Identification of Novel Bacteriophages with Therapeutic Potential That Target
            <i>Enterococcus faecalis</i>

Al-Zubidi, M.; Widziolek, Magdalena; Court, Elizabeth K.; Gains, Ashley F.; Smith, Robert E.; Ansbro, Katherine; Alrafaie, Alhassan M; Evans, Cariad; Murdoch, Craig; Mesnage, Stéphane; Douglas, C. W. I.; Rawlinson, Āndrew; Stafford, Graham P.

doi:10.1128/iai.00512-19

Cited by 55 publications

(53 citation statements)

References 87 publications

(92 reference statements)

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“…Generally, reports from recent years indicated a high biodiversity of bacteriophages specific for E. faecalis strains. Such reports can be exemplified by articles describing isolation and characterization of previously unknown phages of different properties [ 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 ], genetic modification of known phages and their use in experimental phage therapy (including effects on biofilms) [ 46 , 47 ], assessment of phages in therapy using animal models [ 48 , 49 , 50 , 51 , 52 , 53 ], and cloning of phage genes coding for specific lysins and characterization of the gene products in the light of killing E. faecalis cells [ 54 , 55 , 56 , 57 , 58 , 59 , 60 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

Topka-Bielecka

Bloch

Nejman-Faleńczyk

et al. 2020

IJMS

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A newly isolated bacteriophage infecting Enterococcus faecalis strains has been characterized, including determination of its molecular features. This phage, named vB_EfaS-271, has been classified as a Siphoviridae member, according to electron microscopy characterization of the virions, composed of a 50 nm-diameter head and a long, flexible, noncontractable tail (219 × 12.5 nm). Analysis of the whole dsDNA genome of this phage showed that it consists of 40,197 bp and functional modules containing genes coding for proteins that are involved in DNA replication (including DNA polymerase/primase), morphogenesis, packaging and cell lysis. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. vB_EfaS-271 reveals a relatively narrow host range, as it is able to infect only a few E. faecalis strains. On the other hand, it is a virulent phage (unable to lysogenize host cells), effectively and quickly destroying cultures of sensitive host bacteria, with a latent period as short as 8 min and burst size of approximately 70 phages per cell at 37 °C. This phage was also able to destroy biofilms formed by E. faecalis. These results contribute to our understanding of the biodiversity of bacteriophages, confirming the high variability among these viruses and indicating specific genetic and functional features of vB_EfaS-271.

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Section: Introductionmentioning

confidence: 99%

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

Topka-Bielecka

Bloch

Nejman-Faleńczyk

et al. 2020

IJMS

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“…Phages are being considered for the treatment of multi-drug resistant (MDR) bacterial infections, including enterococcal infections. Recent studies have demonstrated the potential for phage-based therapies against systemic and biofilm associated enterococcal infections (18–22). The decolonization of intestinal MDR E. faecalis may be achieved through the action of phage predation which selects for cell wall variants that are rendered sensitive to antibiotic therapy (23).…”

Section: Introductionmentioning

confidence: 99%

Parallel genomics uncover novel enterococcal-bacteriophage interactions

Chatterjee

Willett

Nguyen

et al. 2019

Preprint

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23 24 25 26 suggests that therapeutic phages could more broadly influence bacterial community composition 53 outside of their intended host targets. 54Recent studies have demonstrated the potential for phage-based therapies against systemic and 67 biofilm associated enterococcal infections (18)(19)(20)(21)(22). The decolonization of intestinal MDR E. 68 faecalis may be achieved through the action of phage predation which selects for cell wall variants 69 that are rendered sensitive to antibiotic therapy (23). However, a potential barrier to the wide-70 spread use of phage therapy against E. faecalis is the development of phage resistance. To 71 confront this issue, we must understand the molecular mechanisms used by phages to infect E. 72 faecalis and how E. faecalis overcomes phage infection to become resistant. Only then can this 73 biology be exploited to better develop phage therapies that mitigate the risk of developing phage 74 resistance. 75The study of phage-bacteria interactions has provided key insights into phage infection that 76 could lead to the development of novel antibacterial therapies. Phages replicate in bacteria by 77 sequence-defined mariner technology transposon sequencing (SMarT TnSeq) (33). 10 7 CFU of 104 logarithmically growing E. faecalis TnSeq library pool was plated on solid media in the absence 105 and presence of phage VPE25 at a multiplicity of infection (MOI) of 0.1. Cells from the input library 106 prior to plating and cells plated on plates containing no phage were used as controls. Tn insertions 107 in E. faecalis genomic DNA were sequenced as described by Dale et al. (33). Sequencing reads 108 were mapped to the E. faecalis OG1RF genome to identify bacterial mutants with altered phage 109 sensitivity. The relative abundance of 22 E. faecalis mutants was enriched (adjusted P value < 110 0.05, log2 fold change > 0) in the presence of VPE25 relative to cultures that lacked phage and 111 the input library (Table S1, Fig. 1A). Five of the 22 phage-resistant enriched mutants harbored Tn 112 insertions in OG1RF_10588 (Table S1, Fig. 1A), previously identified to encode the VPE25 113 receptor Phage Infection Protein of E. faecalis (PipEF) (32). This indicates that the Tn mutant 114

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“…Phages are being considered for the treatment of multidrug-resistant (MDR) bacterial infections, including enterococcal infections. Recent studies have demonstrated the potential for phagebased therapies against systemic and biofilm-associated enterococcal infections (18)(19)(20)(21)(22). The decolonization of intestinal MDR E. faecalis may be achieved through the action of phage predation which selects for cell wall variants that are rendered sensitive to antibiotic therapy (23).…”

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confidence: 99%

Parallel Genomics Uncover Novel Enterococcal-Bacteriophage Interactions

Chatterjee

Willett

Nguyen

et al. 2020

mBio

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Bacteriophages (phages) have been proposed as alternative therapeutics for the treatment of multidrug-resistant bacterial infections. However, there are major gaps in our understanding of the molecular events in bacterial cells that control how bacteria respond to phage predation. Using the model organism Enterococcus faecalis, we used two distinct genomic approaches, namely, transposon library screening and RNA sequencing, to investigate the interaction of E. faecalis with a virulent phage. We discovered that a transcription factor encoding a LytR family response regulator controls the expression of enterococcal polysaccharide antigen (epa) genes that are involved in phage infection and bacterial fitness. In addition, we discovered that DNA mismatch repair mutants rapidly evolve phage adsorption deficiencies, underpinning a molecular basis for epa mutation during phage infection. Transcriptomic profiling of phage-infected E. faecalis revealed broad transcriptional changes influencing viral replication and progeny burst size. We also demonstrate that phage infection alters the expression of bacterial genes associated with intraand interbacterial interactions, including genes involved in quorum sensing and polymicrobial competition. Together, our results suggest that phage predation has the potential to influence complex microbial behavior and may dictate how bacteria respond to external environmental stimuli. These responses could have collateral effects (positive or negative) on microbial communities, such as the host microbiota, during phage therapy. IMPORTANCE We lack fundamental understanding of how phage infection influences bacterial gene expression and, consequently, how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole-genome transcriptomic profiling during phage infection has revealed the differential regulation of genes important for group behaviors and polymicrobial interactions. Our work suggests that therapeutic phages could more broadly influence bacterial community composition outside their intended host targets.

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Identification of Novel Bacteriophages with Therapeutic Potential That Target Enterococcus faecalis

Cited by 55 publications

References 87 publications

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

Parallel genomics uncover novel enterococcal-bacteriophage interactions

Parallel Genomics Uncover Novel Enterococcal-Bacteriophage Interactions

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