Future microbiology · 2026
Genomic impact of prophages on carbapenem-resistant Klebsiella pneumoniae: distribution and functional gene profiles.
СтатьяПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод в очереди
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Ayas Nisanur, Uskudar Guclu Aylin, Yalcin Suleyman
Аннотация
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.
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.