Fig. 2

Phylogenetic tree and predicted recombination events of 526 CC271 isolates in China. a Recombination-masked WGS phylogeny; colors of the branches correspond to groups, which consist primarily of isolates with the corresponding ST and serotype. Red represents 19F ST236 (including Taiwan19F-14), orange represents 19F ST271-A, blue represents 19F ST271-B, purple represents 2 19F ST320 isolates, green represents 19A ST320, and gray represents a group consisting of other rare STs that are not focused. Blue and green shaded box represents the monophyletic group of 19F ST271-B and 19A ST320. b The predicted recombinations in CC271 isolates. Column corresponds to location in the reference genome, and row corresponds to taxon in the phylogeny. Red blocks represent putative recombination events shared by multiple isolates through common descent, and blue blocks represent putative recombination events occurred in a single isolate. c Annotation of the S. pneumoniae Taiwan19F-14 reference genome. Each block represents a coding sequence. Coding sequences of pbp2x, cps locus, and pbp2b are colored in red. pbp2x is located upstream of cps locus