Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny

Shigella flexneri is a major health burden in low-and middle-income countries, where it is a leading cause of mortality associ-ated with diarrhoea in children, and shows an increasing incidence among travellers and men having sex with men. Like all Shigella spp., S. flexneri has evolved from commensal Escherichia coli following the acquisition of a large plasmid pINV, which contains genes essential for virulence. Current sequence typing schemes of Shigella are based on combinations of chromo-somal genetic loci, since pINV-encoded virulence genes are often lost during growth in the laboratory, making these elements inappropriate for sequence typing. By performing comparative analysis of pINVs from S. flexneri strains isolated from differ-ent geographical regions and belonging to different serotypes, we found that in contrast to plasmid-encoded virulence genes, plasmid maintenance genes are highly stable pINV-encoded elements. For the first time, to our knowledge, we have developed a S. flexneri plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of the vapBC and yacAB toxin???antitoxin (TA) systems, and the parAB partitioning system. This enables typing of S. flexneri pINV plasmids into distinct ???virulence sequence types??? (vSTs). Furthermore, the phylogenies of vST alleles and bacterial host core genomes sug-gests an intimate co-evolution of pINV with the chromosome of its bacterial host, consistent with previous findings. This work demonstrates the potential of plasmid maintenance loci as genetic characteristics to study as well as to trace the molecular phylogenesis of S. flexneri pINV and the phylogenetic relationship of this plasmid with its bacterial host.

Automated summary

This study found that plasmid maintenance genes are highly stable pINV-encoded elements in different strains of S. flexneri. The researchers also developed a plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of certain genes, which can classify pINV plasmids into distinct "virulence sequence types" (vSTs). Furthermore, the study suggests an intimate co-evolution of pINV with the chromosome of its bacterial host based on phylogenetic analysis. The findings demonstrate the potential of plasmid maintenance loci as genetic characteristics for studying the molecular phylogenesis of S. flexneri pINV and the phylogenetic relationship between this plasmid and its bacterial host.