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Identifying phage Lysins through genomic analysis of prophages from Acinetobacter baumannii

Maria Leonor Raposo1,2, Ana Carolina Pimentel1,2, Vera Manageiro3,4,5

  • 1Faculdade de Ciências, BioISI - Instituto de Biossistemas e Ciências Integrativas, Universidade de Lisboa, Lisbon, Portugal.

Frontiers in Microbiology
|April 16, 2025
PubMed

Insights

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical threat. Researchers found numerous prophages in CRAB genomes, many encoding lysins, which are promising new therapies against antibiotic-resistant infections.

Area of Science:

  • Microbiology and Virology
  • Genomics and Bioinformatics
  • Infectious Diseases and Therapeutics

Background:

  • Acinetobacter baumannii is a Gram-negative opportunistic pathogen causing global nosocomial infections.
  • Increasing antibiotic resistance, particularly carbapenem resistance (CRAB), makes it a critical priority for new treatments.
  • Prophages, viral DNA integrated into bacterial genomes, are increasingly recognized for their therapeutic potential.

Purpose of the Study:

  • To screen for and characterize prophages within Acinetobacter baumannii genomes.
  • To identify prophage-encoded genes, specifically those for putative lysins.
  • To evaluate the therapeutic potential of these prophages and their encoded lysins against CRAB.

Main Methods:

  • Screened 158 Acinetobacter baumannii genomes (139 complete, 19 clinical isolates) for prophage regions.
  • Utilized bioinformatics software and manual curation to identify and analyze complete prophages.
  • Conducted phylogenetic analyses to understand prophage diversity and taxonomic classification.
  • Identified and quantified genes encoding putative lysins within prophage regions.

Main Results:

  • Identified 950 prophage regions, with 348 classified as complete prophages.
  • Complete prophages varied in size (28.6–103.9 kbp) with an average GC content of 39%.
  • Discovered 166 genes encoding putative lysins within complete prophages, with potential in incomplete regions as well.
  • Only 18 complete prophages were taxonomically classified to the genus Vieuvirus.

Conclusions:

  • Acinetobacter baumannii genomes are rich in prophage sequences.
  • Prophage-encoded lysins represent a significant reservoir of potential therapeutic agents.
  • These findings offer promising avenues for developing novel treatments against antibiotic-resistant Acinetobacter baumannii infections.
Keywords:
Acinetobacter baumanniiantibiotic resistancelysinsphylogenyprophages

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