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Whole-genome phylogenetic tree of the 39 E. coli isolates. Phylogenetic relationship of E. coli isolates based on core SNPs from whole-genome sequencing. Isolate and farm IDs are presented in the inner ring. The phylogroups are represented by different colors in the middle ring. The next ring indicates the multi-locus sequence type (MLST; Warwick scheme); the outermost ring indicates the O and H antigen groups assigned by genoserotyping. The image was generated with ITOL (v. 6).
