Fig. 3.

Distribution of restriction-modification genes and virulence/AMR genes in bovine IMI-associated S. aureus . The phylogenomic tree of 65 bovine IMI-associated S. aureus and relevant genetic content show lineage-specific R-M genes. Virulence and AMR genes are either ST-specific or isolate-specific. In the Type I R-M system, the green circular boxes indicate the Type I R-M system genes (hsdR and hsdMS) that are located in νSaα and νSaβ and are part of the core genome. The blue circular boxes show additional Type I R-M hsdRMS genes which are not a part of the S. aureus core genome. The hsdR and hsdM genes are highly conserved within the S. aureus species; however, several hsdS alleles exist. While each of the hsdMS genes shown in green are interchangeable, part of the same R-M system, and should, in combination with the hsdR, form a functional complex, the Type I R-M system genes shown in blue would not be expected to be interchangeable, and would instead form a separate, and independent Type I R-M system. The black circular boxes represent Type II R-M genes that encode a pair of enzymes: a methyltransferase and a restriction endonuclease. The red and the black square boxes represent virulence and AMR genes, respectively. The open circular boxes in all shapes and colours indicate the presence of a pseudogene. The red and green checkmarks indicate signal molecule (AIP-I and AIP-II) and capsular polysaccharide (CP5 and CP8). The highlighted isolates were associated with clinical mastitis. M1 is used to indicate that the milk sample was collected on the day clinical mastitis was diagnosed, and M2 indicates the sample was collected 14 days after a diagnosis of clinical mastitis was made. An extended report of each of the R-M genes identified in all isolates included in this study can be found in Fig. S1.