One pan-genome per infection was generated by merging all genes in the presence/absence matrix produced by the Roary pipeline version 3.11.2 [106], and sequences from all single isolates from that same infection were aligned for SNP calling using the Freebayes tool [107]. Annotations of SNPs were conducted by snpEff [108] based on the annotation of the pan-genome that was carried out with GAMOLA2[109].

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