Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained from seven hospitals during a one-week period in 2010. We employed a framework integrating Staphylococcus protein A typing and full-genome next-generation sequencing. Single nucleotide polymorphisms were analyzed using phylodynamics. Twenty-six t002, 48 t008, and 23 other strains were identified. Phylodynamic analysis of 30 t008 strains showed ongoing exponential growth of the effective population size the basic reproductive number (R0) ranging from 1.24 to 1.34. No evidence of hospital clusters was identified. The lack of phylogeographic clustering suggests that community introduction is a major contributor to emergence of CA-MRSA strains within hospitals. Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control.