Genome Sequencing and Analysis of BCG Vaccine Strains

Abstract

BackgroundAlthough the Bacillus Calmette-Guérin (BCG) vaccine against tuberculosis (TB) has been available for more than 75 years, one third of the world's population is still infected with Mycobacterium tuberculosis and approximately 2 million people die of TB every year. To reduce this immense TB burden, a clearer understanding of the functional genes underlying the action of BCG and the development of new vaccines are urgently needed.Methods and FindingsComparative genomic analysis of 19 M. tuberculosis complex strains showed that BCG strains underwent repeated human manipulation, had higher region of deletion rates than those of natural M. tuberculosis strains, and lost several essential components such as T-cell epitopes. A total of 188 BCG strain T-cell epitopes were lost to various degrees. The non-virulent BCG Tokyo strain, which has the largest number of T-cell epitopes (359), lost 124. Here we propose that BCG strain protection variability results from different epitopes. This study is the first to present BCG as a model organism for genetics research. BCG strains have a very well-documented history and now detailed genome information. Genome comparison revealed the selection process of BCG strains under human manipulation (1908–1966).ConclusionsOur results revealed the cause of BCG vaccine strain protection variability at the genome level and supported the hypothesis that the restoration of lost BCG Tokyo epitopes is a useful future vaccine development strategy. Furthermore, these detailed BCG vaccine genome investigation results will be useful in microbial genetics, microbial engineering and other research fields.

Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG)

“…Our analysis revealed that compared with the M. tuberculosis H37Rv reference sequence, ~120 genes were lost in BCG strains including 33 genes that encode as many as 380 M. tuberculosis T cell epitopes. These results confirm and extend the findings of Zhang et al using a smaller dataset corresponding to one third of the currently known M. tuberculosis T cell epitopes [30]. In contrast to the findings of that study, we found that BCG Pasteur, and not BCG Phipps, has the largest number of T cell epitope sequences depleted from its genome.…”

“…RD2 delimits the border between the early and the late BCG vaccines. The unique presence of the 60 RD2-encoded epitopes in BCG Russia and Japan led the same authors to propose that these strains represent superior candidates for development of a new vaccine against TB [30]. However, the results of clinical trials do not provide evidence for a correlation between the strain of vaccine used and the efficacy in preventing tuberculosis [7] [31] [32] [33].…”

MTBVAC from discovery to clinical trials in tuberculosis-endemic countries

“…The majority (82%) of these absent epitopes are contained in 6 antigenic proteins encoded in RD1 and RD2 deleted in BCG strains. These and related studies further suggested that epitope sequence variation in BCG potentially affects human T cell recognition that could result in ineffective priming of the host immune system [16,17,[50][51][52].…”

“…It is thought that over-attenuation of BCG due to loss of important immunodominant antigens (e.g. those in the region of difference 1 (RD1) region) in the process of its attenuation by repeated subcultivation passaging in nonstandardized conditions could be one of the reasons [16,17]. Moreover, large number of human clinical trials suggest that revaccination with BCG does not provide additional benefit, which could be due to preexisting heterologous immunity resulting from infection with nontuberculous environmental mycobacteria (NTM), a process known as masking and blocking [18,19].…”

Prospects in Mycobacterium bovis Bacille Calmette et Guérin (BCG) vaccine diversity and delivery: Why does BCG fail to protect against tuberculosis?

“…Recent studies showed that 188 T cell epitopes essential to the human immune response to M.tb infection had been lost, to varying degrees, in all BCG substrains [48]. BCG Tokyo-172 substrain had the highest number of T cell epitopes in relation to M.tb strains; however this BCG substrain has consistently induced poor immunity against TB in animal models and in clinical trials [4;40].…”