Fig. 5. Phylogenetic trees of 515 multidrug-resistant E. coli isolates from pig farms together with 287 publicly available draft genomes of human commensal E. coli across China.

a Circular tree showing the phylogenetic relationship of the 802 E. coli isolates. The tree was generated based on the core genome SNPs using the snippy-multi program implemented in Snippy v 4.4.0 (https://github.com/tseemann/snippy), and was rooted on the E. fergusonii sequence. The snippy based tree was inferred using FastTree2, and was visualized using the Interactive Tree Of Life (iTOL v.5). Raw data for the Snippy tree and its annotation codes are provided in Supplementary Data 12; b Venn diagram showing the shared and unique sequence types between pig farm-originating E. coli and human commensal E. coli.