S. aureus clinical isolate sequencing.

DNA was isolated from bacterial cultures grown overnight using the DNeasy blood and tissue kit (catalog number 69504; Qiagen) according to the manufacturer’s instructions. Whole-genome sequencing was performed at the Genome Technology Access Center at the Washington University in St. Louis School of Medicine using an Illumina NovaSeq 6000 instrument with an S4 flow cell and 2-by-150 paired-end reads. Sequence reads were aligned to the reference genome using NovoAlign. USA300_FPR3757 (NCBI accession number {"type":"entrez-nucleotide","attrs":{"text":"NC_007793.1","term_id":"87159884","term_text":"NC_007793.1"}}NC_007793.1) was used for the USA300 reference genome, and N315 (NCBI accession number {"type":"entrez-nucleotide","attrs":{"text":"BA000018.3","term_id":"47118324","term_text":"BA000018.3"}}BA000018.3) was used for the USA100 reference genome. The alignments were sorted with SAMtools. Picard Tools was used to remove duplicate reads. Variant files and BAM alignments for each clinical isolate were analyzed using Geneious Prime v. 2021.0.1.