Figure 1. Clonal phylogeny and distribution of the carbapenem-associated genetic elements.

The columns “STs” and “strains” between the tree and heatmap indicate sequence type and the name of each strain. STs that were not determined by perfect matching of the alleles are kept blank. Orange and green in the 1^st and 2^nd columns of the heatmap indicate the presence of a kmer or gene. Red and pink indicate carbapenem-resistant strains used for GWAS discovery and validation, respectively. The branches showing >0.5 probability of kmer gain, gene gain, and gene loss are indicated by orange, green, and black bold lines, respectively. There are several carbapenem-resistant strains that possess the kmer but not the surface adhesin locus. These strains had a shorter BLAST alignment length than was required to define the presence of the gene: 36–48% of the locus length was found in the strains 1146103, 18689, 1462234, 754286, 951631, 1499986, and 496487.