Genomic impact of prophages on carbapenem-resistant <i>Klebsiella pneumoniae</i> : distribution and functional gene profiles

AIM: (CRKP). MATERIALS AND METHODS: Multiple stressors, including mitomycin-C, were applied to CRKP isolates of ST985, ST101, ST307, and ST2096 to trigger prophage induction. Induced lysates and bacterial genomes were sequenced. Prophages were identified using PHASTEST; resistance, virulence, anti-CRISPR, and tRNA genes were screened; and pangenome, phylogenomic, proteome and intergenomic analyses were performed. RESULTS: were detected. Multiple defense systems, DNA-methyltransferases, diverse anti-CRISPR proteins, the CBASS inhibitor, and the anti-termination protein Q were determined. Some anti-CRISPR loci and pathogenicity-associated gene regions were detected prophages but were absent in induced phages, suggesting structural rearrangements during induction. CONCLUSION: Prophages constitute dynamic genetic reservoirs enriched in virulence, stress-tolerance, and immune-evasion determinants rather than antimicrobial resistance. These findings highlight the significant role of prophages in shaping CRKP pathogenicity and evolutionary adaptation.