MLST was determined by submitting contigs to pubMLST (pubmlst.org, The Department of Zoology, University of Oxford, UK) and MLST-based trees were visualized with goeBURST [110] (S2 Fig). Agr-typing was performed by comparing reference sequences for agrD type I, II and III (WP_001830021.1, WP_002447813.1, WP_002468352.1, respectively) using the blast algorithm against the isolates from this study (CLC Workbench, Qiagen, Hilden, Germany). We screened for CRISPR-Cas by searching for cas1, cas2 and cas10, and if positive, the cas locus was typed as described previously [111]. CRISPR regions were identified with CRISPRFinder [112]. The combination of a complete cas-gene locus and confirmed CRISPR-region are annotated as putative functional CRISPR-Cas system.

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