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A comparative genomic microarray comprising 2,457 genes from two whole genomes of  S. aureus  was employed for the comparative genome hybridization analysis of 50 strains of divergent clonal lineages, including methicillin-resistant  S. aureus  (MRSA), methicillin-susceptible  S. aureus  (MSSA), and swine strains in China. Large-scale validation was confirmed via polymerase chain reaction in 160 representative clinical strains. All of the 50 strains were clustered into seven different complexes by phylogenetic tree analysis. Thirteen gene clusters were specific to different  S. aureus  clones. Ten gene clusters, including seven known (vSa3, vSa4, vSaα, vSaβ, Tn5801, and phage ϕSa3) and three novel (C8, C9, and C10) gene clusters, were specific to human MRSA. Notably, two global regulators,  sarH2  and  sarH3 , at cluster C9 were specific to human MRSA, and plasmid pUB110 at cluster C10 was specific to swine MRSA. Three clusters known to be part of SCCmec, vSa4 or Tn5801, and vSaα as well as one novel gene cluster C12 with homology with Tn554 of  S. epidermidis  were identified as MRSA-specific gene clusters. The replacement of ST239- spa  t037 with ST239- spa  t030 in Beijing may be a result of its acquisition of vSa4, phage ϕSa1, and ϕSa3. In summary, thirteen critical gene clusters were identified to be contributors to the evolution of host specificity and antibiotic resistance in Chinese  S. aureus .

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Identification of Gene Clusters Associated with Host Adaptation and Antibiotic Resistance in Chinese Staphylococcus aureus Isolates by Microarray-Based Comparative Genomics