List of core genome sites included in our analysis. Site numbers are relative to the published ST59 genome used as a reference for mapping short reads (GenBank accession CP003166). (TXT 20378 kb)

Output from in silico antibiotic resistance testing. Genes associated with antibiotic resistance were detected using SRST2. Gene presence is denoted by the name of the gene (asterisks indicates at least one mismatched SNP or indel and a question mark indicates some low-depth bases, as described on the SRST2 website: https://github.com/katholt/srst2 ). Gene absence is denoted by a hyphen. The amino acid residue (IUPAC single letter code) is given for gyrA, grlA and grlB sites associated with fluoroquinolone resistance. Presence or absence of PVL based on mapping of short reads to lukF-PV and lukS-PV reference sequences is also reported. (XLSX 16 kb)

Genes associated with either USA or East Asia clade. Genes whose presence differed significantly between the USA and East Asia clades are listed. We also report the proportion of isolates within the USA and East Asia clades for which each gene was present and note those that share the same pattern of presence or absence across the isolates (identified by having the same â column patternâ ). Results for genes whose presence differed significantly between the USA and Taiwan isolates (as opposed to the USA and East Asia clades) are presented in a separate worksheet. (XLSX 26 kb)

Genes associated with either USA or East Asia clade. Genes whose presence differed significantly between the USA and East Asia clades are listed. We also report the proportion of isolates within the USA and East Asia clades for which each gene was present and note those that share the same pattern of presence or absence across the isolates (identified by having the same â column patternâ ). Results for genes whose presence differed significantly between the USA and Taiwan isolates (as opposed to the USA and East Asia clades) are presented in a separate worksheet. (XLSX 26 kb)

List of core genome sites included in our analysis. Site numbers are relative to the published ST59 genome used as a reference for mapping short reads (GenBank accession CP003166). (TXT 20378 kb)

Output from in silico antibiotic resistance testing. Genes associated with antibiotic resistance were detected using SRST2. Gene presence is denoted by the name of the gene (asterisks indicates at least one mismatched SNP or indel and a question mark indicates some low-depth bases, as described on the SRST2 website: https://github.com/katholt/srst2 ). Gene absence is denoted by a hyphen. The amino acid residue (IUPAC single letter code) is given for gyrA, grlA and grlB sites associated with fluoroquinolone resistance. Presence or absence of PVL based on mapping of short reads to lukF-PV and lukS-PV reference sequences is also reported. (XLSX 16 kb)