Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette–Guérin (BCG) Tokyo 172: A comparative study of BCG vaccine substrains

To investigate the molecular characteristics of bacillus Calmette–Guérin (BCG) vaccines, the complete genomic sequence of Mycobacterium bovis BCG Tokyo 172 was determined, and the results were compared with those for BCG Pasteur and other M. tuberculosis complex. The genome of BCG Tokyo had a length of 4,371,711 bp and contained 4033 genes, including 3950 genes coding for proteins (CDS). There were 18 regions of difference (showing differences of more than 20 bp), 20 insertion or deletion (ins/del) mutations of less than 20 bp, and 68 SNPs between the two BCG substrains. These findings are useful for better understanding of the genetic differences in BCG substrains due to in vitro evolution of BCG.