The genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital.

Pseudomonas aeruginosa, recognized by the World Health Organization as a critical priority pathogen, exhibits significant genomic plasticity and a high potential for developing resistance to multiple antimicrobials. This study provides comprehensive genomic insights into colistin-resistant P. aeruginosa isolates obtained from cancer patients. Phenotypic assays were conducted to evaluate antibiotic susceptibility, biofilm formation, efflux pump activity, swarming motility, and pigment production. Whole genome sequencing of the collected isolates was performed using Oxford-Nanopore technology to examine sequence types, resistome profiles, virulence-associated genes, and mobile genetic elements. Our findings reveled that out of 52 isolates, 10 (19.2%) were resistant to colistin. Ceftolozane/tazobactam demonstrated full efficacy against 60% of colistin resistant P. aeruginosa isolates. Within this colistin resistant subset, high-risk clones ST308 and ST773 emerged as dominant, both harboring blaNDM-1 and exhibiting extensive resistance profiles, including resistance to colistin and, in some cases, ceftolozane/tazobactam. The first detection of ST1143 and ST1693 in Egypt carrying blaOXA-1028 and blaOXA-904, respectively was documented, neither of which had been previously reported in the country. The accessory genome, accounting for up to 34.6% of the total genome, highlights the remarkable genomic plasticity of P. aeruginosa, and its capacity for horizontal acquisition of resistance and virulence genes via mobile genetic elements, such as integrative and conjugative elements (ICEs). Virulome analysis revealed the presence of the exoU gene in high-risk clones, a marker closely linked to hypervirulence in infection models, whereas other sequence types were associated with less virulent factors, such as exoS. Despite phenotypic variability in biofilm formation, pigment production, and motility, the underlying genetic determinants of these traits were highly conserved. Mutational analysis revealed mutations in the regulatory system PhoPQ as the primary mechanism of colistin resistance, with no mcr genes detected. In conclusion, the substantial genomic plasticity of P. aeruginosa, reflected by an extensive accessory genome facilitates horizontal gene transfer (HGT), and significantly influences antimicrobial resistance and virulence. Colistin resistance was predominantly mediated by chromosomal mutations. Virulome and resistome analyses underscores the high pathogenicity and resistance potential of high-risk clones ST773 and ST308. The detection of horizontally acquired elements, such as integrative and conjugative elements (ICEs) carrying resistance genes such as blaNDM-1, underscores their role in disseminating resistance determinants. These findings emphasize the need urgent for targeted antimicrobial stewardship and surveillance strategies within Egyptian healthcare settings.