Molecular Basis for Lytic Bacteriophage Resistance in Enterococci.

Breck A Duerkop,Kelli L Palmer,Wenwen Huo,Lora V Hooper,Pooja Bhardwaj,Jeff F Miller

doi:10.1128/mbio.01304-16

Abstract

ABSTRACTThe human intestine harbors diverse communities of bacteria and bacteriophages. Given the specificity of phages for their bacterial hosts, there is growing interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. A significant barrier to such therapies is the rapid development of phage-resistant bacteria, highlighting the need to understand how bacteria acquire phage resistance in vivo. Here we identify novel lytic phages in municipal raw sewage that kill Enterococcus faecalis, a Gram-positive opportunistic pathogen that resides in the human intestine. We show that phage infection of E. faecalis requires a predicted integral membrane protein that we have named PIPEF (for phage infection protein from E. faecalis). We find that PIPEF is conserved in E. faecalis and harbors a 160-amino-acid hypervariable region that determines phage tropism for distinct enterococcal strains. Finally, we use a gnotobiotic mouse model of in vivo phage predation to show that the sewage phages temporarily reduce E. faecalis colonization of the intestine but that E. faecalis acquires phage resistance through mutations in PIPEF. Our findings define the molecular basis for an evolutionary arms race between E. faecalis and the lytic phages that prey on them. They also suggest approaches for engineering E. faecalis phages that have altered host specificity and that can subvert phage resistance in the host bacteria.

Highlights

The human intestine harbors diverse communities of bacteria and bacteriophages
We find that a variable region in PIPEF specifies phage tropism for distinct E. faecalis strains and that mutations in this variable region confer E. faecalis phage resistance
Phages have long held promise as potential antibacterial therapeutics, and a revival in phage therapy has begun over the last several years

Summary

Introduction

The human intestine harbors diverse communities of bacteria and bacteriophages. Given the specificity of phages for their bacterial hosts, there is growing interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. We identify novel lytic phages in municipal raw sewage that kill Enterococcus faecalis, a Gram-positive opportunistic pathogen that resides in the human intestine. Our findings define the molecular basis for an evolutionary arms race between E. faecalis and the lytic phages that prey on them They suggest approaches for engineering E. faecalis phages that have altered host specificity and that can subvert phage resistance in the host bacteria. We have unraveled one such resistance mechanism in Enterococcus faecalis, a Gram-positive natural resident of the human intestine that has acquired antibiotic resistance and can cause opportunistic infections. There are numerous obligate lytic phages that infect E. faecalis and rapidly kill their bacterial hosts [13] These phages show a remarkable degree of specificity for certain E. faecalis strains. Replication/Biosynthesis DNA restriction modification Host cell lysis Structural morphogenesis DNA packaging Hypothetical that there is an evolutionary “arms race” between E. faecalis and its lytic phages, with underlying mechanisms that promote the evolution of phage resistance in the targeted strains and a corresponding ability of the phage to evolve new host strain specificities

Methods

Results

Conclusion