Fig. 1

Maximum-likelihood (ML) phylogeny of 36 HA-MRSA isolates recovered from Egyptian health care settings. The phylogenetic tree was constructed based on core genome SNPs using Parsnp tool and Gblocks v0.91b to remove contiguous non-conserved regions from the alignment. CIPRES-hosted RAxML-HPC v8 was utilized to construct the ML phylogeny from the core genome alignment with a General Time Reversible model, GAMMA substitution rate and rapid bootstrapping (n = 1000). iTOL was utilized for visualization of the ML tree and the Meta data. Meta data includes ST types, clonal complexes; Spa types, SCCmec type, and PVL presence are color-coded in the inner rings