We describe here the genetic analysis of a vancomycin-susceptible Staphylococcus aureus (VSSA) strain, Mu50Omega, a strain related to vancomycin-intermediate S. aureus (VISA) strain Mu50. Using a combination of Mu50Omega whole-genome sequencing and genome engineering, we observed a stepwise evolution of vancomycin resistance from VSSA to VISA after the mutated vraS and graR genes of Mu50 were engineered into Mu50Omega.