The association of genes from the accessory genome to infection or commensalism was analysed. To that end a gene presence/absence matrix for the accessory genome was built with Roary version 3.11.2 running with the default parameter setting (sequence identity  =  95%) for protein alignment [106]. Each gene’s association was tested with Scoary version 1.6.16 with default parameter settings [122]. Followed by adjustment for multiple testing with the Benjamini-Hochberg[63]. Associated ORFs were annotated by hand according to gene category (main categories mobilome/chromosomal, mobilome divided into plasmid-association, phage-association, SCCmec, ACME, general mobilome (IS elements, transposases)).

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