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

Aim This study aimed to characterize prophage diversity and assess the prophage-encoded genes associated with pathogenicity in carbapenem-resistant Klebsiella pneumoniae (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 Across four CRKP genomes, 16 intact prophages were identified, and 13 were inducible. They exhibited genomic diversity (16–55 kb) with limited shared-gene content. No antimicrobial resistance genes were detected; however, various virulence-, fitness-, and stress-associated genes including, papA, rmlB, pgsA, tagR, algU, fbpC, ybtP, grx1, dusB, aphA, terB, grpE, zur, ren, and piuB 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.