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Genome analysis of Enterococcus faecalis bacteriophage IME-EF3 harboring a putative metallo-beta-lactamase gene
Xiaoyu Li1, Peng Ding, Chuanyin Han
1Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China, lxyandpp@foxmail.com.
Abstract:
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.
Insights
A lytic Enterococcus faecalis bacteriophage, IME-EF3, was isolated and sequenced. Its genome contains a metallo-beta-lactamase gene, highlighting the need for whole genome sequencing before considering phages for therapy.
Area of Science:
- Microbiology
- Genomics
- Bacteriophage research
Background:
- Enterococcus faecalis is an opportunistic pathogen often associated with hospital-acquired infections.
- Bacteriophages are viruses that infect bacteria and are being explored as an alternative to antibiotics.
- Phage therapy requires careful characterization of candidate phages, including their genetic makeup.
Purpose of the Study:
- To isolate and characterize a lytic Enterococcus faecalis bacteriophage from hospital sewage.
- To determine the complete genome sequence of the isolated bacteriophage IME-EF3.
- To assess the potential suitability of bacteriophage IME-EF3 for phage therapy.
Main Methods:
- Isolation of bacteriophage IME-EF3 from hospital sewage.
- High-throughput sequencing for whole genome sequencing of the bacteriophage.
- Genomic analysis to identify putative genes and functional annotations.
- Electron microscopy for morphological characterization.
Main Results:
- Isolation of a lytic Enterococcus faecalis bacteriophage, designated IME-EF3.
- IME-EF3 possesses an isometric head and a long non-contractile tail, consistent with the Siphoviridae family.
- The bacteriophage has a 41 kb linear double-stranded DNA genome encoding 69 putative proteins.
- A metallo-beta-lactamase gene conferring multi-drug resistance was identified within the IME-EF3 genome.
Conclusions:
- Bacteriophage IME-EF3 is a lytic phage belonging to the Siphoviridae family.
- The presence of a metallo-beta-lactamase gene raises concerns for its direct application in phage therapy due to potential horizontal gene transfer.
- Whole genome sequencing is crucial for evaluating phage candidates and ensuring the safety and efficacy of phage therapy.
