Fig. 4

Presence or absence of antibiotic resistance genes amongst global CC59 isolates. SRST2 was used to map the raw sequencing reads for CC59 isolates against the ARG-ANNOT database of genes known to be associated with antibiotic resistance. The distribution of genes is plotted against the core genome phylogeny, with presence of a gene indicated by a blue rectangle. Column names are in the form “X_Y”, where X is the abbreviated name of the gene, and Y is the abbreviated name of the class(es) of antibiotic to which the gene is associated with resistance. The presence of amino acid variants associated with ciprofloxacin resistance is plotted, with resistant genotypes indicated in blue (e.g. A_BCD, where A is the gene name, C is the position of the variant amino acid, B is the residue of the susceptible wild type and D is the residue of the resistant type). Presence of Panton-Valentine leukocidin (PVL) is also indicated by blue rectangles and a subclade of the East Asia clade associated with PVL carriage is indicated by a yellow dot