Fig. 3

Composition of the S. aureus accessory genomes. a-c Comparison of human- and animal-derived isolates showing the (a) distribution of SCCmec elements, (b) distribution of AMR and virulence determinants, and (c) the number of different rep families. d-f Comparison of the three dominant STs (ST5, ST8, and ST30) showing the (d) the number of accessory genes, (e) distribution of AMR and virulence determinants, and (f) the number of different rep families. Intensity of box shading in panels b and e indicates the proportion of genomes harboring at least one gene conferring resistance to an antimicrobial class (red) and virulence mechanism (blue). In panels c, d and f, colored dots represent genomes in each category. In the violin plots, the mean value is represented by the red dot, box represents the interquartile range, horizontal line in the middle of the box represents the median, and the lower and upper whiskers represent the lowest data point without the outliers and the highest data point without outliers, respectively. Details of the distribution of specific genes related to AMR, virulence and plasmids are presented in Supplementary Table S1