Figure 3

ClonalFrame 75% majority-rule consensus phylogeny (node posterior probabilities are at least 0.75). Posterior probabilities for major lineages are shown at nodes. Dashed circles show each clonal complex (CC) and grey shading shows isolates assigned to the two clusters (A and B) determined by the Structure analysis. Taxa labels are colored as follows: red = canine isolate, blue = bovine isolate, green = feline isolate. The first number in the label shows isolate ID. For canine isolates, tissue source follows the isolate ID, which is followed by the ST. Tissue source abbreviations are as follows: thr = throat, vag = vaginal, uri = urine, der = dermis, wou = wound exudate. For bovine and feline isolates, the ID is followed by the geographic location of collection (ITA = Italy, BEL = Belgium, NY = New York state, USA). Strain 227.NY.1 (underlined) is the strain who’s genome was sequenced in this study. Circles with white centers indicate those strains that contained the plasmid discussed in the text. The strain shaded in dark grey (166.thr.7) was grouped with CC4 members based on ClonalFrame analysis but it was not contained within CC4 based on eBURST.