Fig. 1

Phylogenetic tree of the collection and the metadata. The neighbor-joining tree for 328 genomes under study. The tree was reconstructed from the pairwise sequence (SNP) distance values, by ape package in R. The SNPs were called with Snippy (see “Methods”). We rooted the tree using midpoint rooting. The resistance profile shows the distribution of major resistance determinants, i.e., Carb (carbapenemase), ESBL, AGly (aminoglycosides), Flq (fluroquinolone), and Tet (tetracyclines) (see Supplemental Table S1 for the full list of resistance determinants). The virulence and resistance scores were computed from Kleborate, based on the presence of key virulence and resistance determinants (see “Methods”) [27]. Numbers on the distributions of virulence score and count of resistance genes and classes and resistance score show the absolute value. The terms “mut” and “acq” stand mutations and acquired resistance genes, respectively. The coverage strips show the percentage of sites of the plasmid sequences to which short reads for each strain were mapped