Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium.

We isolated and characterized a novel virulent bacteriophage, IME-EFm1, specifically infecting multidrug-resistant Enterococcus faecium. IME-EFm1 is morphologically similar to members of the family Siphoviridae. It was found capable of lysing a wide range of our E. faecium collections, including two strains resistant to vancomycin. One-step growth tests revealed the host lysis activity of phage IME-EFm1, with a latent time of 30 min and a large burst size of 116 p.f.u. per cell. These biological characteristics suggested that IME-EFm1 has the potential to be used as a therapeutic agent. The complete genome of IME-EFm1 was 42 597 bp, and was linear, with terminally non-redundant dsDNA and a G+C content of 35.2 mol%. The termini of the phage genome were determined with next-generation sequencing and were further confirmed by nuclease digestion analysis. To our knowledge, this is the first report of a complete genome sequence of a bacteriophage infecting E. faecium. IME-EFm1 exhibited a low similarity to other phages in terms of genome organization and structural protein amino acid sequences. The coding region corresponded to 90.7 % of the genome; 70 putative ORFs were deduced and, of these, 29 could be functionally identified based on their homology to previously characterized proteins. A predicted metallo-ß-lactamase gene was detected in the genome sequence. The identification of an antibiotic resistance gene emphasizes the necessity for complete genome sequencing of a phage to ensure it is free of any undesirable genes before use as a therapeutic agent against bacterial pathogens.

Genome analysis of Enterococcus faecalis bacteriophage IME-EF3 harboring a putative metallo-beta-lactamase gene.

Lytic Enterococcus faecalis bacteriophage IME-EF3 was isolated from hospital sewage, and its genome was sequenced using high-throughput sequencing. Genomic analysis and electron microscopy suggested that IME-EF3 was a member of the family Siphoviridae. The phage has an isometric head and a long non-contractile tail with a 41 kb linear double-stranded DNA genome. The genome encodes 69 putative proteins, with 32 annotated functionally, including proteins related to phage structure, packaging, transcription, replication, and a lysis module. Interestingly, a metallo-beta-lactamase gene responsible for multi-drug resistance was found in the genome of IME-EF3. The possibility of horizontal gene transfer of the metallo-beta-lactamase gene suggests that phage IME-EF3, although lytic, might not be suitable for phage therapy unless one would devise a way to delete the metallo-beta-lactamase gene. Hence, whole genome sequencing should always be a prerequisite for identifying a phage therapy candidate.