Genomic Plasticity and Antimicrobial Resistance Landscape of Egyptian Pseudomonas aeruginosa Clinical Strains

Pseudomonas aeruginosa is an opportunistic pathogen of significant clinical concern, characterized by high morbidity and mortality rates. Despite its clinical relevance, genomic data from Egyptian isolates remain insufficiently studied. In this study, we performed an in silico comparative genomics and pangenome analysis of 37 publicly available Egyptian P. aeruginosa clinical isolates, using PAO1 as the reference strain. Antimicrobial resistance (AMR) profiles were predicted using ResFinder, revealing high resistance rates to β-lactams, third-generation cephalosporins (100%), and fluoroquinolones (75%), while colistin, minocycline, aztreonam, and ceftriaxone retained full efficacy. Thirty-six isolates (97.3%) were classified as multidrug resistant (MDR), and no extended drug resistant (XDR) strains were detected. Pangenome analysis identified 11,255 genes, with core genes comprising 46.04% of the genome, and a substantial accessory component (21.54% shell and 32.01% cloud genes), highlighting marked genomic diversity. Comparative genome mapping demonstrated a conserved chromosomal backbone among isolates, with localized genomic variations corresponding to prophages, genomic islands, and other mobile genetic elements. These regions likely contribute to the observed heterogeneity in AMR profiles and other strain-specific phenotypes. Our findings provide a detailed genomic snapshot of Egyptian P. aeruginosa isolates, highlighting their high MDR prevalence, substantial accessory genome content, and genomic plasticity. This integrative genomic approach contributes valuable baseline data for regional surveillance, supports antimicrobial stewardship efforts, and offers insights into the evolutionary dynamics shaping P. aeruginosa pathogenicity.