Swab samples were collected from each of 7 sites during each of 5 visits, including from nares and areas rarely affected by AD in children (forearms). Patient treatment for AD with standard treatment of care, with or without bleach baths, was monitored closely between the first four visits (STAR Methods). From each swab, up to 10 colonies were cultured and processed for whole-genome sequencing. We then grouped isolates from each patient into lineages such that isolates from the same lineage are fewer than 100 mutations across the core genome and performed more detailed evolutionary analysis using alignment of raw reads to lineage-specific assemblies built from reads of all isolates in a lineage. Isolates separated by 0 mutations in this more detailed analysis are then grouped into a single genotype.
