1. Whole-genome sequence reads of Shigella sonnei used in this study have been deposited to the European Nucleotide Archive. The run accession numbers and related metadata are detailed in Table S1 which has been deposited in FigShare: http://figshare.com/articles/The_introduction_and_establishment_of_fluoroquinolone_resistant_Shigella_sonnei_into_Bhutan/1610693