For each isolate, the entire resistance gene content (resistome) was identified by mapping the assembly to a manually curated resistome database as described previously (Chung The et al., 2015). MLST was performed for all Shigella isolates by profiling the seven MLST genes (adk, fumC, gyrB, icd, mdh, purA, recA). Mutations in specific genes were manually assessed by retrieving their alignments from the annotations and the effects of non-synonymous mutations were predicted using the sift web server (http://sift.jcvi.org/) (Sim et al., 2012). An in silico plasmid incompatibility-type PCR was performed using an in-house script and bespoke primer set.