PMC

Phylogenomic analysis of Acinetobacter genomes. Phylogenetic analysis of 254 newly sequenced Acinetobacter genomes and 61 genomes that had been previously sequenced. Genomes were aligned and SNPs were called using the program MUMmer. GATK Unified Genotyper was used to call and determine ambiguity of SNPs and to generate a VCF file. RAxML 7.2.8 was used to infer the phylogenetic tree with 100 bootstrap replicates. The phylogeny was rooted with the A. baumannii TYTH-1 complete genome.

Heat map of known virulence-associated factors in A. baumannii. The amino acid sequences for genes previously identified as being associated with virulent phenotypes were obtained from the National Center for Biotechnology database (). LS-BSR analysis to detect if these genes were present in the newly sequenced A. baumannii isolates was performed using TBLASTN. The BSR values were generated as described previously. The heat map generated was visualized with phylogeny using Tree of Life v3.0 software.