Genomic inversions in two major Pseudomonas aeruginosa clonal lineages detected by long-read sequencing

Recombination events are a major driver of Pseudomonas aeruginosa genome evolution causing high genome plasticity. before full genome sequencing of bacteria became feasible, bacterial genomes were analysed and compared by physical genome mapping. Mapping of clonally related strains from chronic airway infections of people with cystic fibrosis has revealed the occurrence of large chromosomal deletions, insertions and inversions as genome architecture re-shaping events. Since then, P. aeruginosa genomes were barely screened for inversions despite sequencing of thousands of isolates, presumably because conventional second generation sequencing could not resolve the recombination breakpoints. By long-read PacBio or MinION sequencing of isolates of the two major P. aeruginosa clones we could demonstrate the general applicability of these methods for the reliable detection of inversions in bacterial chromosomes. The sequencing data displayed the involvement of highly mobile IS elements, transposons or other accessory DNA elements. These sequences typically flank the inverted segments and presumably triggered the recombinations that occur more frequently than documented in genome sequencing projects.