Fig. 1: Population structure and predicted antimicrobial resistance genotypes of 15,743 A. baumannii genomes.

a, b Genetic diversity of the ESKAPE bacteria by their STs. A. baumannii is divided into two groups, with or without ST2. a The bar chart shows the Simpson diversity index (SDI) of STs for each ESKAPE member. b The pie chart of the top 10 STs and the others for each ESKAPE member. c The supertree of A. baumannii based on 2266 softcore genes in the 5824 representative genomes. The highlighted clusters in the tree showed the most compatible IC/CC for each of the nine previously designated international clones (ICs) in A. baumannii, as shown in the labels. The ICs were predicted using Pasteur’s MLST scheme as clonal complexes (CCs), which were shown in the outer ring. Genomes that had inconsistent IC assignments between the supertree and the MLST were marked with triangles, with the false positives (n = 121) and the false negatives (n = 89) color-coded in blue and red, respectively. d Global distributions of the IC1 and IC2 strains, color-coded as in (a). e Histogram of the yearly isolation frequencies of IC1, IC2, and the others. The inset shows the relative frequencies of IC1 and IC2 each year. f The yearly variations of the numbers of AMR genes (blue) and categories of drug resistances (red) between 2003 and 2020. The correlation coefficient of linear regression for each number series was shown nearby. g Bubble plots of the numbers of country presences (X-axis) versus the numbers of ARG carriages (Y-axis) for the IC/CCs. The slope of linear regression (r) is 0.51 and the significance (p) is calculated using the two-tailed student’s t-test. The map was modified from open-source data in [https://github.com/antvis/L7].