TABLE 1.

Comparison of MLST and SNP-based approaches used in study to assess genetic similarity between genomes.

Comparison of WGS-based typing methods used in study
Method	Approach	Reference	Genomic comparison result
cgMLST	Alignment to scheme of core loci found to be present in ≥ 98% of the representative Salmonella genomes used to build the EnteroBase (Achtman et al., 2012) allele scheme (n = 3,002)	Repository of allele calls for a set of core loci	Allele distance matrix; UPGMA phylogenetic tree
wgMLST (chromosome-associated loci)	Alignment to a scheme of all chromosome-associated loci (including core) (n = 22,457)	Repository of allele calls for a set of chromosome-associated loci	Allele distance matrix; UPGMA phylogenetic tree
wgMLST (all loci)	Alignment to scheme of all 22,457 chromosomal and an additional 2,901 plasmid loci, as well as 7-gene MLST loci (n = 25,365)	Repository of allele calls for a set of chromosome-associated loci and accessory loci, and 7-gene MLST scheme (Achtman et al., 2012)	Allele distance matrix; UPGMA phylogenetic tree
hqSNP	Mapping to reference genome; phage regions and plasmid contigs were masked	Closely related reference genome; [SNPs with less reliability were filtered out to produce a list of high quality SNPs (hqSNPs)]	SNP alignment and SNP distance matrix; maximum-likelihood phylogenetic tree

Adapted from Uelze et al. (2020).