Fig. 3: ColV-like plasmids (ColVLPs) and co-resident plasmids in a 100 Sequence Type (ST) E. coli draft genome database.
From: Convergence of plasmid-driven virulence and antibiotic resistance in Escherichia coli
Presence of additional replicons in ColVLP+ draft genomes of the A 100ST database and B top 10 ColVLP+ STs within the 100ST database. The 100ST database consists of 9969 draft E. coli genomes from the top 100 STs in Enterobase. Replicon co-carriage network in the C 100ST, D ST95 and E ST131 (Clade B) databases. The ST95 and ST131 (Clade B) databases consist of 2118 and 344 draft genomes, respectively. ColVLPs were plotted as a separate node from IncF plasmids (IncF non-ColVLP). Total plasmid co-carriage events (n ≥ 10) were plotted using Cytoscape v3.9.1. Red lines denote the top four associations with ColVLPs. Line thickness between nodes is proportional to the number of co-carriage events. F Percent of ColVLP+ isolates in the 100ST, ST95 and ST131 Clade B databases. ColVLP+ isolates were tallied regardless of co-carriage events. Plasmid combinations of ColVLP+ isolates in the G 100ST, H ST95 and I ST131 (Clade B) databases. Plasmid combination frequency was normalised to the total number of ColVLP+ isolates in each database. The top six combinations of each database are shown. ColVLPs were identified using the criteria of Liu et al.6. Additional replicons were identified using ABRicate v0.8 against the PlasmidFinder42 database using a 100% query length threshold. Figure acronyms: ST sequence type. Source data are provided as a Source data file in Supplementary Data 5,7 and 8.
