Fig. 4: Population chromosome and plasmidome show stable genome sizes (bp) over time and plasmid-borne resistance traits in old E. faecalis isolates.

a Chromosome (pink) and plasmidome (yellow-green) sizes show no increase over the years of isolation for hybrid assemblies (top panel) or predictions (bottom panel), as derived from mlplasmids⁷⁹. Bar plots represent mean genome sizes (bp), and each black node represents a single isolate. Years are shown in intervals of 6 and 4 years for hybrid assemblies and predictions, respectively. b Mash distances (k = 21, s = 1000) based on the plasmidome (left panel) and chromosome (right panel) predictions show no prominent host specialisation in E. faecalis. Isolation source is depicted on top of the dendrogram: hospitalised patient (red), wild bird (dark blue), non-hospitalised person (light blue), old human isolates (black), environment (green), farm animal (pink) and others (grey). Dissimilarity matrices of the isolates are depicted as heat maps, coloured as indicated in the colour key. Histograms on top the colour keys show distributions of Mash distances. Source data are provided as a Source Data file. c Oxford Nanopore Technologies (ONT) sequencing of the old E. faecalis isolates revealed old plasmids carrying multiple antimicrobial and metal resistance genes. Plasmid lengths and isolation years are indicated under the plasmid name. Red arrows indicate plasmid-associated genes and transposases, yellow arrows indicate antimicrobial resistance genes; light grey, mercury resistance and light blue, arsenical resistance genes.