:1533-43.
10. Nakamura Y, Obase Y, Suyama N, Miyazaki Y, Ohno H, Oka M, et al. A small outbreak of pulmonary tuberculosis in non-close contact patrons of a bar. Intern Med 2004;43:263-7.
11. Asgharzadeh M, Kafil HS. Current trends in molecular epidemiology studies of Mycobacterium tuberculosis. Biotechnol. Mol Biol Rev 2007;2:108-15.
12. Doroudchi M, Kremer K, Basiri EA, Kadivar MR, Van SD, Ghaderi AA. IS6110-RFLP and spoligotyping of Mycobacterium tuberculosis isolates in Iran. Scand J Infect Dis 2000;32:663-8.
13. Bauer J, Andersen AB, Kremer K, Miorner H. Usefulness of spoligotyping To discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark. J Clin Microbiol 1999;37:2602-6.
14. Kodmon C, Niemann S, Lukacs J, Sor E, David S, Somoskovi A. Molecular epidemiology of drugresistant tuberculosis in Hungary. J Clin Microbiol 2006;44:4258-61.
15. Gori A, Bandera A, Marchetti G, Degli EA, Catozzi L, Nardi GP, et al. Spoligotyping and Mycobacterium tuberculosis. Emerg Infect Dis 2005;11:1242-8.
16. Baker LV, Brown TJ, Maxwell O, Gibson AL, Fang Z, Yates MD, et al. Molecular analysis of isoniazid-resistant Mycobacterium tuberculosis isolates from England and Wales reveals the phylogenetic significance of the ahpC -46A polymorphism. Antimicrob.Agents Chemother 2005;49:1455-64.
17. Scott AN, Menzies D, Tannenbaum TN, Thibert L, Kozak R, Joseph L, et al. Sensitivities and specificities of spoligotyping and mycobacterial interspersed repetitive unit-variablenumber tandem repeat typing methods for studying molecular epidemiology of tuberculosis. J Clin Microbiol 2005;43:89-94.
18. Supply P, Magdalena J, Himpens S, Locht C. Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 1997;26:991-1003.
19. Prod'hom G, Guilhot C, Gutierrez MC, Varnerot A, Gicquel B, Vincent V. Rapid discrimination of Mycobacterium tuberculosis complex strains by ligation-mediated PCR fingerprint analysis. J Clin Microbiol 1997;35:3331-4.
20. Kremer K, Arnold C, Cataldi A, Gutierrez MC, Haas WH, Panaiotov S, et al. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005;43:5628-38.
21. Mostrom P, Gordon M, Sola C, Ridell M, Rastogi N. Methods used in the molecular epidemiology of tuberculosis. Clin Microbiol Infect 2002;8:694-704.
22. Reisig F, Kremer K, Amthor B, van SD, Haas WH. Fast ligation-mediated PCR, a fast and reliable method for IS6110-based typing of Mycobacterium tuberculosis complex. J Clin Microbiol 2005;43:5622-7.
23. Sims EJ, Goyal M, Arnold C. Experimental versus in silico fluorescent amplified fragment length polymorphism analysis of Mycobacterium tuberculosis: improved typing with an extended fragment range. J Clin Microbiol 2002;40:4072-6.
24. Mortimer P, Arnold C. FAFLP: last word in microbial genotyping? J Med Microbiol 2001;50:393-5.
25. Garcia DV, Alonso RN, Andres S, Ruiz MJ, Bouza E. Characterization of clonal complexity in tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat typing. J Clin Microbiol 2005;43:5660-4.
26. Hunter P,Gaston M. Numerical Index of the Discriminatory Ability of Typing Systems: an Application of Simpson's Index of Diversity. J Clin Microbiol 1988;26:2465-6.
27. Gaston MA, Hunter PR. Efficient selection of tests for bacteriological typing schemes. J Clin Pathol 1989;42:763-6.
28. Skuce RA, McCorry TP, McCarroll JF, Roring SM, Scott AN, Brittain D. Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets. Microbiology 2002;148: 519-28.
29. Kassama Y, Shemko M, Shetty N, Fang Z, Macintire G, Gant V, et al. An improved fluorescent amplified fragment length polymorphism method for typing Mycobacterium tuberculosis. J Clin Microbiol 2006;44:288-9.
30. Burger M, Raskin S, Brockelt SR, Amthor B, Geiss HK, Haas WH. DNA fingerprinting of Mycobacterium tuberculosis complex culture isolates collected in Brazil and spotted onto filter paper. J Clin Microbiol 1998;36:573-6.
31. Banu S, Gordon SV, Palmer S, Islam MR, Ahmed S, Alam KM. Genotypic analysis of Mycobacterium tuberculosis in Bangladesh and prevalence of the Beijing strain. J Clin Microbiol 2004;42:674-82.
32. Evans JT, Hawkey PM, Smith EG, Boese KA, Warren RE, Hong G. Automated high-throughput mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis strains by a combination of PCR and non denaturing high-performance liquid chromatography. J Clin Microbiol 2004;42:4175-80.
33. Godreuil S, Torrea G, Terru D, Chevenet F, Diagbouga S, Supply P, et al. First molecular epidemiology study of Mycobacterium tuberculosis in Burkina Faso. J Clin Microbiol 2007;45:921-7.
34. Chin PJ, Jou R. A modified automated high-throughput mycobacterial interspersed repetitive unit method for genotyping Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2005;53: 325-7.
35. Maes M, Kremer K, van Soolingen D, Takiff H, de Waard J. 24-Locus MIRU-VNTR genotyping is a useful tool to study the molecular epidemiology of tuberculosis among Warao Amerindians in Venezuela. Tuberculosis 2008;88:490-4.
36. Sun YJ, Bellamy R, Lee AS, Ng ST, Ravindran S, Wong SY, et al. Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore. J Clin Microbiol 2004;42:1986-93.
37. Haas WH, Bretzel G, Amthor B, Schilke K, Krommes G, Rusch-Gerdes S, et al. Comparison of DNA fingerprint patterns of isolates of Mycobacterium africanum from east and west Africa. J Clin Microbiol 1997;35:663-6.
38. Dahle UR, Nordtvedt S, Winje BA, Mannsaaker T, Heldal E, Sandven P, et al. Tuberculosis in contacts need not indicate disease transmission. Thorax 2005;60:136-7.
39. Durmaz R, Gunal S, Yang Z, Ozerol IH, Cave MD. Molecular epidemiology of tuberculosis in Turkey. Clin Microbiol Infect 2003;9:873-7.
40. Garcia MR, Rodriguez JC, Navarro JF, Samper S, Martin C, Royo G. Molecular epidemiology of tuberculosis in Elche, Spain: a 7-year study. J Med Microbiol 2002;51:273-7.
41. Martinez M, Garcia D, Alonso VM, Andres S, Bouza E, Cabezas T, et al. Impact of laboratory cross-contamination on molecular epidemiology studies of tuberculosis. J Clin Microbiol 2006;44:2967-9.
42. van der Zanden AG, Kremer K, Schouls LM, Caimi K, Cataldi A, Hulleman A, et al. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J Clin Microbiol 2002;40:4628-39.
43. Asgharzadeh M, Shahbabian K, Majidi J, Aghazadeh AM, Amini C, Jahantabi AR, et al. IS6110 restriction fragment length polymorphism typing of Mycobacterium tuberculosis isolates from East Azerbaijan Province of Iran. Mem Inst Oswaldo Cruz. 2006;101:517-21.
44. Barlow RE, Gascoyne-Binzi DM, Gillespie SH, Dickens A, Qamer S, Hawkey PM. Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates. J Clin Microbiol 2001;39:2453-7.
45. Jou R, Chiang CY, Huang WL. Distribution of the Beijing family genotypes of Mycobacterium tuberculosis in Taiwan. J Clin Microbiol 2005;43:95-100.
46. Lari N, Rindi L, Sola C, Bonanni D, Rastogi N, Tortoli E, et al. Genetic diversity, determined on the basis of katG463 and gyrA95 polymorphisms, Spoligotyping, and IS6110 typing, of Mycobacterium tuberculosis complex isolates from Italy. J Clin Microbiol 2005;43:1617-24.
47. Gomez JE, Leon CI, Inirida M, Leen R, Françoise P. IS6110 fingerprinting of sensitive and resistant strains (1991-1992) of Mycobacterium tuberculosis in Colombia. Mem Inst Oswaldo Cruz 2002;97:1005-8.
48. Cadmus S, Palmer S, Okker M, Dale J, Gover K, Smith N, et al. Molecular analysis of human and bovine tubercle bacilli from a local setting in Nigeria. J Clin Microbiol 2006;44:29-34.
49. Gazouli M, Ikonomopoulos J, Koundourakis A, Bartos M, Pavlik I, Overduin P, et al. Characterization of Mycobacterium tuberculosis complex isolates from Greek patients with sarcoidosis by Spoligotyping. J Clin Microbiol 2005;43:4858-61.
50. Jou R, Chen HY, Chiang CY, Yu MC, Su IJ. Genetic diversity of multidrug-resistant Mycobacterium tuberculosis isolates and identification of 11 novel rpoB alleles in Taiwan. J Clin Microbiol 2005;43:1390-4.
51. Goguet de la Salmoniere YO, Li HM, Torrea G, Bunschoten A, van EJ, Gicquel B. Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis. J Clin Microbiol 1997;35:2210-4.
52. Niobe-Eyangoh SN, Kuaban C, Sorlin P, Cunin P, Thonnon J, Sola C, et al. Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J Clin Microbiol 2003;41:2547-53.
53. Zozio T, Allix C, Saribas Z, Alp A, Durmaz R, Fauville-Dufaux M, et al. Genotyping of Mycobacterium tuberculosis clinical isolates in two cities of Turkey: description of a new family of genotypes that is phylogeographically specific for Asia Minor. BMC Microbiol 2005;5:44.
54. Singh UB, Suresh N, Bhanu NV, Arora J, Pant H, Sinha S, et al. Predominant tuberculosis spoligotypes, Delhi, India. Emerg Infect Dis 2004;10:1138-42.
55. Kremer K, van SD, Frothingham R, Haas WH, Hermans PW, Martin C, et al. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol 1999;37:2607-18.
56. Gopaul KK, Brown TJ, Gibson AL, Yates MD, Drobniewski FA. Progression toward an improved DNA amplification-based typing technique in the study of Mycobacterium tuberculosis epidemiology. J Clin Microbiol 2006;44:2492-8.
57. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes S, Willery E, et al. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variablenumber tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006;44:4498-510.
58. Lee AS, Tang LL, Lim IH, Bellamy R, Wong SY. Discrimination of single-copy IS6110 DNA fingerprints of Mycobacterium tuberculosis isolates by high-resolution minisatellitebased typing. J Clin Microbiol 2002;40:657-9.
59. Zanini MS, Moreira EC, Lopes MT, Oliveira RS, Leao SC, Fioravanti RL, et al. Mycobacterium bovis: polymerase chain reaction identification in bovine lymphonode biopsies and genotyping in isolates from Southeast Brazil by spolygotyping and restriction fragment length polymorphism. Mem Inst Oswaldo Cruz 2001;96:809-13.
60. Murray M, Alland D. Methodological problems in the molecular epidemiology of tuberculosis. Am J Epidemiol 2002;155:565-71.
61. Sarmiento OL, Weigle KA, Alexander J, Weber DJ, Miller WC. Assessment by meta-analysis of PCR for diagnosis of smear-negative pulmonary tuberculosis. J Clin Microbiol 2003;41:3233-40.
62. National TB Controllers Association/CDC Advisory Group on Tuberculosis Genotyping. Guide to the Application of Genotyping to Tuberculosis Prevention and Control. Atlanta, GA: US Department of Health and Human Services, CDC; 2004.
63. Brudey K, Gutierrez MC, Vincent V, Parsons LM, Salfinger M, Rastogi N, et al. Mycobacterium africanum genotyping using novel spacer oligonucleotides in the direct repeat locus. J Clin Microbiol 2004;42:5053-7.
64. McNabb SJ, Kammerer JS, Hickey AC, Braden CR, Shang N, Rosenblum LS, et al. Added epidemiologic value to tuberculosis prevention and control of the investigation of clustered genotypes of Mycobacterium tuberculosis isolates. Am J Epidemiol 2004;160:589-97.