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Novel genome polymorphisms in BCG vaccine strains and impact on efficacy.

Leung AS, Tran V, Wu Z, Yu X, Alexander DC, Gao GF, Zhu B, Liu J - BMC Genomics (2008)

Bottom Line: Moreover, we have uncovered various polymorphisms in the phoP-phoR locus.Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy.These findings have important implications for the development of a new generation of vaccines.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada. andreas.leung@utoronto.ca

ABSTRACT
Bacille Calmette-Guérin (BCG) is an attenuated strain of Mycobacterium bovis currently used as a vaccine against tuberculosis. Global distribution and propagation of BCG has contributed to the in vitro evolution of the vaccine strain and is thought to partially account for the different outcomes of BCG vaccine trials. Previous efforts by several molecular techniques effectively identified large sequence polymorphisms among BCG daughter strains, but lacked the resolution to identify smaller changes. In this study, we have used a NimbleGen tiling array for whole genome comparison of 13 BCG strains. Using this approach, in tandem with DNA resequencing, we have identified six novel large sequence polymorphisms including four deletions and two duplications in specific BCG strains. Moreover, we have uncovered various polymorphisms in the phoP-phoR locus. Importantly, these polymorphisms affect genes encoding established virulence factors including cell wall complex lipids, ESX secretion systems, and the PhoP-PhoR two-component system. Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy. These findings have important implications for the development of a new generation of vaccines.

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Refined genealogy of BCG vaccines. The genealogy is modified from a previous model [24]. Genetic markers identified in this work are highlighted.
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Figure 3: Refined genealogy of BCG vaccines. The genealogy is modified from a previous model [24]. Genetic markers identified in this work are highlighted.

Mentions: The loss of the RD1-encoded ESX-1 protein secretion system during 1908–1921 contributes to the attenuation of BCG ([55], see also Fig. 3). However, because reintroduction of ESX-1 into BCG does not restore full virulence, other genetic lesions are also involved [56]. Whole genome sequence comparison reveals 2,223 single nucleotide polymorphisms (SNPs) between BCG-Pasteur and M. tb H37Rv, and 736 SNPs between BCG-Pasteur and M. bovis AF2122/97 [24]. NimbleGen analysis revealed 1,010 SNPs between BCG-Pasteur and M. tb H37Rv. Of which, 945 SNPs were correctly identified when comparing to the complete genome sequence of BCG-Pasteur. Thus the NimbleGen technique has a limited ability to detect SNPs but the majority of identified SNPs are accurate. Our NimbleGen analysis also revealed numerous SNPs (ranging from ~400 to ~1,800) between individual BCG strains and M. tb H37Rv, and the majority of changes detected by the NimbleGen technique are also present in BCG-Pasteur (data not shown). This suggests that the loss of RD1 and the accumulation of a number of point mutations during the 230 passages in vitro likely account for the initial loss of virulence by 1921. Subsequent dissemination of BCG to various parts of the world, accompanied by changes in the manufacturing process, further affected the residual virulence and immunogenicity of individual BCG strains. As such, some strains are more virulent than others in animal models of infection [57] and also exhibit differential ability to induce adverse reactions (reactogenicity) following vaccination in neonates [58]. Our current work begins to provide some explanation for these observed differences (Fig. 3).


Novel genome polymorphisms in BCG vaccine strains and impact on efficacy.

Leung AS, Tran V, Wu Z, Yu X, Alexander DC, Gao GF, Zhu B, Liu J - BMC Genomics (2008)

Refined genealogy of BCG vaccines. The genealogy is modified from a previous model [24]. Genetic markers identified in this work are highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553098&req=5

Figure 3: Refined genealogy of BCG vaccines. The genealogy is modified from a previous model [24]. Genetic markers identified in this work are highlighted.
Mentions: The loss of the RD1-encoded ESX-1 protein secretion system during 1908–1921 contributes to the attenuation of BCG ([55], see also Fig. 3). However, because reintroduction of ESX-1 into BCG does not restore full virulence, other genetic lesions are also involved [56]. Whole genome sequence comparison reveals 2,223 single nucleotide polymorphisms (SNPs) between BCG-Pasteur and M. tb H37Rv, and 736 SNPs between BCG-Pasteur and M. bovis AF2122/97 [24]. NimbleGen analysis revealed 1,010 SNPs between BCG-Pasteur and M. tb H37Rv. Of which, 945 SNPs were correctly identified when comparing to the complete genome sequence of BCG-Pasteur. Thus the NimbleGen technique has a limited ability to detect SNPs but the majority of identified SNPs are accurate. Our NimbleGen analysis also revealed numerous SNPs (ranging from ~400 to ~1,800) between individual BCG strains and M. tb H37Rv, and the majority of changes detected by the NimbleGen technique are also present in BCG-Pasteur (data not shown). This suggests that the loss of RD1 and the accumulation of a number of point mutations during the 230 passages in vitro likely account for the initial loss of virulence by 1921. Subsequent dissemination of BCG to various parts of the world, accompanied by changes in the manufacturing process, further affected the residual virulence and immunogenicity of individual BCG strains. As such, some strains are more virulent than others in animal models of infection [57] and also exhibit differential ability to induce adverse reactions (reactogenicity) following vaccination in neonates [58]. Our current work begins to provide some explanation for these observed differences (Fig. 3).

Bottom Line: Moreover, we have uncovered various polymorphisms in the phoP-phoR locus.Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy.These findings have important implications for the development of a new generation of vaccines.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada. andreas.leung@utoronto.ca

ABSTRACT
Bacille Calmette-Guérin (BCG) is an attenuated strain of Mycobacterium bovis currently used as a vaccine against tuberculosis. Global distribution and propagation of BCG has contributed to the in vitro evolution of the vaccine strain and is thought to partially account for the different outcomes of BCG vaccine trials. Previous efforts by several molecular techniques effectively identified large sequence polymorphisms among BCG daughter strains, but lacked the resolution to identify smaller changes. In this study, we have used a NimbleGen tiling array for whole genome comparison of 13 BCG strains. Using this approach, in tandem with DNA resequencing, we have identified six novel large sequence polymorphisms including four deletions and two duplications in specific BCG strains. Moreover, we have uncovered various polymorphisms in the phoP-phoR locus. Importantly, these polymorphisms affect genes encoding established virulence factors including cell wall complex lipids, ESX secretion systems, and the PhoP-PhoR two-component system. Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy. These findings have important implications for the development of a new generation of vaccines.

Show MeSH
Related in: MedlinePlus