Figure 2.

Core genome phylogeny of the 100 XDR P. aeruginosa outbreak strains included in this study, taking recombinational events into account. Out of these 100 strains, 23 strains (all from cluster 2) were excluded by the Gubbins algorithm because they were genetically identical with one of the other strains. Thus, only 36 strains of cluster 2 (constituted of a total of 59 strains) are shown. Grouping into clusters 1–8 is indicated in translucent colors: (i) two major clusters 1 and 2 (green and orange, respectively), and (ii) six small clusters 3, 4, 5, 6, 7, and 8 (red, gray, yellow, violet, turquoise, and blue, respectively). Sampling source (hospital A and B) is indicated for each strain in non-translucent colors (dark green and dark orange, respectively). As evident from the branches in the far left of the figure, the phylogenetic tree shows two major clusters, designated clusters 1 and 2, alongside with the six additional small clusters, designated cluster 3–8. In the middle left of the figure, the color coding (green/orange) indicates in which of the two hospitals (hospital A/B, respectively) the individual strains were sampled. In the middle and to the right of the figure, the colored barcode lines (red and blue) represent predicted recombinations, either shared by multiple isolates through common descent (red blocks), or occurring on terminal branches which are unique to individual isolates (blue blocks). In the far right of the figure, the source of the strains [P, patient (bold) or E, environment (italic)] and the MLST type are indicated. MLST, multi-locus sequence typing; XDR, extensively drug-resistant.