Fig. 4

Phylogenetic tree of the examined isolates, constructed from SNPs identified by the CSI Phylogeny pipeline, using NC_007795.1 as the reference. The alignment of the high-quality SNPs contained 9391 sites and the percentage of genomes covered by all isolates was 91.8%. The maximum-likelihood phylogeny was inferred using RAxML v8.1.22 with GTRGAMMA model and 1000 bootstrap replicates. VF40237–16-SP1, VF40237–16-SP2, VF40237–16-SP3, 7–2018-SP4: outbreak-associated clinical isolates; VF27322–15: isolate from a sporadic case of methicillin-resistant S. pseudintermedius infection; NC_017568.1: reference isolate. The median, minimum, and maximum pairwise SNP differences among isolates are shown near the root of each cluster, with the minimum and maximum in parentheses. Scale bar, number of substitutions per site