Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Abstract

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery(1,2), spreading efficiently via low-dose fecal-oral transmission(3,4). Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality(4-6). Classical approaches have shown that S. sonnei is genetically conserved and clonal(7). We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage.

Figure 1. Bayesian maximum clade credibility phylogeny for S. sonnei

Branches defining major lineages in bold (each had 100% posterior support); pie charts indicate ML estimates for geographic origin of major nodes, according to inset legend (lower left). Time (x-axis) is relative to the Common Era; divergence dates (median estimate and 95% HPD) are given in blue for major nodes. Distribution of antimicrobial resistance determinants is indicated in the heatmap according to the legends provided, which reflect percentage of bases in each gene sequence that are covered by reads from each isolate (top right). Geographically localised clonal expansions are highlighted on the right, labeled with their median estimated divergence date.