Fig. 3: The phylogeny and spatiotemporal dynamics of ESL genomes.

a The mutational phylogeny of the ESL based on 23,524 SNPs in the 1.6MB LRB (Fig. 2). The nine clusters of the ESL were shown as colored circles on the tree. The sizes of the circles were proportional to the number of associated genomes. b The relative frequencies of nine clusters in the ESL for each year between 2003 and 2020. c The estimated effective population sizes of the IC2 and all of its Clusters. The dashed line in 2006 shows the year of emergence for Clade 2.5.6. d The spatiotemporal tree by TreeTime. The branches were color-coded based on their clusters (as in the Key). The red dots represent the 99 Chinese IC2 strains sequenced in the study. Additionally, the allelic variations of three virulence factors (capsule, type 4 pilus, and hemO gene cluster) and four antimicrobial genes conferring resistances to carbapenem, sulbactam, tetracycline, and macrolide were also shown in the bottom, according to the Key. e The geographic distribution and major transmission patterns of Clusters 2.1–2.4 in IC2. f The geographic distribution and major transmission patterns of Cluster 2.5 with a focus on the rapid dissemination of Clade 2.5.6. Source data are provided as a Source Data file.