Fig. 3

The phylodynamic of ST2096 strains. A The Bayesian phylodynamic tree for the ST2096 strains. The horizontal red lines show 95% Highest Posterior Distribution (HPD) for the age of the internal node. We showed the distribution of carbapenemase, ESBL positive, with the acquired genes for aminoglycoside and the distribution of missense, stop gained, and frameshift mutations in the mgr gene and the acquired mcr gene. Colors on the patient panel show whether the isolates were retrieved from the same patients. We did not show the results for patients with one representative strain. B Bayesian skyline plot for the size of the population over time. The shaded region corresponds to 95% confidence interval. C Ancestral state reconstruction for the presence of the carbapenemase genes for the ST2096 clone. The pie charts represent the likelihood of the ancestral state. The tree is a Bayesian tree in (A). The tree tips show the presence/absence status of the genes. The clade colors show the BAPS clusters in (A). D Contextualization of the ST2096 clone with the global population. The neighbor-joining tree was reconstructed from the SNP distance matrix for the ST2096 cluster. Five divergent strains were removed before reconstructing the tree