a, A lineage can lose MDR by first losing either one of the two plasmid types and then losing the remaining plasmid. Here we compare the rates of loss of a focal plasmid between ancestral and evolved strains for all single- and double-plasmid-containing cells. b, and c, represent the transition from double-plasmid-containing cells to single-plasmid-containing cells, whereas d, and e, show the transition from single-plasmid-containing cells to plasmid-free cells, with conclusions from (d) having already been drawn from a previous assay (Extended Data Fig. 3c, d). All persistence assays were done with K. pneumoniae as the host in an ancestral context (K(p1), K(p2) or K(p1,p2)) or an evolved context (K 1 (p1 K ), K 1 (p2 E ) or K 1 (p1 K ,p2 E )). In all the evolved contexts, p1 K is the coevolved plasmid and p2 E is recently introduced. Furthermore, for all trajectories in panels (b)-(e), the left cell in the displayed “two-cell transition icon” possesses the focal plasmid; thus, the proportion being tracked refers to this left cell (whereas the right cell refers to a host without the focal plasmid). (b), Persistence of the focal plasmid in a double-plasmid-containing population under selection for the alternate plasmid is initially higher and ultimately different in the evolved context compared to the ancestral context for the p1-type plasmid (ΔBIC = −27.7, Supplementary Table 7) and (c), higher but not meaningfully different compared to the ancestral context for the p2-type plasmid (ΔBIC = 11.7, Supplementary Table 7). (d), Plasmid persistence in a single-plasmid-containing population is higher in the evolved context than the ancestral context for the p1-type plasmid (ΔBIC = −552.3, Supplementary Table 7) and (e) p2-type plasmid (ΔBIC = −893.7, Supplementary Table 7). We also note an interesting result regarding the effect of plasmid coresidency on plasmid persistence in the ancestral strains: the dashed lines in (b) and (d) are tracking the loss of the same plasmid but in the context of the plasmid either on its own or with a coresiding plasmid (see Supplementary Information XI). Graph background shading and line colours are identical to Fig. 5. Dashed and solid lines indicate ancestral and evolved contexts, respectively. Bars indicate s.e.m.