Phylogenetic relationships among methicillin-resistant Staphylococcus aureus isolates from 3 patients (Patients A–C). We applied stable core genome multilocus sequence typing (cgMLST) to identify cluster types with default parameters using the S aureus COL-type strain as a reference and a standard set of 1861 genes for gene-by-gene comparisons. For distance calculations, we used only cgMLST target genes that were present in all 20 isolates, meaning that 42 of the 1861 genes were not used. The minimum spanning tree depicting a cgMLST-based comparison of whole-genome sequencing data. Each branch represents 1 isolate. The numbers on the connecting lines illustrate the number of allelic differences based on a pairwise comparison.