Chapter 10 : Comparative Genomics and Evolution of Mycobacterium bovis BCG

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Recent advances in the field of mycobacterial genetics, genomics, comparative genomics, and related techniques have supplied an enormous amount of new information, which is summarized and discussed in this chapter. Lyophilization of vaccine lots became available in the latter half of the 20th century, exposing different BCG daughter strains to some 1,000 additional passages of in vitro evolution in different laboratories. Specific PCR and sequence analyses of these RD regions, among members of the complex, showed that most of the RD regions absent from BCG were also missing from other strains of , indicating that some of these variable regions reflect the evolutionary divergence of and rather than being genomic modifications that were introduced during the attenuation process of BCG. Using the historical records about when and where BCG strains were distributed, together with information about genetic particularities of certain BCG substrains, reconstruction of the short-term evolution of BCG strains can be established. With prototype sequence information, along with comparative genomic tools such as subtractive hybridization, bacterial artificial chromosome (BAC) libraries, and DNA microarrays, the discovery of genomic deletions has been greatly facilitated. The situation in mycobacterial research has considerably changed in the last few years due to the information contained in the whole-genome sequence of H37Rv. A more efficient anti-TB vaccine seems to be one of the few possible public health interventions that would really have a major impact on the improvement of the worldwide TB situation.

Citation: Brosch R, Behr M. 2005. Comparative Genomics and Evolution of Mycobacterium bovis BCG, p 155-164. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch10

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Figure 1.

BCG genealogy. The vertical axis represents time, and the horizontal axis represents movement of vaccines between laboratories. Solid lines indicate deletions, and the dotted line indicates an SNP in .

Citation: Brosch R, Behr M. 2005. Comparative Genomics and Evolution of Mycobacterium bovis BCG, p 155-164. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch10
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Figure 2

Comparison of the genomic region RD9 from H37Rv and . A 2-kb fragment including highly conserved parts of is absent from BCG, , , and strains but is present in and

Citation: Brosch R, Behr M. 2005. Comparative Genomics and Evolution of Mycobacterium bovis BCG, p 155-164. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch10
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Figure 3

Evolutionary scheme of the complex, indicating that BCG has lost numerous regions of difference, several of which are in common with other strains of the complex. Adapted from reference 10 with permission.

Citation: Brosch R, Behr M. 2005. Comparative Genomics and Evolution of Mycobacterium bovis BCG, p 155-164. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch10
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1. Banu, S.,, N. Honore,, B. Saint-Joanis,, D. Philpott,, M. C. Prevost,, and S. T. Cole. 2002. Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol. Microbiol. 44:919.
2. Behr, M. A.,, M. A. Wilson,, W. P. Gill,, H. Salamon,, G. K. Schoolnik,, S. Rane,, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:15201523.
3. Behr, M. A.,, and P. M. Small. 1999. A historical and molecular phylogeny of BCG strains. Vaccine 17:915922.
4. Behr, M. A.,, and P. M. Small. 1997. Has BCG attenuated to impotence? Nature 389:133134.
5. Behr, M. A.,, B. G. Schroeder,, J. N. Brinkman,, R. A Slayden,, and C. E. Barry III. 2000. A point mutation in the mma3 gene is responsible for impaired methoxymycolic acid production in Mycobacterium bovis BCG strains obtained after 1927. J. Bacteriol. 182:33943399.
6. Berthet, F.-X.,, P. B. Rasmusse,, I. Rosenkrands,, P. Andersen,, and B. Gicquel. 1998. A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology 144:31953203.
7. Boshoff, H. I.,, V. Mizrahi,, and C. E. Barry III. 2002. Effects of pyrazinamide on fatty acid synthesis by whole mycobacterial cells and purified fatty acid synthase I. J. Bacteriol. 184:21672172.
8. Brennan, M. J.,, and G. Delogu. 2001. The PE multigene family: a ‘molecular mantra’ for mycobacteria. Trends Microbiol. 10:246249.
9. Brodin, P.,, K. Eiglmeier,, M. Marmiesse,, A. Billault,, T. Garnier,, S. Niemann,, S. T. Cole,, and R. Brosch. 2002. Bacterial artificial chromosome-based comparative genomic analysis identifies Mycobacterium microti as a natural ESAT- 6 deletion mutant. Infect. Immun. 70:55685578.
10. Brosch, R.,, S. V. Gordon,, M. Marmiesse,, P. Brodin,, C. Buchrieser,, K. Eiglmeier,, T. Garnier,, C. Gutierrez,, G. Hewinson,, K. Kremer,, L. M. Parsons,, A. S. Pym,, S. Samper,, D. van Soolingen,, and S. T. Cole. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. USA 99:36843689.
11. Brosch, R.,, S. V. Gordon,, A. Billault,, T. Garnier,, K. Eiglmeier,, C. Soravito,, B. G. Barrell,, and S. T. Cole. 1998. Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics. Infect. Immun. 66:22212229.
12. Brosch, R.,, S. V. Gordon,, C. Buchrieser,, A. S. Pym,, T. Garnier,, and S. T. Cole. 2000. Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur. Yeast (Comp. Funct. Genomics) 17:111123.
13. Brosch, R.,, A. S. Pym,, S. V. Gordon,, and S. T. Cole. 2001. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9:452458.
14. Calmette, A.,, and C. Guérin. 1920. Nouvelles recherches experimentales sur la vaccination des bovides contre la tuberculose. Ann. Inst. Pasteur 34:553560.
15. 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. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, A. Krogh,, J. McLean,, S. Moule,, L. Murphy,, K. Oliver,, J. Osborne,, M. A. Quail,, M. A. Rajandream,, J. Rogers,, S. Rutter,, K. Soeger,, J. Skelton,, R. Squares,, S. 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 393:537544.
16. Dreyer, G.,, and R. L. Vollum. 1931. Mutation and pathogenicity experiments with BCG. Lancet i:914.
17. Fernandes, N. D.,, Q. L. Wu,, D. Kong,, X. Puyang,, S. Garg,, and R. N. Husson. 1999. A mycobacterial extracytoplasmic sigma factor involved in survival following heat shock and oxidative stress. J. Bacteriol. 181:42664274.
18. Fine, P. E. M.,, I. A. M. Carneiro,, J. B. Milstein,, and C. J. Clements. 1999. Issues Relating to the Use of BCG in Immunization Programmes. A Discussion Document. WHO/V&B/ 99.23. Department of Vaccines and Biologicals, World Health Organization, Geneva, Switzerland.
19. Fleischmann, R. D.,, D. Alland,, J. A. Eisen,, L. Carpenter,, O. White,, J. Peterson,, R. DeBoy,, R. Dodson,, M. Gwinn,, D. Haft,, E. Hickey,, J. F. Kolonay,, W. C. Nelson,, L. A. Umayam,, M. Ermolaeva,, S. L. Salzberg,, A. Delcher,, T. Utterback,, J. Weidman,, H. Khouri,, J. Gill,, A. Mikula,, W. Bishai,, W. R. Jacobs, Jr.,, J. C. Venter,, and C. M. Fraser. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184:54795490.
20. Garnier, T.,, K. Eiglmeier,, J. C. Camus,, N. Medina,, H. Mansoor,, M. Pryor,, S. Duthoy,, S. Grondin,, C. Lacroix,, C. Monsempe,, S. Simon,, B. Harris,, R. Atkin,, J. Doggett,, R. Mayes,, L. Keating,, P. R. Wheeler,, J. Parkhill,, B. G. Barrell,, S. T. Cole,, S.V. Gordon,, and R. G. Hewinson. 2003. The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. USA 100:78777882.
21. Gordon, S. V.,, R. Brosch,, A. Billault,, T. Garnier,, K. Eiglmeier,, and S. T. Cole. 1999. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol. Microbiol. 32:643655.
22. Guinn, K. I.,, M. J. Hickey,, S. K. Mathur,, K. L. Zakel,, J. E. Grotzke,, D. M. Lewinsohn,, S. Smith,, and D. R. Sherman. 2004. Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis. Mol. Microbiol. 51:359370.
23. Gutacker, M. M.,, J. C. Smoot,, C. A. Migliaccio,, S. M. Ricklefs,, S. Hua,, D. V. Cousins,, E. A. Graviss,, E. Shashkina,, B. N. Kreiswirth,, and J. M. Musser. 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms. Resolution of genetic relationships among closely related microbial strains. Genetics 162:15331543.
24. 24 Haas, F.,, and S. S. Haas,. 1996. The origins of Mycobacterium tuberculosis and the notion of its contagiousness, p. 319. In W. N. Rom, and S. Garay (ed.), Tuberculosis. Little, Brown & Co., Boston, Mass..
25. Harboe, M.,, T. Oettinger,, H. G. Wiker,, I. Rosenkrands,, and P. Andersen. 1996. Evidence for occurrence of the ESAT-6 protein in Mycobacterium tuberculosis and virulent Mycobacterium bovis and for its absence in Mycobacterium bovis BCG. Infect. Immun. 64:1622.
26. Hart, P. D. A.,, and I. Sutherland. 1977. BCG and vole bacillus vaccines in the prevention of tuberculosis in adolescence and early adult life. Br. Med. J. 2:293295.
27. Horwitz, M. A.,, G. Harth,, B. J. Dillon,, and S. Maslesa-Galic. 2000. Recombinant bacillus Calmette-Guerin (BCG) vaccines expressing the Mycobacterium tuberculosis 30-kDa major secretory protein induce greater protective immunity against tuberculosis than conventional BCG vaccines in a highly susceptible animal model. Proc. Natl. Acad. Sci. USA 97:1385313858.
28. Hsu, T.,, S. M. Hingley-Wilson,, B. Chen,, M. Chen,, A. Z. Dai,, P. M. Morin,, C. B. Marks,, J. Padiyar,, C. Goulding,, M. Gingery,, D. Eisenberg,, R. G. Russell,, S. C. Derrick,, F. M. Collins,, S. L. Morris,, C. H. King,, and W. R. Jacobs, Jr. 2003. The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue. Proc. Natl. Acad. Sci. USA 100:1242012425.
29. Kato-Maeda, M.,, J. T. Rhee,, T. R. Gingeras,, H. Salamon,, J. Drenkow,, N. Smittipat,, and P. M. Small. 2001. Comparing genomes within the species Mycobacterium tuberculosis. Genome Res. 11:547554.
30. Lewis, K. N.,, R. Liao,, K. M. Guinn,, M. J. Hickey,, S. Smith,, M. A. Behr,, and D. R. Sherman. 2003. Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guérin attenuation. J. Infect. Dis. 187:117123.
31. Lupski, J. R.,, J. R. Roth,, and G. M. Weinstock. 1996. Chromosomal duplications in bacteria, fruit flies, and humans. Am. J. Hum. Genet. 58:2127.
32. Mahairas, G. G.,, P. J. Sabo,, M. J. Hickey,, D. C. Singh,, and C. K. Stover. 1996. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J. Bacteriol. 178:12741282.
33. Minnikin, D. E, S. M. Minnikin, G. Dobson, M. Goodfellow, F. Portaels, L. van den Breen, and D. Sesardic. 1983. Mycolic acid patterns of four vaccine strains of Mycobacterium bovis BCG. J. Gen. Microbiol. 129:889891.
34. Mostowy, S.,, D. Cousins,, J. Brinkman,, A. Aranaz,, and M. A. Behr. 2002. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J. Infect. Dis. 186:7480.
35. Mostowy, S.,, A. G. Tsolaki,, P. M Small,, and M. A. Behr. 2003. The in vitro evolution of BCG vaccines. Vaccine 21: 42704274.
36. Mukamolova, G. V.,, O. A Turapov,, D. I. Young,, A. S. Kaprelyants,, D. B. Kell,, and M. Young. 2002. A family of autocrine growth factors in Mycobacterium tuberculosis. Mol. Microbiol. 46:623635.
37. Oettinger, T.,, M. Jorgensen,, A. Ladefoged,, K. Haslov,, and P. Andersen. 1999. Development of the Mycobacterium bovis BCG vaccine: review of the historical and biochemical evidence for a genealogical tree. Tubercle Lung Dis. 79:243250.
38. Ponnighaus, J. M.,, P. E. Fine,, J. A. Sterne,, R. J. Wilson,, E. Msosa,, P. J. Gruer,, P. A. Jenkins,, S. B. Lucas,, N. G. Liomba,, and L. Bliss. 1992. Efficacy of BCG vaccine against leprosy and tuberculosis in northern Malawi. Lancet 339: 636639.
39. Pym, A. S.,, P. Brodin,, R. Brosch,, M. Huerre,, and S. T. Cole. 2002. Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol. Microbiol. 46:709717.
40. Pym, A. S.,, P. Brodin,, L. Majlessi,, R. Brosch,, C. Demangel,, A. Williams,, K. E. Griffiths,, G. Marchal,, C. Leclerc,, and S. T. Cole. 2003. Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat. Med. 9:533539.
41. Riehle, M. M.,, A. F. Benett,, and A. D. Lang. 2001. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. USA 98:525530.
42. Salamon, H.,, M. Kato-Maeda,, P. M. Small,, J. Drenkow,, and T. R. Gingeras. 2000. Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Res. 10:20442054.
43. Sassetti, C. M.,, and E. J. Rubin. 2003. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. USA 100:1298912994.
44. Scorpio, A.,, and Y. Zhang. 1996. Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus. Nat. Med. 2:662667.
45. Skjot, R. L. V.,, T. Oettinger,, I. Rosenkrands,, P. Ravn,, I. Brock,, S. Jacobsen,, and P. Andersen. 2000. Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens. Infect. Immun. 68:214220.
46. Sorensen, A. L.,, S. Nagai,, G. Houen,, P. Andersen,, and A. Andersen. 1995. Purification and characterization of a low molecular mass T-cell antigen secreted by Mycobacterium tuberculosis. Infect. Immun. 63:17101717.
47. Sreevatsan, S.,, X. Pan,, K. E. Stockbauer,, N. D. Connell,, B. N. Kreiswirth,, T. S. Whittam,, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:98699874.
48. Stanley, S. A.,, S. Raghavan,, W. W. Hwang,, and J. S. Cox. 2003. Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc. Natl. Acad. Sci. USA 100:1300113006.
49. Stead, W. W. 1997. The origin and erratic global spread of tuberculosis. How the past explains the present and is the key to the future. Clin. Chest Med. 18:6577.
50. Streng, K. O. 1940. Etude des caracteres d’attennuation du bacille BCG suivant le nombre de passages de ce germe sur pomme de terre a la bile de boeuf. Ann. Inst. Pasteur 64:196202.
51. Sula, L.,, and I. Radkovsky. 1976. Protective effects of M. microti vaccine against tuberculosis. J. Hyg. Epidemiol. Microbiol. Immunol. 20:16.
52. Wiker, H. G.,, S. Nagai,, R. G. Hewinson,, W. P. Russell,, and M. Harboe. 1996. Heterogenous expression of the related MPB70 and MPB83 proteins distinguish various substrains of Mycobacterium bovis BCG and Mycobacterium tuberculosis H37Rv. Scand. J. Immunol. 43:374380.
53. Yuan, Y.,, D. D. Crane,, R. M. Simpson,, Y. Zhu,, M. J. Hickey,, D. R. Sherman,, and C. E. Barry III. 1998. The 16-kDa α-crystallin (Acr) protein of Mycobacterium tuberculosis is required for growth in macrophages. Proc. Natl. Acad. Sci. USA 95:95789583.


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Table 1

Genomic deletions in certain BCG substrains

Citation: Brosch R, Behr M. 2005. Comparative Genomics and Evolution of Mycobacterium bovis BCG, p 155-164. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch10

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