Chapter 33 : Molecular Epidemiology of Tuberculosis

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Molecular epidemiology is the integration of molecular techniques to track specific strains of pathogens with conventional epidemiologic approaches to understanding the distribution of disease in populations. This chapter describes the genetic elements of that may be exploited as strain-specific markers, the strain-typing methods that are based on these elements, and some of the DNA fingerprinting results obtained to date and speculates on future directions in this field. complex bacteria constitute a remarkably homogeneous group, as revealed by the inability of multilocus enzyme electrophoresis to differentiate individual strains and the minimal DNA polymorphism in restriction fragments of randomly chosen chromosomal DNA fragments. Most investigators use the technique of Southern blotting to exploit the presence of the above-described genetic elements to reveal restriction fragment length polymorphisms (RFLP) among strains. The application of molecular techniques in this setting suggests that tuberculosis control efforts should be focused on this population to prevent the emergence and spread of multidrug-resistant (MDR) tuberculosis in Europe. Differences in the genetic stabilities of such genetic elements can be used to exploit these elements as molecular clocks in the evolution of divergent strains. A major future challenge of DNA fingerprinting of will be to determine the paces of change of the various elements and to match these to study specific epidemiologic questions.

Citation: Small P, van Embden J. 1994. Molecular Epidemiology of Tuberculosis, p 569-582. In Bloom B (ed), Tuberculosis. ASM Press, Washington, DC. doi: 10.1128/9781555818357.ch33
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Figure 1.

IS-based DNA fingerprinting results of initial (lanes A) and subsequent (lanes B) isolates of from patients with tuberculosis isolated from serial sputum samples. In each patient, the time interval between samples was 7 to 29 months, and subsequent isolates demonstrated increasing antimicrobial resistance. Serial RFLP patterns either are identical or differ by one additional band (arrow). The last two lanes contain negative and positive control DNA. (Reprinted by permission of the [ ].)

Citation: Small P, van Embden J. 1994. Molecular Epidemiology of Tuberculosis, p 569-582. In Bloom B (ed), Tuberculosis. ASM Press, Washington, DC. doi: 10.1128/9781555818357.ch33
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1. Aber, V. R.,, B. W. Allen,, D. A. Mitchison,, P. Ayuma,, E. A. Edwards,, and A. B. Keyes. 1980. Quality control in the tuberculosis laboratory. 1. Laboratory studies on isolated positive cultures and the efficiency of direct smear examination. Tubercle 61: 123 133.
2. Beck-Sague, C.,, S. W. Dooley,, M. D. Hutton,, J. Otten,, A. Breeden,, J. T. Crawford,, A. E. Pitchenik,, C. Woodley,, G. Cauthen,, and W. R. Jarvis. 1992. Hospital outbreak of multidrug-resistant Mycobacterium tuberculosis infections. JAMA 268: 1280 1286.
3. Brudney, K.,, and J. Dobkin. 1991. Resurgent tuberculosis in New York City: human immunodeficiency virus, homelessness, and the decline of tuberculosis control programs. Am. Rev. Respir. Dis. 144: 745 749.
4. Cave, M. D.,, K. D. Eisenach,, P. F. McDermott,, J. H. Bates,, and J. T. Crawford. 1991. 756/70: conservation of sequence in the Mycobacterium tuberculosis complex and its utilization in DNA fingerprinting. Mol. Cell. Probes 5: 73 80.
5. Centers for Disease Control. 1991. Nosocomial transmission of multidrug resistant tuberculosis among HIV-infected persons, Florida and New York, 1988-1991. Morbid. Mortal. Weekly Rep. 40: 585591.
6. Centers for Disease Control. 1992. Transmission of multidrug-resistant tuberculosis among immunocompromised persons in a correctional system. New York 1991. Morbid. Mortal. Weekly Rep. 41: 507509.
7. Collins, D. M. Personal communication.
8. Collins, D. M.,, and G. W. de Lisle. 1984. DNA restriction endonuclease analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG. J. Gen. Microbiol. 130: 1019 1021.
9. Collins, D. M.,, S. K. Erasmuson,, D. M. Stephens,, G. F. Yates,, and G. W. de Lisle. 1993. DNA fingerprinting of Mycobacterium bovis strains by restriction fragment analysis and hybridization with insertion elements IS/087 and IS 6110. J. Clin. Microbiol. 31: 1143 1147.
10. Collins, D. M.,, and D. M. Stephens. 1991. Identification of insertion sequence, IS 1081, in Mycobacterium bovis. FEMS Microbiol. Lett. 83: 11 16.
11. Crawford, J. T. Personal communication
12. Daley, C. L.,, P. M. Small,, G. F. Schecter,, G. K. Schoolnik,, R. A. McAdam,, W. R. Jacobs, Jr.,, and P. C. Hopewell. 1992. 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. 326: 231 235.
13. Das, S.,, S. L. Chan,, B. W. Allen,, D. A. Mitchison,, and D. B. Lowrie. 1993. 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. Tuberc. Lung Dis. 74: 47 51.
14. Dooley, S. W.,, M. E. Villarino,, M. Lawrence, et al. 1992. Nosocomial transmission of tuberculosis in a hospital unit for HIV-infected patients. JAMA 267: 2632 2634.
15. Doran, T. J.,, A. L. M. Hodgson,, J. K. Davies,, and A. J. Radford. 1992. Characterization of a novel repetitive DNA sequence from Mycobacterium bovis. FEMS Microbiol. Lett. 96: 179 186.
16. Dwyer, B.,, K. Jackson,, K. Raios,, A. Sievers,, E. Wilshire,, and B. Ross. 1993. DNA restriction fragment analysis to define an extended cluster of tuberculosis in homeless men and their associates. J. Infect. Dis. 167: 490 494.
17. Edlin, B. R.,, J. I. Tokars,, M. H. Grieco,, J. T. Crawford,, J. Williams,, E. M. Sordillo,, K. R. Ong,, J. O. Kilburn,, S. W. Dooley,, K. G. Castro,, W. R. Jarvis,, and S. D. Holmberg. 1992. An outbreak of multidrug-resistant tuberculosis among hospitalized patients with the acquired immunodeficiency syndrome. N. Engl. J. Med. 326: 1514 1521.
18. Fischl, M. A.,, R. B. Uttamchandani,, G. L. Daikos, et al. 1992. An outbreak of tuberculosis caused by multiple-drug resistant tubercle bacilli among patients with HIV infection. Ann. Intern. Med. 117: 177 183.
19. Fomukong, N. G.,, and J. W. Dale. Transpositional activity of IS 986 in M. smegmatis. Submitted for publication.
20. Fomukong, N. G.,, J. W. Dale,, T. W. Osborn,, and J. M. Grange. 1992. Use of gene probes on the insertion sequence IS 986 to differentiate between BCG vaccine strains. J. Appl. Bacteriol. 72: 125 133.
21. Genewein, A.,, A. Telenti,, C. Bernasconi,, C. Mordasini,, S. Weiss,, A. Maurer,, H. Rieder,, K. Schopfer,, and T. Bodmer. 1993. Molecular approach to identifying route of transmission of tuberculosis in the community. Lancet 342: 841 844.
22. Godfrey-Faussett, P.,, P. R. Mortimer,, P. A. Jenkins,, and N. G. Stoker. 1992. Evidence of transmission of tuberculosis by DNA fingerprinting. Br. Med. J. 305: 221 223.
23. Godfrey-Faussett, P.,, and N. G. Stoker. 1992. Aspects of tuberculosis in Africa. 3. Genetic fingerprinting for clues to the pathogenesis of tuberculosis. Trans. R. Soc. Trop. Med. 86: 472 475.
24. Groenen, P. M. A.,, A. E. van 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 method. Mol. Microbiol. 10: 1057 1065.
25. Gruft, H.,, R. Johnson,, R. Claflin,, and A. Loder. 1984. Phage-typing and drug-resistance patterns as tools in mycobacterial epidemiology. Am. Rev. Respir. Dis. 130: 96 97.
26. Haas, W. H.,, W. R. Butler,, C. L. Woodley,, and J. T. Crawford. 1993. Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex. J. Clin. Microbiol. 31: 1293 1298.
27. 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 1S987 from Mycobacterium bovis BCG is located in a hot spot integration region for insertion elements in M. tuberculosis complex strains. Infect. Immun. 59: 2695 2705.
28. Hermans, P. W. M.,, D. van Soolingen,, J. W. Dale,, A. R. Schuitema,, R. A. McAdam,, D. Catty,, and J. D. A. van Embden. 1990. Insertion element IS986 from Mycobacterium tuberculosis: a useful tool for diagnosis and epidemiology of tuberculosis. J. Clin. Microbiol. 28: 2051 2058.
29. Hermans, P. W. M.,, D. van Soolingen,, and J. D. A. van Embden. 1992. 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. 174: 4157 4165.
30. Jeffreys, A. J.,, A. MacLeod,, K. Tamaki,, D. L. Neil,, and D. G. Monckton. 1991. Minisatellite repeat coding as a digital approach to DNA typing. Nature (London) 354: 204 209.
31. Lawrence, J. G.,, D. E. Dykhuizen,, R. F. Dubose,, and D. L. Hartl. 1989. Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli. Mol. Biol. Evol. 6: 1 14.
32. Lederberg, J.,, R. E. Shope,, and E. J. Oaks. 1993. Emerging Infections: Microbial Threats to the Health of the United States, p. 1. National Academy Press, Washington, D.C..
33. Mazurek, G. H.,, M. D. Cave,, K. D. Eisenach,, R. J. Wallace, Jr.,, J. H. Bates,, and J. T. Crawford. 1991. Chromosomal DNA fingerprint patterns produced with IS 6110 as strain-specific markers for epidemiologic study of tuberculosis. J. Clin. Microbiol. 29: 2030 2033.
34. McAdam, R. A.,, P. W. M. Hermans,, D. van Soolingen,, Z. F. Zainuddin,, D. Catty,, J. D. A. van Embden,, and J. W. Dale. 1990. Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the ISi family. Mol. Microbiol. 4: 1607 1613.
35. Mendiola, M. V.,, C. Martin,, I. Otal,, and B. Gicquel. 1992. Analysis of regions responsible for IS 6110 RFLP in a single Mycobacterium tuberculosis strain. Res. Microbiol. 143: 767 772.
36. Otal, I.,, C. Martin,, V. Vincent-Levy-Frebault,, D. Thierry,, and B. Gicquel. 1991. Restriction fragment length polymorphism analysis using IS 6110 as an epidemiological marker in tuberculosis. J. Clin. Microbiol. 29: 1252 1254.
37. Palittapongarnpim, P.,, S. Chomic,, A. Fanning,, and D. Kunimoto. 1993a. DNA fingerprinting of Mycobacterium tuberculosis by ligation-mediated polymerase chain reaction. Nucleic Acids Res. 3: 761 762.
38. Palittapongarnpim, P.,, S. Chomic,, A. Fanning,, and D. Kunimoto. 1993b. DNA fragment length polymorphism analysis of M. tuberculosis isolates by arbitrarily primed polymerase chain reaction. J. Infect. Dis. 167: 975 978.
39. Palittapongarnpim, P. S.,, S. Rienthong,, and W. Panbangred. 1993c. Comparison of restriction fragment length polymorphism of M. tuberculosis isolated from cerebrospinal fluid and sputum: a preliminary report. Tuberc. Lung Dis. 74: 204 207.
40. Plikaytis, B. B. Personal communication.
41. Ross, B. C, and B. Dwyer. 1993. Rapid, simple method for typing isolates of Mycobacterium tuberculosis by using the polymerase chain reaction. J. Clin. Microbiol. 31: 329 334.
42. Ross, C.,, K. Raios,, K. Jackson,, and B. Dwyer. 1992. Molecular cloning of a highly repeated element from Mycobacterium tuberculosis and its use as an epidemiological tool. J. Clin. Microbiol. 30: 942 946.
43. Ryan, F. 1993. Tuberculosis: the Greatest Story Never Told, p. 173. Swift Publishers, Bromsgrove, Worchestershire, England.
44. Shafer, R. W.,, P. M. Small,, C. Larkin,, S. P. Singh,, P. Kelly,, M. F. Sierra,, G. K. Schoolnik,, and K. D. Chirgwin. Temporal trends and transmission patterns during the emergence of multidrug-resistant tuberculosis in New York City: a molecular epidemiological assessment. Submitted for publication.
45. Small, P. M.,, P. C. Hopewell,, S. P. Singh,, A. Paz,, J. Parsonnet,, D. C. Ruston,, G. F. Schecter,, C. L. Daley,, and G. K. Schoolnik. The contemporary urban epidemiology of tuberculosis: a population-based study using conventional and molecular methods. Submitted for publication.
46. Small, P. M.,, and B. Kreiswirth. Unpublished observations.
47. Small, P. M.,, N. McClenny,, S. P. Singh,, G. K. Schoolnik,, L. S. Tomkins,, and P. A. Mickelsen. 1993a. Molecular strain typing of Mycobacterium tuberculosis to confirm cross-contamination in the myco-bacteriology laboratory and modification of procedures to minimize occurrence of false-positive cultures. J. Clin. Microbiol. 31: 1677 1682.
48. Small, P. M.,, and A. Moss. 1993. Molecular epidemiology and the new tuberculosis. Infect. Agents Dis. 2: 132 138.
49. Small, P. M.,, R. W. Schafer,, P. C. Hopewell,, S. P. Singh,, M. J. Murphy,, E. Desmond,, M. F. Sierra,, and G. K. Schoolnik. 1993b. Exogenous reinfection with multidrug-resistant M. tuberculosis in patients with advanced HIV infection. N. Engl. J. Med. 328: 1137 1144.
50. Tabet, S. R.,, G. M. Goldbaum,, T. M. Hoot on,, K. D. Eisenach,, M. D. Cave,, and C. M. Nolan. 1994. Restriction fragment length polymorphism analysis detecting a community-based tuberculosis outbreak among persons infected with human immunodeficiency virus. J. Infect. Dis. 169: 189 192.
51. Thierry, D.,, M. D. Cave,, K. D. Eisenach,, J. T. Crawford,, J. H. Bates,, B. Gicquel,, and J. L. Guesdon. 1990. IS6//0, an IS-like element of M. tuberculosis complex. Nucleic Acids Res. 18: 188.
52. van Embden, J. D. A. Unpublished data.
53. van Embden, J. D. A.,, M. D. Cave,, J. T. Crawford,, J. W. Dale,, K. D. Eisenach,, B. Gicquel,, P. W. M. Hermans,, C. Martin,, R. McAdam,, T. M. Shinnick,, and P. M. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31: 406 409.
54. van Embden, J. D. A.,, P. M. Small,, and B. Gicquel. Unpublished data.
55. van Embden, J. D. A.,, D. van Soolingen,, P. M. Small,, and P. W. M. Hermans. 1992. Genetic markers for the epidemiology of tuberculosis. Res. Microbiol. 143: 385 391.
56. Vannier, A. N.,, J. J. Tarrand,, and P. R. Murray. 1988. Mycobacterial cross contamination during radiometric culturing. J. Clin. Microbiol. 26: 1867 1868.
57. van Soolingen, D.,, and D. M. Collins. Personal communication.
58. van Soolingen, D.,, P. E. W. de Haas,, P. W. M. Hermans,, P. M. A. Groenen,, and J. D. A. van Embden. 1993. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J. Clin. Microbiol. 31: 1987 1995.
59. van Soolingen, D.,, P. W. M. Hermans,, P. E. W. de Haas,, D. R. Soil,, and J. D. A. van Embden. 1991. The occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains; evaluation of insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 29: 2578 2586.
60. van Soolingen, D.,, P. W. M. Hermans,, P. E. W. de Haas,, and J. D. A. van Embden. 1992. Insertion element IS 1081-associated restriction fragment length polymorphism in Mycobacterium tuberculosis complex species: a reliable tool for recognizing Mycobacterium bovis BCG. J. Clin. Microbiol. 30: 1772 1777.
61. Yuen, L. K.,, B. C. Ross,, K. M. Jackson,, and B. Dwyer. 1992. Characterization of Mycobacterium tuberculosis strains from Vietnamese patients by Southern blot hybridization. J. Clin. Microbiol. 31: 1615 1618.
62. Zainuddin, Z. F.,, and J. W. Dale. 1989. Polymorphic repetitive DNA sequences in Mycobacterium tuberculosis detected with a gene probe from a Mycobacterium fortuitum plasmid. J. Gen. Microbiol. 135: 2347 2355.


Generic image for table
Table 1.

Insertion sequences and repetitive DNA in

Citation: Small P, van Embden J. 1994. Molecular Epidemiology of Tuberculosis, p 569-582. In Bloom B (ed), Tuberculosis. ASM Press, Washington, DC. doi: 10.1128/9781555818357.ch33

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