Insertion sequence evolutionary patterns highlight convergent genetic inactivations and recent genomic island acquisitions among epidemic Burkholderia cenocepacia.

The Burkholderia cenocepacia B&B clone was found previously to be responsible for an epidemic outbreak within an intensive care unit in France. This clone belongs to the ST32 clonal complex, which is one of the most prevalent among French cystic fibrosis patients and is known to be related to the highly virulent ET12 clonal complex. Genomic repartition biases of insertion sequences (ISs) were investigated to improve our understanding of the evolutionary events leading to B. cenocepacia diversification and the emergence of such epidemic lineages. IS were used for tracking convergent genetic inactivations and recent DNA acquisitions. B. cenocepacia IS families and subgroups were compared in terms of genetic diversity and genomic architecture using fully sequenced genomes, PCR screening and DNA blot analysis. These analyses revealed several features shared by the B&B and ET12 epidemic clones. IS elements showed a frequent localization on genomic islands (GI) and indicated convergent evolution towards inactivation of certain loci. The IS407 subgroup of the IS3 family was identified as a good indicator of recently acquired GIs in clone ET12. Several IS407 elements showed strain-specific or clonal complex-specific localizations. IS407 DNA probing of a DNA library built from the B. cenocepacia B&B epidemic clone led to the identification of a recently acquired IS407-tagged GI likely to be conjugative and integrative. The B&B clone showed significant differences in its IS architecture from that of ST32 strains isolated from Czech cystic fibrosis patients.