Chapter 10 : Comparative Genomics and Evolution of Mycobacterium bovis BCG

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Comparative Genomics and Evolution of Mycobacterium bovis BCG, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817657/9781555812959_Chap10-1.gif /docserver/preview/fulltext/10.1128/9781555817657/9781555812959_Chap10-2.gif


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
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1.
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
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
Permissions and Reprints Request Permissions
Download as Powerpoint


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: 9 19.
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: 1520 1523.
3. Behr, M. A.,, and P. M. Small. 1999. A historical and molecular phylogeny of BCG strains. Vaccine 17: 915 922.
4. Behr, M. A.,, and P. M. Small. 1997. Has BCG attenuated to impotence? Nature 389: 133 134.
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: 3394 3399.
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: 3195 3203.
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: 2167 2172.
8. Brennan, M. J.,, and G. Delogu. 2001. The PE multigene family: a ‘molecular mantra’ for mycobacteria. Trends Microbiol. 10: 246 249.
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: 5568 5578.
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: 3684 3689.
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: 2221 2229.
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: 111 123.
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: 452 458.
14. Calmette, A.,, and C. Guérin. 1920. Nouvelles recherches experimentales sur la vaccination des bovides contre la tuberculose. Ann. Inst. Pasteur 34: 553 560.
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: 537 544.
16. Dreyer, G.,, and R. L. Vollum. 1931. Mutation and pathogenicity experiments with BCG. Lancet i: 9 14.
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: 4266 4274.
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: 5479 5490.
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: 7877 7882.
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: 643 655.
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: 359 370.
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: 1533 1543.
24. 24 Haas, F.,, and S. S. Haas,. 1996. The origins of Mycobacterium tuberculosis and the notion of its contagiousness, p. 3 19. 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: 16 22.
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: 293 295.
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: 13853 13858.
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: 12420 12425.
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: 547 554.
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: 117 123.
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: 21 27.
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: 1274 1282.
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: 889 891.
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: 74 80.
35. Mostowy, S.,, A. G. Tsolaki,, P. M Small,, and M. A. Behr. 2003. The in vitro evolution of BCG vaccines. Vaccine 21: 4270 4274.
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: 623 635.
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: 243 250.
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: 636 639.
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: 709 717.
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: 533 539.
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: 525 530.
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: 2044 2054.
43. Sassetti, C. M.,, and E. J. Rubin. 2003. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. USA 100: 12989 12994.
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: 662 667.
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: 214 220.
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: 1710 1717.
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: 9869 9874.
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: 13001 13006.
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: 65 77.
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: 196 202.
51. Sula, L.,, and I. Radkovsky. 1976. Protective effects of M. microti vaccine against tuberculosis. J. Hyg. Epidemiol. Microbiol. Immunol. 20: 1 6.
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: 374 380.
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: 9578 9583.


Generic image for table
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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error