Genome sequence of a T4-like phage, Escherichia phage vB_EcoM-Sa45lw, infecting Shiga toxin-producing Escherichia coli strains

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

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2019
Publication Date: 8/8/2019
Citation: Liao, Y., Zhang, Y., Salvador, A., Wu, V.C. 2019. Genome sequence of a T4-like phage, Escherichia phage vB_EcoM-Sa45lw, infecting Shiga toxin-producing Escherichia coli strains. Microbiology Resource Announcements. 8:e00804-19. https://doi.org/10.1128/MRA.00804-19.
DOI: https://doi.org/10.1128/MRA.00804-19

Interpretive Summary: There are increasing numbers of foodborne outbreaks associated with the contamination of Shiga toxin-producing E. coli (STEC) on produce around the world, resulting in severe illnesses as well as economic loss. Using lytic bacteriophages has been considered as a promising biocontrol approach to prevent the development of antibiotic-resistant strains. Therefore, there is a need to isolate and characterize more bacteriophages against these pathogens. Here, we report a complete genome sequence of a T4-like coliphage, Escherichia phage vB_EcoM-Sa45lw, isolated from surface water in a produce-growing area. The results of this study show that the phage vB_EcoM-Sa45lw belongs to Myoviridae family, the group with a contractile tail. The phage genome has 282 predicted genes in which 137 genes encode proteins with known functions, including DNA replication and packaging, structural proteins, and host cell lysis. Additionally, no virulence genes or antibiotic resistance genes are found. Phage vB_EcoM-Sa45lw is highly related to Escherichia phage wV7 that infects E. coli O157:H7 strains, with subtle difference of amino acid sequence on the receptor recognition protein. The findings of this study reveal that phage vB_EcoM-Sa45lw is a new member of T4-like phage. Additionally, the phage, lytic against generic E. coli and STEC strains, has a wider host range than most T4-like coliphages.

Technical Abstract: Shiga toxin-producing E. coli (STEC) is notorious for causing hemolytic uremic syndrome through the consumption of a variety of contaminated foods, such as meats and leafy greens. Using lytic bacteriophages for controlling bacterial pathogens has been increasingly considered because it can reduce the development of antibiotic-resistant strains. However, the number of genomically characterized coliphages are relatively scarce as compared to their bacterial hosts. In this study, the complete genome sequence of a T4-like coliphage is described. Escherichia phage vB_EcoM-Sa45lw (or Sa45lw), with morphology belonging to Myoviridae family, was previously isolated from surface water collected in a produce-growing area. The phage has double-stranded DNA with the genome size of 167,353 bp, an average G+C content of 35.4% and 11 tRNAs. These genomic characteristics are closely similar to T4 or other T4-like coliphages, such phages wV7, AR1, and PE37. Additionally, the packaging mechanism of phage Sa45lw was predicted to be headful packaging, similar to phage T4. These findings show that phage Sa45lw belongs to the T4virus genus of the subfamily Tevenvirinae in family Myoviridae. A total of 282 ORFs were predicted in the phage genome, and 137 ORFs encode the proteins categorized into 4 functional groups: virion structure, host lysis, DNA replication and transcription regulation, and additional function. None of the ORFs contain virulence genes, such as stx gene or antibiotic resistance genes. Furthermore, ORF258 of Sa45lw encodes a large distal long tail fiber subunit, as a receptor recognition protein from the bacterial host membranes, sharing 92.12%, 86.11% and 83.41% amino acid identity to the counterparts in coliphages wV7, AR1 and PE37, respectively. This finding likely accounts for the different host range of phage Sa45lw—against K12, STEC O157 and O45 strains—as the three T4-like reference phages primarily infect STEC O157.