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

Virus Genes. 2014 Aug;49(1):145-51. doi: 10.1007/s11262-014-1079-3. Epub 2014 May 13.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacteriophages / enzymology
  • Bacteriophages / genetics*
  • Bacteriophages / isolation & purification
  • Bacteriophages / ultrastructure
  • DNA, Viral / chemistry*
  • DNA, Viral / genetics*
  • Enterococcus faecalis / virology*
  • Genome, Viral*
  • Hospitals
  • Microscopy, Electron, Transmission
  • Molecular Sequence Data
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sewage / virology
  • Siphoviridae / enzymology
  • Siphoviridae / genetics
  • Siphoviridae / isolation & purification
  • Siphoviridae / ultrastructure
  • Virion / ultrastructure
  • beta-Lactamases / genetics*


  • DNA, Viral
  • Sewage
  • beta-Lactamases

Associated data

  • GENBANK/KF728385
  • RefSeq/NC_023595