Fig. 1: Genomic evidence for adaptive evolution during the outbreak.

a Maximum likelihood phylogeny of the 110 outbreak isolates rooted with the index isolate. Isolates are colour coded according to location of isolation as indicated by the key in the figure. Clusters of >2 isolates are assigned with letters A-H. The columns and boxes next to the tree show the presence of mutations in significantly enriched genes and intergenic regions. Colour coding indicates different functional groups as underlined at the top. Separate boxes indicate independent mutations. Zoomed-in clusters on the right illustrate the acquisition of enriched mutations in four of the clusters. These data are available for interactive viewing on Microreact (https://microreact.org/project/6BG86F2TGdDpZ4Q5xAvMGh). b Number of chromosomal genetic changes per isolate relative to isolation date. Colour coding of isolates according to isolation location as in 1a. Manhattan plots illustrating gene (c) and intergenic region (d) mutational enrichment analysis. Genes and intergenic regions that exceed a Bonferroni-corrected significance threshold of α = 0.05 (orange line) are named. e Number of GEA mutations per isolate with GEA mutations in clinical (n = 40) vs colonizing (n = 30) isolates. Bars show medians with 95% CI. The two groups were compared using Mann-Whitney test; two-tailed p-value is shown. f Chord graph illustrating the number of isolates carrying combinations of mutations between any of two enriched genes/intergenic regions. The combinations that were found in at least two isolates are shown with increased opacity. The same colour coding of functional groups as in (b). The graph was created using the Flourish Studio visualization tool. Source data are provided as a Source Data file.