Fig. 1

Core SNV phylogeny of A. baumannii strains. A core phylogeny was constructed using 50,472 SNVs that were present in at least 80 % of all strains. SNVs were identified using kSNP and the tree was built using RAxML. Clade A-E designation reflect primary clade structure previously designated [30, 44] where strains in Clade A-D through the ACICU branch are all Global Clone II, or multi-locus sequence type (MLST) ST2, strains [60]. Internal nodes with bootstrap support of at least 50 % are indicated. Black circles near terminal nodes indicate highly-supported monophyletic groups of strains from individual patients. Strain names are color-coded based on the hospital from which the isolate was obtained and the first the numbers after ABUH refer to patient and strain identifiers in Additional file 1: Table S2. Colored dots represent the presence of specific genes or genomic regions of interest as listed in the key