Sequencing reads were assembled using the genome assembler pipeline Shovill v1.1.0. Briefly, the Shovill pipeline included read trimming using Trimmomatic v0.39, de novo assembly with SPAdes v3.15.5 and genome polishing with Pilon v1.24. After the pipeline, additional polishing was performed by mapping the reads back to the contigs with BWA v0.7.17 and sorting the resulting SAM/BAM files using SAMtools v1.15.1. Pilon v1.24 was then used to correct bases, fix mis-assemblies and fill gaps. The reformat.sh script from the Bbmap package v38.76 (-minlength=1000) was used to filter out contigs less than 1000bp. The draft genome assemblies were then annotated with Bakta v1.7.0. Single nucleotide polymorphism (SNP) detection between WT (WTref) and SS (SSref) samples were then performed using snippy v4.6.0, where both WT and SS samples were inputted as the reference genome in turn. A subset of the snippy output files are uploaded here and contain all variants found.