Unraveling the biological and evolutionary consequences of in vivo IS6110 transposition in Mycobacterium tuberculosis through next generation sequencing
Next generation sequencing of flanking sites for the IS6110 element in clinical strains of M. tuberculosis
The insertion sequence IS6110 of Mycobacterium tuberculosis has been used extensively for epidemiological purposes, but the analysis of its biological effects has been limited by difficulties in identifying the precise chromosomal locations of insertion sites. Therefore, we developed a generally applicable method for the multiplexed sequencing and identification of insertion sites of transposable elements. This method enabled us to probe more than 500 clinical strains and map the “in vivo” transpositions of the IS6110 element. Using this strategy, we identified 6,976 insertions, 964 of which were unique in both coding and non-coding regions of the Mycobacterium tuberculosis genome. Several of the interrupted genes that we identified were proposed to be essential for virulence or in vitro growth. Specific IS6110 signatures were used to trace the evolution of the various clades and clusters within M. tuberculosis families. In addition, insertions correlated with strain traits or epidemiological data. These findings imply that the analysis of IS6110 transposition is not only useful in epidemiology but can also provide insight into the mechanism of strain evolution and the specification of in vivo traits.