Whole Staphylococcus aureus genomes cultured longitudinally from diabetic foot ulcers

The goal of this study was to characterize the genomic and phenotypic contributors to strain-dependent effects of S. aureus on diabetic wound healing. S. aureus isolates were cultured from deep fluid swabs as part of a longitudinal prospective cohort study of 100 patients with neuropathic diabetic foot ulcers (DFU). As described in accompanying publications, subjects with neuropathic DFU were enrolled and underwent standardized sharp debridement at visit 0. Deep fluid swabs (Levine's technique) were collected every two weeks until healing, amputation, or the end of 26 weeks. Swabs were plated under multiple media conditions including chromogenic selection plates for S. aureus, and 221 S. aureus isolates total were cultured from 60 S. aureus-positive DFU. Sampling took place between September 2008 and October 2012 at the University of Iowa Hospitals and Clinics and the Iowa City Veteran's Affairs Medical Center. All isolates were sequenced with either paired-end Illumina or a combination of paired-end Illumina and Oxford Nanopore sequencing. Quality-control filtering yielded 220 de novo-assembled S. aureus whole genome sequences (described in Campbell, McCready-Vangi et al. 2023). Metadata by sequence (including patient ID and week collected) is included with the BioProject and more extensive clinical metadata by patient will be made available in Campbell, McCready-Vangi et al. (2023) as a supplementary table.