Comparative Genomic Analysis of ESKAPE Pathogens Reveals a Fully Accessory Resistome and Extreme Genomic Divergence in Acinetobacter baumannii

The ESKAPE pathogens are a leading cause of multidrug-resistant hospital infections. This study aimed to define the evolutionary forces shaping their resistomes by investigating whether a conserved core of antibiotic resistance genes (ARGs) exists or if resistance is driven by horizontal acquisitions. Using a comparative genomic approach, we analyzed 12 complete genomes (two strains per species) with Prokka, Roary, and AMRFinderPlus. We identified 129 unique ARGs, with no universal core gene conserved across all species. The resistome was entirely accessory, comprising 66 species-associated and 63 strictly strain-specific genes, including high-risk determinants like  bla KPC-2 and  mecA . A key finding was the extreme genomic divergence in Acinetobacter baumannii, where the two strains shared only a single core gene. Furthermore, the frequent co-occurrence of ARGs with heavy metal resistance operons (e.g.,  ars, mer ) suggests significant environmental co-selection. We conclude that resistome plasticity in these pathogens is extreme, shaped predominantly by horizontal gene transfer rather than vertical inheritance, and is coupled with broader genomic instability. These findings fundamentally underscore that antimicrobial resistance surveillance must operate at the strain level and that effective interventions require a One Health approach to manage environmental selection pressures.