Complete genome sequence of a Shiga toxin-converting bacteriophage, Escherichia phage Lys12581Vzw, induced from an outbreak Shiga toxin-producing Escherichia coli strain

Authors: ZHANG, YUJIE - Shanghai Ocean University; Liao, Yen-Te; Salvador, Alexandra; SUN, XIAOHONG - Shanghai Ocean University; Wu, Vivian

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2019
Publication Date: 9/5/2019
Citation: Zhang, Y., Liao, Y., Salvador, A., Sun, X., Wu, V.C. 2019. Complete genome sequence of a Shiga toxin-converting bacteriophage, Escherichia phage Lys12581Vzw, induced from an outbreak Shiga toxin-producing Escherichia coli strain. Microbiology Resource Announcements. 8:e00793-19. https://doi.org/10.1128/MRA.00793-19.
DOI: https://doi.org/10.1128/MRA.00793-19

Interpretive Summary: Lysogenic bacteriophages (or temperate phages), usually integrated in a bacterial genome, have been considered as potential mobile elements for the transfer of crucial genes, such as Shiga toxin genes. With the increase of new STEC strains associated with recent foodborne outbreaks around the world, there is a need to explore further information of Shiga toxin converting phages which play an important role in the emergence of new STEC strains. Here, we report a genomic characterization of a new member of Shiga toxin converting bacteriophage, Escherichia phage Lys12581Vzw, induced from an outbreak STEC O145 strain. The results of this study show that the phage Lys12581Vzw belongs to Podoviridae family, a group phage with a short tail. The phage genome has a total of 81 predicted coding regions and 45 of which encode proteins with known functions, including crucial proteins contributing to the virulence and the replication of the stx converting phage. Phage Lys12581Vzw is closely related to two published stx2 converting phages, Enterobacteria phage VT2-Sakai and Bacteriophage 933W, induced from STEC O157 strains, with 95% nucleotide sequence similarity. The findings of this study reveal that the stx2 phage, Lys12581Vzw, is a new member of Shiga toxin converting phage and provide the genomic features for better understanding the emergence of new pathogens in the future.

Technical Abstract: Shiga toxin-producing E. coli (STEC), as one of the major foodborne pathogens, has been widely associated with multiple foodborne outbreaks in the United States. Previous studies showed Shiga toxin, the main virulence factors of STEC, is encoded in the sequence of lambdoid temperate bacteriophage (as known as prophage) within the bacterial genome. The prophages, including those containing stx genes, are usually induced by SOS response and subsequently released in the environment as potential mobile elements that likely contribute to virulence genes transfer among susceptible strains. However, genomic characterizations of the stx converting phages which were induced from host strains are scarce. Thus, we report a new member of Shiga toxin converting phage, Escherichia phage Lys12581Vzw, which was induced from an outbreak STEC O145 strain. The phage has a double-stranded DNA with a genome size of 62,668 bp (3257 x coverage) and an average G+C content of 50.1%. Based on the analysis of genomic sequences and transmission electron microscopy, the phage belongs to the Podoviridae family with Mu-like packaging mode. There are 81 open reading frames (ORFs) predicted, of which 45 ORFs are annotated with functional proteins, such as DNA replication and modification (restriction endonuclease, DNA primase and methylase), membrane-related proteins (lysis protein, membrane protein and cell division inhibitor), antirepressor, virion structure, integrase, Shiga toxin, and tRNA. Most functional ORFs contributed to the virulence and the propagation of Shiga toxin converting phages. Additionally, the genome of Lys12581Vzw shares 95% average nucleotide identity to two published stx2 converting phages, Enterobacteria phage VT2-Sakai and Bacteriophage 933W, which were induced from different Shiga toxin-producing E. coli O157:H7 strains. This result of the phage genome provides valuable insights into the diversity of Shiga toxin converting phages induced from STEC strains.