Fig. 2.—

Phylogeny of C. suis isolates. The genome drafts from US strains (Joseph et al. 2016), reference strain S45 and strain MD56 (Donati et al. 2014) are included. Indicated alongside Swiss samples are the farms from which the isolates originate, showing the diversity within each farm, and the antibiotic regimen used. Presence of tetC in the genome is indicated. Seven paired isolates taken from the same pig before and after the fattening period are also indicated in matched colors. The location of the assembly of sample 14-23b in the phylogeny suggests that it contains mixed isolates from both clades, in addition to being of low coverage (mean 12×). Bootstraps on all branches are in excess of 97% except where shown. Scale bar indicates number of substitutions per site.