Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages

Abstract

The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7–46.8 kb (43.8–44 mol% G+C) encoding 74–81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily “Tunavirinae” with further classification into five genera, namely “Tlslikevirus” (TLS, FSL SP-126), “Kp36likevirus” (KP36, F20), Tunalikevirus (T1, ADB-2 and Shf1), “Rtplikevirus” (RTP, vB_EcoS_ACG-M12) and “Jk06likevirus” (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49). The fact that the viruses related to JK06 have been isolated independently in Israel (JK06) (GenBank Assession #, NC_007291), Canada (vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96) and Mexico (phiKP26, phiJLA23) (between 2005 and 2011) indicates that these similar phages are widely distributed, and that horizontal gene transfer does not always prevent the characterization of bacteriophage evolution. With this new scheme, any new discovered phages with same type can be more properly identified. Genomic- and proteomic- based taxonomic classification of phages would facilitate better understanding phages diversity and genetic traits involved in phage evolution.

A proposed new bacteriophage subfamily: “Jerseyvirinae”

“…Using an alternative approach, employing NCBI BLASTN and TBLASTX, a genus can be defined as a group in which members share ≥65 % DNA sequence identity, while members of the same subfamily should show ≥40 % protein homologs (Kropinski, Edwards and Mahadevan, unpublished results). These values are those derived by Niu et al in their assessment of the T1-likeviruses [45].…”

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

“…The other two Enterobacteriaceae lytic phages that have bacterial genome matches with better than 50% identity, E1 and IME-EC2 (singleton lytic clusters 26 and 33), appear to be examples of past horizontal transfer of virion assembly genes between temperate and lytic phages. Salmonella lytic phage E1 (Niu et al , 2014) has a number of phage ES18-like (temperate cluster 5) virion assembly genes and an early region that is weakly related to lytic T1-like phages (lytic cluster 1); the proteins encoded by these two regions are mostly in the 30–40% identity range to ES18 and T1, respectively. Lytic Escherichia phage IME-EC2 (Hua et al , 2014) has virion assembly genes that are related to temperate P22-like phages (temperate cluster 9) with protein identities to those phages mostly in the 30–70% range (closest MCP match is about 70% identity to the CUS-3-like subgroup of the P22-like phages) (see Figure S1).…”

Capsule-Targeting Depolymerase, Derived from Klebsiella KP36 Phage, as a Tool for the Development of Anti-Virulent Strategy

“…NCBI BLAST results revealed that depoKP36 shares about 67–88% amino-acid identities in the N-terminal region with other putative tail fiber proteins from Klebsiella and Enterobacter phages, belonging to the same family of Siphoviridae and more specifically the “ KP36likevirus ” genus [22,43]. Such high homology within morphologically similar phages may indicate the presence in this part of a domain anchoring the tail fiber to the phage particle.…”

“…Transmission electron microscopy and genome sequence analyses revealed that this phage belongs to the family Siphoviridae , and is currently classified as a member of the “ KP36likevirus ” genus within subfamily Tunavirinae [22]. …”