The use of restriction fragment length polymorphism (RFLP) analysis for epidemiological studies of tuberculosis in developing countries

International Journal of Tuberculosis and Lung Disease

Volumn 2, Issue 1, 1998, Pages 16-26

  Cohn, D L ^a,b,c,e   O'Brien, R J ^a,d  

^a WORLD HEALTH ORGANIZATION   (Switzerland)

^b Denver Disease Control Service   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^e DENVER PUBLIC HEALTH   (United States)

Author keywords

DNA; Fingerprinting; Molecular epidemiology; RLP; Transmission; Tuberculosis

Indexed keywords

DEVELOPING COUNTRY; DISEASE TRANSMISSION; DNA FINGERPRINTING; HOSPITAL INFECTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MYCOBACTERIUM TUBERCULOSIS; PATHOGENESIS; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; TUBERCULOSIS;

AIDS-RELATED OPPORTUNISTIC INFECTIONS; CROSS INFECTION; DEVELOPED COUNTRIES; DEVELOPING COUNTRIES; DNA FINGERPRINTING; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; DRUG RESISTANCE, MICROBIAL; HUMANS; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RECURRENCE; TUBERCULOSIS, PULMONARY;

EID: 0031887119     PISSN: 10273719     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (77)

1. Bottger E C, Teske A, Kirschner P, et al. Disseminated infections with Mycobacterium genavense in patients with AIDS. Lancet 1992; 340: 76-80.
2. Springer B, Kirschner P, Rost-Meyer G, Schroder K H, Kroppenstedt R M, Bottger E C. Mycobacterium interjectum, a new species isolated from a patient with chronic lymphadenitis. J Clin Microbiol 1993; 31: 3083-3089.
3. Clarridge J E III, Shawar R M, Shinnick T M, Plikyatis B. Large-scale use of polymerase chain reaction for detection of Mycobacterium tuberculosis in a routine mycobacteriology laboratory. J Clin Microbiol 1993; 31: 2049-2056.
4. Noordhock G T, Kolk A H J, Bjune G, et al. Sensitivity and specificity of PCR for detection of Mycobacterium tuberculosis: a blind comparison study among seven laboratories. J Clin Microbiol 1994; 32: 277-284.
5. Eisenach K D, Crawford J T, Bates J H. Genetic relatedness among strains of the Mycobacterium tuberculosis complex: analysis of restriction fragment heterogeneity using cloned DNA probes. Am Rev Respir Dis 1986; 133: 1055-1068.
6. Shoemaker S A, Fisher J H, Jones W D, Scoggin C H. Restriction fragment analysis of chromosomal DNA defines different strains of Mycobacterium tuberculosis. Am Rev Respir Dis 1986; 134: 210-213.
7. van Soolingen D, Hermans P W M, de Haas P E W, Soll Dr, van Embden J D A. The occurence and stability of insertion sequences in Mycobacterium tuberculosis complex strains; evaluation of IS-dependent DNA polymorphism as a tool in the epidemiolgy of tuberculosis. J Clin Microbiol 1991; 29: 2578-2586.
8. Chevrel-Dellagi D, Abderrahman A, Haltiti R, Koubaji H, Gicquel B, Dellagi K. Large-scale DNA fingerprinting of Mycobacterium tuberculosis strains as a tool for epidemiological studies of tuberculosis. J Clin Microbiol 1993; 31: 2446-2450.
9. Small P M, Hopewell P C, Singh S P, et al. The epidemiology of tuberculosis in San Francisco: a population based study using conventional and molecular methods. N Engl J Med 1994; 330: 1703-1709.
10. Genewein A, Telenti A, Bernasconi C, et al. Molecular approach to identifying route of transmission of tuberculosis in the community. Lancet 1993; 342: 841-844.
11. Tabet S R, Goldbaum G M, Hooten T M, Eisenach K D, Cave M D, Nolan C M. Restriction fragment length polymorphism analysis detecting a community-based tuberculosis outbreak among persons infected with human immunodeficiency virus. J Infect Dis 1994; 169: 189-192.
12. Friedman C R, Stoeckle M Y, Kreiswirth B N, et al. Transmission of multidrug-resistant tuberculosis in a large urban setting. Am J Respir Crit Care Med 1995; 152: 355-359.
13. Bifani P J, Plikaytis B B, Kapur V, et al. Origin and interstate spread of a New York City multidrug-resistant Mycobacterium tuberculosis clone family. JAMA 1996; 275: 452-457.
14. Alland D, Kalkut G E, Moss A R, et al. Transmission of tuberculosis in New York city: an analysis by DNA fingerprinting and conventional epidemiologic methods. N Engl J Med 1994; 330: 1710-1716.
15. Dwyer B, Jackson K, Raios K, Sievers A, Wilshire E, Ross B, DNA restriction fragment analysis to define an extended cluster of tuberculosis in homeless men and their associates. J Infect Dis 1993; 167: 490-494.
16. Jereb J A, Burwen D R, Dooley S W, et al. Nosocomial out-break of tuberculosis in a renal transplant unit: application of a new technique for restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates. J Infect Dis 1993; 168: 1219-1224.
17. Coronado V G, Beck-Sague C M, Hutton M D, et al. Transmission of multidrug-resistant Mycobacterium tuberculosis among persons with human immunodeficiency virus infection in an urban hospital: epidemiologic and restriction fragment length polymorphism analysis. J Infect Dis 1993; 168: 1052-1055.
18. Small P M, Shafer R W, Hopewell P C, et al. Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in patients with advanced HIV infection. N Engl J Med 1993; 328: 1137-1144.
19. Godfrey-Faussett P, Githui W, Batchelor B, et al. Recurrence of HIV-related tuberculosis in an endemic area may be due to relapse or reinfection. Tubercle Lung Dis 1995; 75: 199-202.
20. Daley C L, Small P M, Schecter G F, et al. An outbreak of tuberculosis with accelerated progression among persons infected with the human immunodeficiency virus: an analysis using restriction fragment-length polymorphisms. N Engl J Med 1992; 326: 231-235.
21. Das S, Chan S, Allen B W, Mitchison D A, Lowrie D B. Application of DNA fingerprinting with IS986 to sequential mycobacterial isolates obtained from pulmonary tuberculosis patients in Hong Kong before, during and after short-course chemotherapy. Tubercle Lung Dis 1993; 74: 47-51.
22. Burman W J, Stone B L, Reves R R, et al. The incidence of false-positive cultures for Mycobacterium tuberculosis. Am J Respir Crit Care Med 1997; 155: 321-326.
23. Fomukong N G, Tang T H, Al-Maamary S, et al. Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110. Tubercle Lung Dis 1994; 75: 435-440.
24. Hermans P W, Messadi F, Guebrexabher H, et al. Analysis of the population structure of Mycobacterium tuberculosis in Ethiopia, Tunisia, and the Netherlands: usefulness of DNA typing for global tuberculosis epidemiology. J Infect Dis 1995; 171: 1504-1513.
25. van Soolingen D, Qian L, de Haas P E W, et al. Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J Clin Microbiol 1995; 33: 3234-3238.
26. Small P M. Editorial: towards an understanding of the global migration of Mycobacterium tuberculosis. J Infect Dis 1995; 171: 1593-1594.
27. Godfrey-Faussett P, Stoker N G, Scott JAG, Pasvol G, Kelly P, Clancy L. DNA fingerprints of Mycobacterium tuberculosis do not change during the development of rifampicin resistance. Tubercle Lung Dis 1993; 74: 240-243.
28. Horn D L, Hewlett D, Haas W H, et al. Superinfection with rifampin-isoniazid-streptomycin-ethambutol (RISE)-resistant tuberculosis in three patients with AIDS: confirmation by polymerase chain reaction fingerprinting. Ann Intern Med 1994; 121: 115-116.
29. Heym B, Honore N, Truffot-Pernot C, et al. Implications of multidrug resistance for the future of short-course chemotherapy of tuberculosis: a molecular study. Lancet 1994; 344: 293-298.
30. Kline S E, Hedemark L L, Davies S F. Outbreak of tuberculosis among regular patrons or a neighorhood bar. N Engl J Med 1995; 333: 222-227.
31. Thierry D, Cave M D, Eisenach K D, et al. IS6110, an IS-like element of Mycobacterium tuberculosis complex. Nucl Acids Res 1990; 18: 188.
32. Hermans P W M, van Soolingen D, Dale J W, et al. Insertion element IS986 from Mycobacterium tuberculosis: a useful tool for diagnosis and epidemiology of tuberculosis. J Clin Microbiol 1990; 28: 2051-2058.
33. Thierry D, Brisson-Noel A, Vincent-Levy-Frebault V, Nguyen S, Guesdon J L, Gicquel B. Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis. J Clin Microbiol 1990; 28: 2668-2673.
34. van Soolingen D, de Haas P E W, Hermans P W M, van Embden J D A. DNA fingerprinting of Mycobacterium tuberculosis. Methods Enzymol 1994; 235: 196-205.
35. van Soolingen D, Hermans P W M, de Haas P E W, van Embden J D A. Insertion element IS1081-associated restriction fragment length polymorphism in Mycobacterium tuberculosis complex species; a reliable tool for recognizing M. bovis BCG. J Clin Microbiol 1992; 30: 1772-1777.
36. Ross B C, Raios K, Jackson K, Dwyer B. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J Clin Microbiol 1992; 30: 942-946.
37. van Soolingen D, de Haas P E W, Hermans P W M, Groenen P M A, van Embden J D A. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol 1993; 31: 1987-1995.
38. Hermans P W M, van Soolingen D, van Embden J D A. Characterization of a major polymorphic tandem repeat in Mycobacterium tuberculosis and its potential use in the epidemiology of Mycobacterium kansasii and Mycobacterium gordonae. J. Bacteriol 1992; 174: 4157-4165.
39. Hermans P W M, van Soolingen D, Bik E M, de Haas P E W, Dale J W, van Embden J D A. The insertion element IS987 from Mycobacterium bovis is located in a hot spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect immun 1991; 59: 2695-2705.
40. Wild I J F, Werely C, Beyers N, Donald P, van Helden P D, Oligonucleotide (GTG)5 as a marker for Mycobacterium tuberculosis strain identification. J Clin Microbiol 1994; 32: 1318-1321.
41. van Embden J D A, Cave M D, Crawford J T, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993; 31: 406-409.
42. Cave M D, Eisenach K D, Templeton G, et al. Stability of DNA fingerprint pattern produced with IS6110 in strains of Mycobacterium tuberculosis, J Clin Microbiol 1994; 32: 262-266.
43. Plikaytis B D, Plikaytis B B, Shinnick T M. Computer-assisted pattern recognition model for the identification of slowly growing mycobacteria including Mycobacterium tuberculosis. J Gen Microbiol 1992; 138: 2265-2273.
44. Burman W J, Reves R R, Hawkes A P, et al. DNA fingerprinting with two probes decreases clustering of Mycobacterium tuberculosis. Am J Respir Crit Care Med 1997; 155: 1140-1146.
45. Plikaytis B B, Crawford J T, Woodley C L, et al. Rapid, amplification-based fingerprinting of Mycobacterium tuberculosis. J Gen Microbiol 1993; 139: 1537-1542.
46. Ross B C, Dwyer B. Rapid, simple method for typing isolates of Mycobacterium tuberculosis by using polymerase chain reaction. J Clin Microbiol 1993; 31: 329-334.
47. Haas W H, Butler W R, Woodley C L, Crawford J T. Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex. J Clin Microbiol 1993; 31: 1293-1298.
48. Goyal M, Saunders N A, van Embden J D A, Young D B, Shaw R J. Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism. J Clin Microbiol 1997; 35: 647-651.
49. Edlin B R, Tokars J I, Grieco M H, et al. An outbreak of multidrug-resistant tuberculosis among hospitalized patients with the acquired immunodeficiency syndrome. N Engl J Med 1992; 326: 1514-1521.
50. Pearson M L, Jereb J A, Frieden T R, et al. Nosocomial transmission of multidrug-resistant Mycobacterium tuberculosis: a risk to patients and health care workers. Ann Intern Med 1992; 117: 191-196.
51. Yang Z H, de Haas P E W, Wachmann C H, van Soolingen D, van Embden J D A, Andersen A B. Molecular epidemiology of tuberculosis in Denmark in 1992. J Clin Microbiol 1995; 33: 2077-2081.
52. Wurtz R, DeMarais P, Trainor W, McAuie J, Kocka F, Moster L, Dietrich S. Specimen contamination in mycobacteriology laboratory detected by pseudo-outbreak of multidrug-resistant tuberculosis analysis by routine epidemiology and confirmation by molecular technique. J Clin Microbiol 1996; 34: 1017-1019.
53. Shafer R W, Small P M, Larkin C, et al. Temporal trends and transmission patterns during the emergence of multidrug-resistant tuberculosis in New York City: a molecular epidemiologic assessment. J Infect Dis 1995; 171: 170-176.
54. Braden C R, Templeton G L, Cave M D, et al. Interpretation of restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates from a state with a large rural popluation. J Infect Dis 1997; 175: 1446-1452.
55. Godfrey-Faussett P, Stoker N G. Aspects of tuberculosis in Africa. 3: genetic 'fingerprinting' for clues to the pathogenesis of tuberculosis. Trans Roy Soc Trop Med Hyg 1992; 86: 472-475.
56. Chevrel-Dellagi D, Abderrahman A, Haltiti R, Koubaji H, Gicquel B, Dellagi K. Large-scale DNA fingerprinting of Mycobacterium tuberculosis strains as a tool for epidemiological studies of tuberculosis. J Clin Microbiol 1993; 31: 2446-2450.
57. Palittapongarnpim P, Rienthong S, Panbangred W. Comparison of restriction fragment length polymorphism of Mycobacterium tuberculosis isolated from cerebrospinal fluid and sputum: a preliminary report. Tubercle Lung Dis 1993; 74: 204-207.
58. Yuen L K W, Ross B C, Jackson K M, Dwyer B. Characterization of Mycobacterium tuberculosis strains from Vietnamese patients by Southern Blot hybridization. J Clin Microbiol 1993; 31: 1615-1618.
59. Yang Z H, Mtoni I, Chonde M, et al. DNA fingerprinting and phenotyping of Mycobacterium tuberculosis isolates from human immunodeficiency virus (HIV)-seropositive and HIV-seronegative patients in Tanzania. J Clin Microbiol 1995; 33: 1064-1069.
60. Torrea G, Levee G, Grimont P, Martin C, Chanteau S, Gicquel B. Chromosomal DNA fingerprinting analysis using the insertion sequence IS6110 and the repetitive element DR as strain-specific markers for epidemiological study of tuberculosis in French Polynesia. J Clin Microbiol 1995; 33: 1899-1904.
61. Huh Y J, Ahn D I, Kim S J. Limited variation of DNA fingerprints (IS6110 and IS1081) in Korean strains of Mycobacterium tuberculosis. Tubercle Lung Dis 1995; 76: 324-329.
62. Yuen K Y, Chan C M, Chan K S, Yam W C, Ho P L, Chau P Y. IS6110 based amplityping assay and RFLP fingerprinting of clinical isolates of Mycobacterium tuberculosis. J Clin Pathol 1995; 48: 924-928.
63. Das S, Paramasivan C N, Lowrie D B, Prabhakar R, Narayanan R P. IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, South India. Tubercle Lung Dis 1995; 76: 550-554.
64. van Guens H A, Meijer J, Styblo K. Results of contact investigation in Rotterdam, 1967-1969. Bull Int Union Tuberc 1975; 50: 107-121.
65. Rose C E, Zerbe G O, Lantz S O, Bailey W C. Establishing priority during investigation of tuberculosis contacts. Am Rev Respir Dis 1979; 119: 603-609.
66. DeCock K, Soro B, Coulibaly I M, Lucas S B. Tuberculosis and HIV infection in sub-Saharan Africa. JAMA 1992; 268: 1581-1587.
67. Narain J, Raviglione M, Kochi A. HIV-associated tuberculosis in developing countries: epidemiology and strategies for prevention. Tubercle Lung Dis 1992; 73: 311-321.
68. Geiseler P J, Nelson H E, Crispen R G, Moses V K. Tuberculosis in physicians: a continuing problem. Am Rev Respir Dis 1986; 133: 773-778.
69. Menzies D, Fanning A, Yuan L, Fitzgerald M. Tuberculosis among health care workers. N Engl J Med 1995; 332: 92-98.
70. Centers for Disease Control and Prevention (CDC). Guidelines for preventing the transmission of Mycobacterium tuberculosis in health-care facilities. MMWR 1994; 43(RR-13): 1-132.
71. WHO Global Tuberculosis Programme and the International Union Against Tuberculosis and Lung Disease. Control of tuberculosis transmission in health care settings. WHO Wkly Epidem Rec 1993; 50: 369-371.
72. Godfrey-Faussett P, Murray J, Shearer S, et al. Molecular epidemiology of TB in South Africa gold mines (Abstract 472-PA10). Tubercle Lung Dis 1995; 76 (suppl 2): 50.
73. Perriens J H, Colebunders R L, Karahunga C, et al. Increased mortality and tuberculosis treatment failure rate among human immunodeficiency virus (HIV) seropositive compared with HIV seronegative patients with pulmonary tuberculosis treated with 'standard' chemotherapy in Kinshasa, Zaire. Am Rev Respir Dis 1991; 144: 750-855.
74. Perriens J H, St. Louis M E, Yiadiul B, et al. Pulmonary tuberculosis in HIV-infected patients in Zaire: a controlled treatment trial of treatment for 6 to 12 months. N Engl J Med 1995; 332, 779-784.
75. O'Brien R J, Perriens J H. Preventive therapy for tuberculosis in HIV infection: the promise and the reality. AIDS 1995; 9: 665-673.
76. Cohn D L, Bustreo F, Raviglione M R. Drug-resistant tuberculosis: review of the worldwide situation and the WHO/ IUATLD global surveillance project. Clin Infect Dis 1997; 24 (suppl 1): S121-30.
77. World Health Organization. Global Tuberculosis Programme. Tuberculosis and HIV research: working towards solutions. WHO/TB/95 193.