FIGURE 1.

Maximum likelihood phylogeny constructed using core SNPs identified among 570 Salmonella isolate genomes. Publicly available genomes are denoted by black tip labels (n = 442), while genomes of bovine- and bovine farm-associated strains isolated in conjunction with this study are denoted by colored tip labels (n = 128). In cases where a discrepancy existed between the traditional serotype designation of an isolate and one or more in silico methods (i.e., SISTR and SeqSero2), the serotype assigned using two out of the three methods was selected as the final serotype to be used for phylogeny annotation. The phylogeny is rooted at the midpoint with branch lengths reported in substitutions per site. Core SNPs were identified among all genomes using kSNP3, while the phylogeny was constructed and annotated using IQ-TREE and bactaxR/ggtree, respectively.