Impact of insertion sequences on convergent evolution of Shigella species

Shigellaspecies are specialised lineages ofEscherichia colithat have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies ofShigellaevolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individualShigellaspecies have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent inShigellagenomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations ofShigella dysenteriaeSd1,Shigella sonneiandShigella flexneri. We find that five IS (IS1, IS2, IS4, IS600and IS911) have undergone expansion in allShigellaspecies, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced inS.dysenteriaeand least advanced inS.sonnei; and using genome-scale models of metabolism we show thatShigellaspecies display convergent loss of coreE.colimetabolic capabilities, withS.sonneiandS.flexnerifollowing a similar trajectory of metabolic streamlining to that ofS.dysenteriae. This study highlights the importance of IS to the evolution ofShigellaand provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species. Author summary Originally classified as a genus due to shared disease features,Shigellaspecies actually represent distinct lineages ofEscherichia colithat have become human-restricted dysentery pathogens via convergent evolution. A hallmark of this host-adaptation is the accumulation of insertion sequences (IS), which interrupt genes and cause deletions or genome rearrangements. Due to technical limitations in identifying IS insertions from short-read data, our understanding of the contribution of IS to the evolution ofShigellaand other host- restricted bacteria has relied on analyses of either single genome representatives, or small numbers of genomes, and there are no large-scale population genomic studies exploring IS dynamics within bacterial species. Here we explore IS variation within and betweenShigellaspecies, revealing their historical and ongoing contributions to evolutionary convergence and metabolic streamlining.