Here are the scripts to generate data and plots (Main and Extended Figures) for the relevant manuscript. Shotgun sequencing data, BSI isolate assemblies, and clinical metadata is available in the NCBI repository under BioProject PRJNA884103 (Reviewer link available https://dataview.ncbi.nlm.nih.gov/object/PRJNA884103?reviewer=45mncs5d0b4fvgqknbn6m74741).
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