Fig. 3

Pan-genome analysis of isolates from the five predominant production companies. The predominant production companies are presented as A, D, E, K, and M. Color-coding of isolate names by production company and color-coding of phylogenetic tree branches by CC follow the same color schemes as Fig. 2. The percent similarity of isolates within a cluster is defined as the percentage of shared genes from a total of 8373 genes. The presence of the classical VAGs epf, mrp, and sly is represented in green and the proposed VAGs ofs and srtF in orange