Phylogenetic tree data for 200 strains used in the associated manuscript.

Data from Figure 6: Associations and dissociations between efflux pump genes and accessory gene functional categories in E. coli.

Data from Figure 6: Associations and dissociations between efflux pump genes and accessory gene functional categories in E. coli.

Figure 5: Network models of the coincidence analysis on selected E. coli genomes by Coinfinder. Networks for (A) gene-gene associations, and (B) dissociations, are shown. Networks were laid out using the Frutchterman Reingold layout algorithm. Nodes are sized based on lineage independence. Node colours of gene networks denote different gene families.

Figure 5: Network models of the coincidence analysis on selected E. coli genomes by Coinfinder. Networks for (A) gene-gene associations, and (B) dissociations, are shown. Networks were laid out using the Frutchterman Reingold layout algorithm. Nodes are sized based on lineage independence. Node colours of gene networks denote different gene families.

Phylogenetic tree data for 200 strains used in the associated manuscript.

Data from Figure 4:Efflux pump encoding genes present in thein the E. coli core genome and accessory genome.Relative proportion of core and accessory genome, and fractions of each that comprise efflux pumps of each of the main efflux pump families (note that no PACE family efflux pump genes were found).ABC—ATP-Binding Cassette Family, MATE—multi-drug and Toxin Extrusion, MFS—Major FacilitatorSuperfamily, PACE—Proteobacterial Antimicrobial Compound Efflux, RND—Resistance-Nodulation cell Division, SMR—Small Drug Resistance.

Data from Figure 4:Efflux pump encoding genes present in thein the E. coli core genome and accessory genome.Relative proportion of core and accessory genome, and fractions of each that comprise efflux pumps of each of the main efflux pump families (note that no PACE family efflux pump genes were found).ABC—ATP-Binding Cassette Family, MATE—multi-drug and Toxin Extrusion, MFS—Major FacilitatorSuperfamily, PACE—Proteobacterial Antimicrobial Compound Efflux, RND—Resistance-Nodulation cell Division, SMR—Small Drug Resistance.

Data from Figure 6: Associations and dissociations between efflux pump genes and accessory gene functional categories in E. coli.

Data from Figure 3: Pangenome of E. coli genomes used in this study. (A)Gene presence/absence matrix representation of the pangenome. A total of 40,442 clusters of gene groups were identified through Roary using 95% BLAST identity. Genes that are present in each isolate are represented by a blue marker. Genes that were found to be present in all strains are situated in the core and the rest of the pangenome is classed as the accessory genome. The tree next to the matrix represents the phylogeny of the input genomes. (B) Relationship between pangenome size and and number of genomes considered. The total number of genes continues to grow logarithmically, while the number of conserved genes declines at a slow rate, highlighting that this is an open pangenome.