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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #360287

Research Project: Ecology and Detection of Human Pathogens in the Produce Production Continuum

Location: Produce Safety and Microbiology Research

Title: Complete Genome Sequence of a Lytic T7-like Phage, Escherichia phage vB_EcoP-Ro45lw, Isolated from Non-Fecal Compost Samples

item Liao, Yen-te
item Liu, Fang - Ocean University Of China
item Wu, Vivian

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary: Lytic bacteriophages (or phages) have been considered as alternative naturally-occurring agents to control bacterial pathogens, such as Shiga toxin-producing E. coli (STEC) strains. With more and more produce contaminated with different serogroups of STEC strains, there is a need to isolate various bacteriophages against these pathogens. Here, we report a genomic characterization of a new member of T7-like bacteriophage, Escherichia phage vB_EcoP-Ro45lw, isolated from non-fecal compost samples that is lytic against STEC O45 strains. The results of this study show that the phage vB_EcoP-Ro45lw belongs to Podoviridae family, the group with a short tail. The phage genome has 50 predicted genes in which 29 of them are coding for proteins with functional functions, including DNA replication, DNA packaging and structural proteins. Additionally, no virulence genes, such as stx genes, are found. Phage vB_EcoP-Ro45lw is close related to Cronobacter phage Dev2 from NCBI database with 89.18% nucleotide sequence similarity. The findings of this study reveal that phage vB_EcoP-Ro45lw is a new member of T7-like podophage lytic against STEC strains.

Technical Abstract: There are growing numbers of produce contaminated with Shiga toxin-producing E. coli (STEC) strains, including the current romaine lettuce outbreak in California, capable of causing severe foodborne illness. Lytic bacteriophages have been considered as promising naturally-occurring agents, alternative to antibiotics, to combat these pathogenic bacteria. With constantly evolving bacteria, the isolation of novel and diverse bacteriophages specific to the pathogens is needed. Here, we report a new member of T7-like bacteriophage, Escherichia phage vB_EcoP-Ro45lw, which was isolated from non-fecal compost samples. The phage has a double-stranded DNA in 39,793 bp length (2352-fold coverage), with an average G+C content of 52.19%, belonging to the branch of T7-like phages under sub-family Autographivirinae in Podoviridae. There are 50 ORFs predicted in which 29 ORFs are annotated with functional proteins, such as T7-like RNA polymerase, endonuclease, DNA primase / helicase, collar, as well as tail tubular proteins A and B, which are related to T7-like phage. Additionally, the genome of vB_EcoP-Ro45lw has close similarity to Cronobacter phage Dev2 with average nucleotide identity (ANIb) of 89.18% over 77.31% coverage of the reference genome. The genomic results suggest that phage vB_EcoP-Ro45lw is a new member of T7-like podophage lytic against STEC strains.