FIG 2.

Comparison of clustering methods for Derby pulsotypes from MW. (A) PFGE analysis of Derby isolates from MW and Hawaii clinics (black dots indicate clinical samples; not all MW samples are shown). The dendrogram splits isolates into three major clusters. (B) Generalized time-reversible/gamma maximum likelihood phylogenetic tree from alignment of core pangenome (generated from Roary [48] alignment via RAxML [49], visualized in iTOL [50]). (C) cgMLST minimum spanning tree for MW Derby pulsotypes. Branch lengths correspond with allelic differences over 3,002 loci in the EnteroBase cg-MLST scheme for Salmonella (45). The minimum spanning tree was generated with GrapeTree using the online web tool (46).