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An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense

Nathan P Bullen1,2, Cydney N Johnson3, Shelby E Andersen3

  • 1Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8.

Biorxiv : the Preprint Server for Biology
|November 28, 2023
PubMed

Insights

Researchers identified a new defense system in multidrug-resistant Enterococcus faecalis that blocks bacteriophage therapy. They also found how bacteriophages evolve to overcome this resistance, offering insights for developing effective phage treatments.

Area of Science:

  • Microbiology and Virology
  • Bacterial Genetics and Resistance Mechanisms
  • Antimicrobial Therapy Development

Background:

  • Rising prevalence of multidrug-resistant (MDR) bacterial infections, particularly MDR enterococci, poses a significant global health threat.
  • Antibiotic development is lagging, necessitating alternative therapeutic strategies like bacteriophage (phage) therapy.
  • Understanding phage resistance mechanisms in MDR bacteria is crucial for the success of phage therapy.

Purpose of the Study:

  • To identify genetic factors contributing to phage resistance in *Enterococcus faecalis*.
  • To elucidate the mechanism by which *E. faecalis* resists specific bacteriophages.
  • To investigate the evolutionary strategies employed by bacteriophages to overcome bacterial resistance.

Main Methods:

  • Utilized a CRISPR interference (CRISPRi) genetic screen to identify phage resistance determinants in *E. faecalis*.
  • Characterized a novel plasmid-borne genetic locus encoding a Type IV restriction enzyme (TIV-RE).
  • Analyzed phage evolution through whole-genome sequencing and functional assays to identify resistance-breaking mutations.

Main Results:

  • Identified a genetic locus on a mobilizable plasmid conferring resistance to phage phi47 in *E. faecalis*.
  • Demonstrated that the identified locus encodes a TIV-RE that restricts phage replication.
  • Discovered that phage phi47 evolves resistance by acquiring a mutation in a TIV-RE inhibitor, termed type IV restriction inhibiting factor A (TifA), which inhibits diverse TIV-REs.

Conclusions:

  • Advanced understanding of phage defense mechanisms in drug-resistant *Enterococcus faecalis*.
  • Provided mechanistic insights into how bacteriophages evolve to overcome bacterial antiphage defense systems.
  • Findings contribute to the rational design of phage therapy strategies against MDR bacterial infections.
Keywords:
BacteriophagesEnterococcus faecalisantiphageplasmidtype IV restriction enzyme

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