Fig. 3.

Diversity in plasmid type and carriage across eight isolates involved in the outbreak. Complement of plasmids carried by eight isolates assembled using PacBio long-read technology, sampled over the time-course of the outbreak. The colour provides the Inc type assignment of the plasmids based on the presence of plasmid replicon sequences and is given in the legend at the bottom. Plasmid copy number relative to coverage over the chromosome is provided to the right of each depicted plasmid. bla_KPC-2-carrying plasmids are denoted with the triangular symbol and are found in the third column. Virulence plasmids are defined as those carrying the rmpA, rmpA2 and/or iuc operon genes. We have also included the virulence plasmid of CX45 (in grey), which we were able to identify from short-read sequencing. The phylogeny on the left provides the core genome phylogeny for these eight isolates, with chromosomal Lineages 1–3 highlighted in colour, as in Figs 1 and 2.