The dataset contains data pertaining to the examination of draft genomes of 388 methicillin-resistant Staphylococcus aureus isolates obtained from intensive care unit patients at three geographically distributed hospitals. The purpose of the study was to determine genomic diversity associated with potential health care worker-associated transmission. Relevant statistics, including linked GenBank and SRA accession numbers for each genome assembly, are included in Table 1 of the associated publication.