Fig. 2

Definition of the plasmid types (A–I) observed in the 86 retrieved vanA complete plasmid sequences. a Network representation of the vanA complete plasmid sequences based on Mash distances (k = 21, s = 1000). Nodes (n = 76) in the network correspond to complete plasmid sequences and edges were defined if nodes shared a minimum Mash distance of 0.025. Edges correspond to connections between sequences with a similar k-mer composition. Nodes were colored according to the defined plasmid type assignment. Based on the modularity values and structure of the network components, we identified the plasmid types: A, B, C, D, E, G, H, and I. Twelve complete plasmid sequences (NC_014726.1, AP022823.1, NC_013317.1, NZ_CP012594.1, NC_005054.1, NZ_CP022486.1, NZ_CP014531.1, NZ_CP040238.1, E8172_3, NZ_CP036247.1, NZ_CP018130.1, NZ_CP019973.1) are not present in the network since they did not share any edges connecting to other nodes (singletons). b Heatmap and hierarchical clustering (ward.D2 method) of the pyani pairwise alignment coverage obtained from the 86 vanA complete plasmid sequences. On the left side, the plasmid types (A, B, C, D, E, F, G, H, I) previously defined in the network (panel a) are indicated. The twelve plasmid sequences corresponding to singletons are also included in this analysis