Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866

Abstract

Shigella sonneiis responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, wepresent the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophageinfections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termedp866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, andtrimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbonewith previously described IncB/O/K/Z-typeShigellaspp. andEscherichiacoliplasmids, but is differentiated by the insertion of antibioticresistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derivedphylogenetic reconstruction showed the evolutionary relationships ofS. sonneistrain 866 and the four establishedShigellaspecies,highlighting the clonal nature ofS. sonnei.