De novo assembly for each read set was performed using the assembler Velvet (version 1.2.03) and VelvetOptimizer, with each read set mapped back to each assembly (Zerbino & Birney, 2008). Contigs < 300 bp were discarded. Assemblies were annotated using the rapid prokaryotic genome annotation tool Prokka (Seemann, 2014). To identify contigs associated with the accessory genome, contigs were first-ordered with S. sonnei Ss046 and its large virulence plasmid pSS046 as references using abacas. The remaining contigs were visualized and examined in Artemis. Presence of specific accessory genetic determinants was confirmed by blast and visualized using act (Carver et al., 2008).