Fig. 3

Maximum likelihood phylogram of the genetic relatedness of selected isolates based on WGS. Isolates are represented by shapes: isolates from Outbreak 1 are triangles, Outbreak 2 are ovals, and Outbreak 3 are rectangles. Black filled shapes are isolates from water and white filled shapes are from clinical isolates. Color outline on shapes represents households. Shapes with the same outline color are from the same household. Black color outline is for four isolates where only one strain was sequenced in the household. The numbers are the household IDs. The length of the radial lines connecting isolates are proportional to number of SNVs between isolates. The SNVs were identified using the strain S002604 as the reference for the core-genome alignment and using only the contigs bigger than 10Kb to remove the potentially low assembly quality regions, which represent less than 5% of the genomes