Fig. 5: Phylogenetic trees of isolates belonging to pandemic UPEC lineages CC69, CC95, and CC73. | Nature Communications

Fig. 5: Phylogenetic trees of isolates belonging to pandemic UPEC lineages CC69, CC95, and CC73.

From: Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages

Fig. 5

Midpoint rooted maximum-likelihood phylogenies based on core genome alignments (CC69: 76 isolates, 25,753 variable sites in 4.006 Mbp core genome; CC95: 107 isolates, 17,674 variable sites in 4.054 Mbp core genome; CC73: 164 isolates, 25,939 variable sites in 3.857 Mbp core genome). Clinical phenotypes are labeled at the branch tips (ring 3). The presence of papGII, papGIII, and iuc is shown (ring 2). When identification was possible, papGII+ PAI types are labeled (ring 1). Fragmented assemblies, lack of resolved reference PAIs, and sequence deletions or insertions within PAIs sometimes prevented the determination of the specific papGII+ PAI type. Isolates part of papGII+ lineages are shaded in red; isolates part of the same lineages but lacking papGII in bright red. Isolates with complete or near-complete genomes used to investigate the genetic context of papGII are annotated. Red branch lines indicate nodes with bootstrap values <70. Branch lengths of distantly related isolates (outgroup) are reduced and indicated as dashed lines. The papGII-negative subclade in CC95 corresponds to the previously defined subgroup B (serotype O18:H7)45. The trees were visualized using iTOL89.

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