Comparative genomic analysis of clinical Pseudomonas aeruginosa isolates from Iraq: insights into genome diversity, antimicrobial resistance, and phylogenetic relatedness.

Pseudomonas aeruginosa is a high-priority opportunistic pathogen of public health concern. Its large, complex genome, rich in transferable genetic elements, enables rapid acquisition of antibiotic resistance and contributes to its natural tolerance to antibiotics and disinfectants. Among fifty-two clinical isolates, shotgun whole-genome sequencing was conducted on four clinical isolates of P. aeruginosa from Erbil, Iraq (PA-1 to PA-4) and the laboratory strain PA-NCIMB 8626. The antibiotic susceptibilities of these strains were assessed using the Kirby-Bauer disk diffusion method. The clinical isolates selected for this study were PA-1 (multidrug-resistant, MDR), PA-2 (susceptible, S), PA-3 (extensively drug-resistant, XDR), and PA-4 (pan-drug-resistant, PDR), in addition to the standard strain NCIMB 8626. All strains underwent shotgun whole-genome sequencing and comprehensive bioinformatics analysis. Genomic DNA sequencing was performed on an MGI T7 platform using a unique DNA nanoball technology, followed by quality control, read assembly, gap closing, and annotation. Since the potential of Iraqi strains remains incompletely understood, whole-genome sequence (WGS) data from five P. aeruginosa strains were analyzed to compare genomic divergence in size, structure, and content, assess evolutionary relationships, and identify genes associated with antibiotic resistance and virulence. Virulence factor profiling identified key genes involved in adhesion, secretion, quorum sensing, iron acquisition, and biofilm formation, with isolate-specific differences. Gene analysis aligned efflux pump-related, β-lactam, and aminoglycoside resistance genes with phenotypic susceptibility profiles, except for one susceptible strain. Phylogenetic and evolutionary analyses indicated genomic diversity without sequence type clumping.