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.
Citation: Niu YD, McAllister TA, Nash JHE, Kropinski AM, Stanford K (2014) Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages. PLoS ONE 9(6): e100426. https://doi.org/10.1371/journal.pone.0100426
Editor: Mark J. van Raaij, Centro Nacional de Biotecnologia – CSIC, Spain
Received: January 9, 2014; Accepted: May 23, 2014; Published: June 25, 2014
Copyright: © 2014 Niu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by the Alberta Livestock and Meat Agency, Agriculture and Agri-Food Canada Peer-Reviewed Project Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Tailed bacteriophages (phages) with double-strand DNA genomes belonging to the order Caudovirales are the most abundant viruses on earth, accounting for 96% of all the phages observed . Based on tail morphology, these viruses are classified by the International Committee on Taxonomy of Viruses (ICTV), into three families−Myoviridae (long contractile tail), Siphoviridae (long non-contractile tail) and Podoviridae (short non-contractile tail). Recent advances in sequencing technologies has led to a proliferation in the sequencing of phage genomes , , enabling comparative genomics and proteomics to better define phage taxonomy. The family Myoviridae now contains three subfamilies, Peduovirinae, Spounavirinae and Tevenvirinae , and 18 genera. The family Podoviridae has been further divided into the Autographivirinae and Picovirinae subfamilies , with a total of eleven genera. The Siphoviridae account for >61% of described phages  and this family also represents the largest group of fully sequenced phages, but no subfamilies, and only nine bacterial-specific phage genera have been described. Classification of the Siphoviridae is currently under review by ICTV (Adriaenssens, personal communication). T1-like phages possess terminally redundant and circularly permuted genomes of ∼50 kb, and are currently classified as members of one genus (Tunalikevirus) within Siphoviridae . Morphologically, they have a polyhedral head 60 nm in diameter with an extremely flexible non-contractile tail 151 nm in length and 8 nm in diameter . At present, ICTV only recognizes nine species of phages within this genus with 1, 1, 6 and 1 infecting Cronobacter, Enterobacter, Escherichia coli, and Shigella, respectively.
Shiga-toxin producing E. coli O157:H7 (STEC O157:H7) remains one of leading causes of foodborne illnesses in North America , . Although the food production continuum has introduced control measures to prevent the pathogen from entering food chain, outbreaks of STEC O157:H7 linked to fresh produce and beef products continue (http://www.cdc.gov/ecoli/outbreaks.html and http://www.phac-aspc.gc.ca/fs-sa/fs-fi/ecoli-eng.php). Lytic phages offer promise in the prevention and therapy of bacterial infections in humans , livestock ,  and plants  and have been employed to decontaminate processed foods and agricultural products , . However, the use of phage therapy to target bacterial pathogens such as STEC O157:H7 ,  and Salmonella ,  in the digestive tract of livestock remains challenging. Factors such as the development of phage resistance, the complexity of predator-prey relationships between phages and hosts, the diversity and abundance of microflora in the gastro-intestinal tract all may undermine the effectiveness of phage therapy. Recently, in-vitro experiments in our laboratory have indicated that competitive interference between different phage types may be another factor impacting effectiveness of phage cocktails , even though this approach is often advocated as a means of avoiding resistance. An improved understanding of phage taxonomy, proteomics and target receptors could lead to the formulation of more effective phage cocktails that overcome resistance development while remaining efficacious.
Previously, four STEC O157:H7-infecting bacteriophages (vB_EcoS_AHP24, AHS24, AHP42 and AKS96) originally isolated from cattle feedlots in southern Alberta, Canada were classified as T1-like Siphoviridae by electron microscopy, but exhibited divergent genotypes based on EcoRI- or HindIII-digestion profiles . This study aimed to further define their genomic and proteomic characteristics as well as infectivity against STEC O157:H7 and non-pathogenic E. coli (ECOR) strains. We also conducted comparative genomic, proteomic and phylogenetic analysis among known T1-like phages in an effort to determine how these viruses could be optimally classified.
Materials and Methods
Bacteriophage, bacteria and media
Four phages infecting STEC O157:H7 strain R508 (phage type, PT14) were isolated from the feces of commercial feedlot cattle in 2007 in Alberta, Canada  with AHP24 (Pen 10), AHS24 (Pen 10) and AHP42 (Pen 6) from Feedlot B and AKS97 (Pen 2) from Feedlot A  with permission. A single discrete plaque from each phage was purified three times by the soft agar (0.6%) overlay method  and propagated as previously discribed . Titers of phages in the stock filtrates were then determined by the soft agar overlay technique . STEC O157:H7 strain R508 was used as a host for plaque purification, propagation and titration of the phage stocks. Other standard laboratory strains of STEC O157:H7 (n = 24) and non-O157 E. coli (n = 73)  used to evaluate host range of four T1-like phages are listed in Table 1. Unless otherwise indicated the bacterial strains were grown in tryptic soy broth and/or tryptic soy agar.
Host range and lytic capability
Host range and lytic capability of the phages for STEC O157:H7 and non-O157 E. coli was assessed using a microplate phage virulence assay . To estimate multiplicity of infection (MOI), high titre phage stocks (109−1010 PFU/ml) were serially diluted and incubated at 37°C for 5 h with 10-fold diluted overnight cultures of STEC O157:H7 in a 96-well microplate. After incubation, wells were examined visually for turbidity and the highest dilution that resulted in complete lysis (no discernable turbidity) of bacteria was recorded. The MOI for each phage-host assay was calculated by dividing the initial number of phages in the highest-dilution wells by the initial number of bacteria added, as determined by plate counts of serially diluted bacterial cultures.
CsCl density gradient centrifugation
Bacterial nucleic acids were removed from filtered phage lysates (∼109 PFU/ml) using DNase1 (Sigma-Aldrich, Oakville, ON, Canada) and RNaseA (Sigma-Aldrich), and the phage lysates were concentrated in polyethylene glycol (PEG) 8000 and purified through two rounds of CsCl density gradient centrifugation .
Genome sequencing and annotation
Phage DNA was extracted from the CsCl-purified phage lysates using the SDS-proteinase K protocol of Sambrook and Russell . Purified phage DNA was submitted to the Plate-forme d'Analyses Génomiques of the Institut de Biologie Intégrative et des Systèmes (Laval University, Québec, QC, Canada) for sequencing. For each sample, a tagged GS-FLX rapid library was made according to the manufacturer's instructions (Roche/454 sequencing, Brandford, USA). Phage libraries were pooled for sequencing on a GS-FLX+ instrument using titanium chemistry according to the manufacturer's instructions (Roche/454). Sequencing reads were assembled with the gsAssembler module of Newbler v. 2.5.3.
Initial genome annotation was completed using myRAST . Geneious v5.4 program (Biomatters Ltd., Auckland, New Zealand) was used to visually scan the sequence for potential genes. All predicted proteins were scanned for homologues using BLASTP and PSI-BLAST . Rho-independent terminators were identified using WebGeSTer at http://pallab.serc.iisc.ernet.in/gester/rungester.html  and TransTermHP . Promoters were identified by neural network promoter prediction  with visual inspection. Transfer RNA (tRNA) genes were screened using Aragorn  at http://22.214.171.124/ARAGORN/and tRNAScan at http://lowelab.ucsc.edu/tRNAscan-SE/. Transmembrane domains were described using TMHMM 2.0 at http://www.cbs.dtu.dk/services/TMHMM/, Phobius at http://phobius.sbc.su.se/ and SPLIT 4.0 at http://split.pmfst.hr/split/4/. The phage genomes were rendered syntenic by opening at the initiation codon for the small subunit terminase gene prior to dotplot alignment, ClustalW alignment and EMBOSS Stretcher analysis. Whole genome sequences of the four phages studied, as well as another 17 T1-like phages (Table 2) from the database of National Center for Biotechnology Information (NCBI) were analyzed by local ClustalW algorithm ,  using default parameters and phylogenetic trees were visualized by FigTree program (available from http://tree.bio.ed.ac.uk/software/figtree/). CLUSTAL omega  was used to align amino acid sequences of T1-like phages. The GenBank accession numbers for AHP24, AHS24, AHP42 and AKS96 sequence are KF771236, KF771238, KF771237 and KF771239, respectively.
Analysis of structural proteins
The in-gel digest and mass spectrometry experiments were performed by the Proteomics platform of the Eastern Quebec Genomics Center (Quebec, Canada). CsCl-purified phage particles were analyzed for structural proteins by standard Tris-glycine 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Samples were mixed with sample loading buffer and boiled for 5 min before loading. Proteins were stained with Coomassie brilliant blue R250 (Bio-Rad Laboratories, Mississauga, ON, Canada) and subsequently characterized using Bionumerics 6.6 software (Applied Maths, Austin, TX, USA). Bands of interest were excised and de-stained with water. Tryptic digestion was performed on a MassPrep liquid handling robot (Waters, Milford, USA) according to the manufacturer's specifications and to the modified protocol , . Briefly, following reduction with 10 mM dithiothreitol (DTT) and alkylation with 55 mM iodoacetamide, the protein was digested by 126 nM of modified porcine trypsin (Sequencing grade, Promega, Madison, WI, USA) at 58°C for 1 h. The proteolytic peptides were then extracted using 1% formic acid, 2% acetonitrile followed by 1% formic acid and 50% acetonitrile. The recovered extracts were pooled, dried by vacuum centrifuge and resuspended into 7 µl of 0.1% formic acid for mass spectrometry. Peptide resuspensions (2 µl) were separated by online reversed-phase (RP) nanoscale capillary liquid chromatography (nanoLC) and analyzed by electrospray mass spectrometry (ES MS/MS). The experiments were performed with a Agilent 1200 nano pump connected to a triple time-of-flight mass spectrometer (AB Sciex 5600, Framingham, MA,USA) equipped with a nanoelectrospray ion source (AB Sciex 5600). Briefly, 2 µl of the peptide resuspension was injected onto a 15 cm×75 µm (internal diameter) PicoFrit column (New Objective, Woburn, MA), packed with reversed phase C18 particles (5 µm diameter; 300 Å pore size; Jupiter 300, Phenomenex, Torrance, CA, USA) and eluted in a linear gradient from 2–50% buffer B (0.1% formic acid in acetonitrile) at flow rate of 300 nl/min for 30 min. Mass spectra were acquired using a data-dependent acquisition mode using Analyst software version 1.6 (AB Sciex 5600). Each full scan mass spectrum (400 to 1250 m/z) was followed by collision-induced dissociation of the twenty most intense ions. Dynamic exclusion was set for a period of 3 sec and a tolerance of 100 ppm.
All MS/MS peak lists were generated with ProteinPilot Version 4.5 (AB Sciex, Framingham, MA, USA) and analyzed using Mascot (Matrix Science, London, UK; version 2.3.02). Proteins were identified by searching against the Uniref100-SiphoViridea database (release 12-05) as well as an in-house protein database derived from genome sequences of AHP24, AHS24, AHP42 and AKS96. Parameters for Mascot used a fragment ion mass tolerance of 0.10 Da and a parent ion tolerance of 0.10 Da. Iodoacetamide derivatives of cysteine were specified as a fixed modification and oxidation products of methionine were specified as a variable modification with up to two missed cleavages allowed. Scaffold version 4.0.1 (Proteome Software Inc., Portland, OR, USA) was used to validate MS/MS based peptide and protein identifications. The protein identification cut off was set at a confidence level of 95% (MASCOT score >33) with a requirement for at least two peptides to match to a protein. Proteins with similar peptides that could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony.
Phages were able to lyse all 24 STEC O157:H7 strains tested, but displayed no activity against any of the 73 non-O157 E. coli strains (Table 1). Phages AHP24 and AHS24 exhibited the same infective pattern, with 17 strains extremely susceptible, 4 strains highly susceptible and 3 strains moderately susceptible. On the basis of MOI value, the lytic capability of these two phages was slightly higher than AHP42 or AKS96.
General genomic feature
All four phages contained circularly permuted genomes of 45.7–46.8 kb (43.8–44 mol% G+C) encoding 74–81 open reading frames (ORFs) and 1 arginyl-tRNA (Tables 3 and S1−S4). Furthermore, 18−21 rho-dependent terminators and 5−10 promoters recognized by host RNA polymerase were identified. The majority (68–72 ORFs, 86–94%) of the proteins displayed homology to proteins of other T1-like phages with 32−39 of DNA replication, morphogenesis, genome packing and lysis (Tables 3 and S1−S4). Based on functional comparison of the ORFs to the NCBI database of non-redundant protein sequences, none of the genes encoded for proteins associated with pathogenesis, integration or antibiotic resistance.
Comparative computational genomic analysis revealed that the four T1-like phages were collinear (>90.8% pairwise similarity), with AHP24 and AHS24 having the highest sequence identity (99.2%). All four phages were 80.8–86.5% identical to phages JK06, vB_EcoS_Rogue1, phiJLA23 and phiKP26 and 65% similar to phiEB49 in Cluster E and <56% related to other known T1-like phages (Fig. 1A, Table 4). At the protein level, computational analysis of CoreGenes demonstrated that compared to phage vB_EcoS_Rogue1, phages AHP24 and AHS24 shared greatest number of proteins (67–68, Avg. 91.2% similarity) in common, followed by AHP42, AKS96, phiKP26 and phiJLA23 (65, 87.8%), phiJLA23, JK06 and phiEB49 (56–58, Avg.77%)(Table 5).
A, Dot plot alignment of nucleotide identity of the 21 known T1-like phages using Gepard . The vertical axis shows the phage IDs and horizontal axis indicates phage clusters (highlighted in red box). The apparent black diagonal lines indicate high degrees of nucleotide sequence identity; while each phage shows 100% identity to itself (displayed as diagonal line). B, Phylogenetic analysis of whole genomes of the 21 known T1-like phages by ClustalW algorithm. Scale bar represents 0.1 substitutions. C, Whole genome comparisons of phages AHP24 (A), KP36 (B), Rogue1 (C), RTP (D), TLS (E) and T1 (F) using a progressive MAUVE alignment . The degree of sequence similarity is indicated by the intensity of the colored region. The contiguous black boxes under the colored region represent the position of the genes; red, large subunit of terminase; green, tail tape measure protein; blue, tail fiber protein I; black, tail fiber protein II; orange, helicase; pink, common hypothetical protein.
To obtain a global phylogenetic overview of the relationships between the T1-like phages, we employed genomic dot-plots of these genome sequences against each other (Fig. 1A). Clearly, nucleotide sequence aligned well within each cluster. Phylogenic analysis of whole genome also demonstrated that phages within each cluster shared close relatedness at nucleotide level (Fig. 1B). Nucleotide similarity of phages within each cluster was 82.6% (Cluster A), 72.8% (Cluster B), 77.6–81.5% (Cluster C), 65.1% (Cluster D) and 64.2–99.2% (Cluster E), whereas nucleotide identity shared between each cluster was 48.6–55.7% (Fig. 1C, Tables 2 and 4). Phages pSf-1 and ESP2949-1 demonstrated lower nucleotide similarity to phages from each genus (Table 4). Computational analysis of CoreGenes showed that phages within same cluster had greater number of homologues (75.7–91.2%) than those among different clusters (43.7–68%; Table 5). Orphan phage species pSf-1 and ESP2949-1 did not have over 55 gene products (<64%) in common as compared with other phages in each cluster. Considering the close relatedness at both nucleotide and protein level exhibited by the phages within each cluster, we propose the establishment of a new subfamily “Tunavirinae” which can be divided into five genera, i.e. “Tlslikevirus” (Cluster A), “Kp36likevirus” (Cluster B), Tunalikevirus (Cluster C), “Rtplikevirus” (Cluster D) and “Jk06likevirus” (Cluster E) (Fig. 1, Tables 4 and 5), each of which is named after the first isolated phage of its type.
Phylogenetic trees were constructed to further investigate common proteomic features for the large subunit of terminase (TerL), portal protein (PorT), tail fiber (FibA) and major capsid proteins (CapS) (Fig. 2). Overall, these analyses substantiated the establishment of the proposed genera. Interestingly, PorT and CapS of phage phiEB49 were more closely related to those from the “Rtplikevirus” (84.4–93% aa identity, ID) than those from the “Jk06likevirus” (70.4–75.2% aa ID). Within the “Jk06likevirus”, CapS from AHP24, AHS24, AHP42 and AKS96 (100% aa ID) was found to be 70.4–72.3% (aa) related to that from phages JK06, Rogue1, phiKP26 and phiJLA23 (97.8–99.7% aa ID). Likewise high diversity of the whole genome presented by orphan phages pSf-1 and ESP2949-1, low amino acid sequence similarities (<73.5%) were identified for each of the proteins studied, as compared to those of other members of the T1-like family.
The evolutionary history was inferred using the Neighbor-Joining method . The optimal tree with the sum of branch length for A, large subunit of terminase ( = 2.05), B, portal protein ( = 2.2), C, tail fiber ( = 1.61), D, major capsid ( = 2.05), is shown; The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches . The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method  and are in the units of the number of amino acid substitutions per site. The analysis involved 20 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 429 positions (A), 244 positions (B), 807 positions (C), 305 positions (D), in each final dataset. Evolutionary analyses were conducted in MEGA5 . Scale bar represents 0.1 substitutions. The asterisk represents phages of which evolutionary relationships of major proteins differed from those of whole genome.
SDS-PAGE revealed that the structural proteins generated identical banding patterns among the four phages (Fig. 3). Further shotgun proteomics by liquid chromatography-tandem mass spectrometry identified up to 52% of the amino acids in seven structural proteins including tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins (Table 6 and Fig. 3). A major capsid protein (Fig. 3, band D) was observed to have a molecular mass of 29.7 kDa, similar to the 33 kDa of the major head subunit P7 protein previously identified from T1 phage . Also, a conserved hypothetical protein with a molecular mass of 14.2 kDa (Table 6; Fig. 3, band G) was similar to P11 (16 kDa) from phage T1, which has been proposed to be a second major head component that stabilizes the later stages of head assembly . A major 23.6 kDa tail protein (Table 6; Fig. 3, band F) was consistent with a major tail protein from phage Rogue1 (gp29, 25.9kDa)  and from phage T1 (P10, 26 kDa) .
A, tail fiber protein; B, tail tape measure protein; C, portal protein; D, major capsid protein; E, minor tail protein; F, major tail protein; G, conserved hypothetical protein.
This study revealed that phages AHP24, AHS24, AHP42 and AKS96 are closely related members of new proposed genus–“Jk06likevirus”. Not surprisingly, the highest degree of nucleotide identity was shared between AHP24 and AHS24, as they were isolated simultaneously from fecal pats and manure slurry from the same feedlot pen . AHP42 and AKS96 originated from different feedlots, but displayed the second highest degree of nucleotide sequence similarity, a result that confirms our previous findings of genomic relatedness of these two isolates based on restriction enzyme profiles . Our ongoing work has also characterized a number of additional STEC O157:H7-infecting phages with TEM morphology, genome size and restriction enzyme profiles (Niu et al. unpublished data) that are similar to the four phages in this study, possibly because they were also obtained from the same commercial feedlots in 2007 . This may suggest that “Jk06likevirus” are widespread in Alberta feedlots. All four phages were active against a broad range of STEC O157:H7 reference strains, but did not target non-O157 E. coli, suggesting that they could be used to control STEC O157:H7 without harming generic commensal E. coli. Also, the four phages exhibited strong lytic capability against vast majority of PT strains of STEC O157:H7, although lytic capability may vary with propagation hosts. This would make them effective biocontrol agents and possible low dosage required for therapeutic application.
A total of 21 phages with genome sizes ranging from 43 to 52 kb, similar genomic structure and TEM morphology have been described. Based on current taxonomic classification of ICTV, these phages were classified as T1-like phage (Tunalikevirus) within Siphoviridae. Undoubtedly, more T1-like phages will be identified in the future and there is a need to establish a more defined taxonomic system in order to explore the evolutionary relationships and genetic linkages in these types of phage. In the present study, we aligned whole genome sequences from all 21 T1-like phages using the ClustalW algorithm, which has been widely used for nucleotide sequence alignment of viruses -. The phylogenetic analysis showed that the T1-related phages fall into five clusters. Moreover, computational EMBOSS Stretcher ,  and CoreGenes programs – showed that phages within each proposed genus were more closely related than those among genera at both the nucleotide and protein level. This was also confirmed by the phylogenetic analysis of four key functional phage proteins. 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. Similar finding have been noted as part of the Phage Hunters Integrating Research and Education (PHIRE) program (http://phagesdb.org/) and for the global distribution of viruses related to Listeria phage A511. The results indicate that a new subfamily, the “Tunavirinae” created within the family Siphoviridae containing the following genera: a modified Tunalikevirus (T1, ADB-2, Shfl1) , , “Tlslikevirus” (TLS, FSL SP-126) , , “Kp36likevirus” (KP36, F20) , , “Rtplikevirus” (RTP, vB_EcoS_ACG-M12) , ; and “Jk06likevirus” (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49) , , , . This would leave two putative orphan species: pSf-1  and ESP2949-1  to be further classified as more phages are characterized. There is a move within ICTV to eliminate the order Caudovirales, and its three families (Myoviridae, Siphoviridae and Podoviridae) as they are not compatible with emerging genomic and proteomic information on phage phylogeny.
Mitigation of STEC O157:H7 has been a challenge in feedlot cattle. The newly discovered four members of “Jk06likevirus” exhibited broad host range and strong lytic capability against STEC O157:H7, emphasizing efficacy and suitability for phage-based biocontrol of this zoonotic pathogen. In this study, we also proposed further classification of the 21 known T1-like phages into one subfamily with five genera, constructing a basis for proper identification of new phages within the same type. Genomic- and proteomic- based taxonomic classification of phages would facilitate a better understanding of phage diversity and genetic traits involved in phage evolution.
Feature of phage AHP24 gene products and their functional assignments.
Feature of phage AHS24 gene products and their functional assignments.
Feature of phage AHP42 gene products and their functional assignments.
We gratefully acknowledge J. Peters and H. Zahiroddini for technical assistance and support, and R. Johnson (Public Health Agency of Canada, Guelph, ON, Canada) for kind provision of bacterial strains.
Conceived and designed the experiments: YDN TAM KS. Performed the experiments: YDN. Analyzed the data: YDN JHEN AMK. Contributed reagents/materials/analysis tools: TAM KS. Wrote the paper: YDN TAM JHEN AMK KS.
- 1. Ackermann H-W (2009) Phage classification and characterization. Methods Mol Biol 501: 127–140.
- 2. Lavigne R, Seto D, Mahadevan P, Ackermann HW, Kropinski AM (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159: 406–414.
- 3. Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI (2012) Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol 10: 607–617.
- 4. Comeau AM, Tremblay D, Moineau S, Rattei T, Kushkina AI, et al. (2012) Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses. PLoS ONE 7: e40102.
- 5. German GJ, Misra R, Kropinski AM (2006) The T1-like bacteriophages, pp. 211–224. In Calendar R (ed.), The bacteriophages, 2nd ed. New York, NY: Oxford University Press.
- 6. King AM, Lefkowitz E, Adams MJ, Carstens EB (2012) Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, California, CA: Elsevier Academic Press.
- 7. Nyachuba DG (2010) Foodborne illness: is it on the rise? Nutr Rev 68: 257–269.
- 8. Public Health Agency of Canada (2011) National enteric surveillance program (NESP) annual summary. Available at https://www.nml-lnm.gc.ca/NESP-PNSME/surveillance-2011-eng.html (accessed 12 December 2013).
- 9. Maura D, Debarbieux L (2011) Bacteriophages as twenty-first century antibacterial tools for food and medicine. Appl Microbiol Biotechnol 90: 851–859.
- 10. Johnson RP, Gyles CL, Huff WE, Ojha S, Huff GR, et al. (2008) Bacteriophages for prophylaxis and therapy in cattle, poultry and pigs. Anim Health Res Rev 9: 201–215.
- 11. Atterbury RJ (2009) Bacteriophage biocontrol in animals and meat products. Microb Biotechnol 2: 601–612.
- 12. Balogh B, Jones JB, Iriarte FB, Momol MT (2010) Phage therapy for plant disease control. Curr Pharm Biotechnol 11: 48–57.
- 13. Stanford K, McAllister TA, Niu YD, Stephens TP, Mazzocco A, et al. (2010) Oral delivery systems for encapsulated bacteriophages targeted Escherichia coli O157:H7 in feedlot cattle. J Food Prot 73: 1304–1312.
- 14. Rozema EA, Stephens TP, Bach SJ, Okine EK, Johnson RP, et al. (2009) Oral and rectal administration of bacteriophages for control of Escherichia coli O157:H7 in feedlot cattle. J Food Prot 72: 241–250.
- 15. Callaway TR, Edrington TS, Brabban A, Kutter B, Karriker L, et al. (2011) Evaluation of phage treatment as a strategy to reduce Salmonella populations in growing swine. Foodborne Pathog Dis 8: 261–266.
- 16. Carvalho CM, Santos SB, Kropinski AM, Ferreira EC, Azeredo J (2012) Phages as Therapeutic Tools to Control Major Foodborne Pathogens: Campylobacter and Salmonella. In Kurtboke I (ed.), Bacteriophages. Rijeka, Croatia: InTech.
- 17. Liu H, Niu YD, Li JQ, Stanford K, McAllister TA (2013) June 18–20. In-Vitro efficacy of bacteriophages T5, T4, T1 and O1 against E. coli O157 :H7, Joint Canadian Society of Animal Science and Canadian Meat Science Association Congress, Banff, Canada.
- 18. Niu YD, Stanford K, Ackermann HW, McAllister TA (2012) Characterization of 4 T1-like lytic bacteriophages that lyse Shiga-toxin Escherichia coli O157:H7. Can J Microbiol 58: 923–927.
- 19. Niu YD, McAllister TA, Xu Y, Johnson RP, Stephens TP, et al. (2009) Prevalence and impact of bacteriophages on the presence of Escherichia coli O157:H7 in feedlot cattle and their environment. Appl Environ Microbiol 75: 1271–1278.
- 20. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual-3rd ed. New York, NY: Cold Spring Laboratory Press, Cold Spring Harbor.
- 21. Ochman H, Selander RK (1984) Standard reference strains of Escherichia coli from natural populations. J Bacteriol 157: 690–693.
- 22. Niu YD, Johnson RP, Xu Y, McAllister TA, Sharma R, et al. (2009) Host range and lytic capability of four bacteriophages against bovine and clinical human isolates of Shiga toxin-producing Escherichia coli O157:H7. J Appl Microbiol 107: 646–656.
- 23. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
- 24. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
- 25. Mitra A, Kesarwani AK, Pal D, Nagaraja V (2011) WebGeSTer DB-a transcription terminator database. Nucleic Acids Res 39: D129–135.
- 26. Kingsford CL, Ayanbule K, Salzberg SL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8: R22.
- 27. Reese MG (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26: 51–56.
- 28. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11–16.
- 29. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964.
- 30. Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6: 175–182.
- 31. Kall L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027–1036.
- 32. Juretic D, Zoranic L, Zucic D (2002) Basic charge clusters and predictions of membrane protein topology. J Chem Inf Comput Sci 42: 620–632.
- 33. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680.
- 34. Li KB (2003) ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19: 1585–1586.
- 35. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
- 36. Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68: 850–858.
- 37. Havlis J, Thomas H, Sebela M, Shevchenko A (2003) Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem 75: 1300–1306.
- 38. Martin DT, Adair CA, Ritchie DA (1976) Polypeptides specified by bacteriophage T1. J Gen Virol 33: 309–319.
- 39. Ramsay N, Ritchie DA (1984) Phage head assembly in bacteriophage T1. Virology 132: 239–249.
- 40. Kropinski AM, Lingohr EJ, Moyles DM, Ojha S, Mazzocco A, et al. (2012) Endemic bacteriophages: a cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals. Virol J 9: 207.
- 41. Westover KM, Rusinko JP, Hoin J, Neal M (2013) Rogue taxa phenomenon: a biological companion to simulation analysis. Mol Phylogenet Evol 69: 1–3.
- 42. Alonso C, Murtaugh MP, Dee SA, Davies PR (2013) Epidemiological study of air filtration systems for preventing PRRSV infection in large sow herds. Prev Vet Med 112: 109–117.
- 43. Mollov D, Lockhart B, Zlesak D (2013) Complete nucleotide sequence of rose yellow mosaic virus, a novel member of the family Potyviridae. Arch Virol 158: 1917–1923.
- 44. Olson SA (2002) EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 3: 87–91.
- 45. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276–277.
- 46. Mahadevan P, King JF, Seto D (2009) CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res Notes 2: 168.
- 47. Mahadevan P, King JF, Seto D (2009) Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes. Int J Comput Biol Drug Des 2: 100–114.
- 48. Mahadevan P, Seto D (2010) Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes. Adv Exp Med Biol 680: 379–385.
- 49. Amarillas L, Chaidez C, Lugo Y, Leon-Felix J (2013) Complete genome sequence of Escherichia coli O157:H7 bacteriophage phiJLA23 isolated in Mexico. Genome Announc 1: art.no. e00219–00212.
- 50. Amarillas L, Chaidez-Quiroz C, Sanudo-Barajas A, Leon-Felix J (2013) Complete genome sequence of a polyvalent bacteriophage, phiKP26, active on Salmonella and Escherichia coli. Arch Virol 158: 2395–2398.
- 51. Roberts MD, Martin NL, Kropinski AM (2004) The genome and proteome of coliphage T1. Virology 318: 245–266.
- 52. Bhensdadia DV, Bhimani HD, Rawal CM, Kothari VV, Raval VH, et al.. (2013) Complete genome sequence of Escherichia phage ADB-2 isolated from a fecal sample of poultry. Genome Announc 1: art.no. e0004313.
- 53. Moreno Switt AI, Orsi RH, den Bakker HC, Vongkamjan K, Altier C, et al. (2013) Genomic characterization provides new insight into Salmonella phage diversity. BMC Genomics 14: 481.
- 54. Mishra CK, Choi TJ, Kang SC (2012) Isolation and characterization of a bacteriophage F20 virulent to Enterobacter aerogenes. J Gen Virol 93: 2310–2314.
- 55. Kęsik-Szeloch A, Drulis-Kawa Z, Weber-Dąbrowska B, Kassner J, Majkowska-Skrobek G, et al. (2013) Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae. Virol J 10: 100.
- 56. Chibeu A, Lingohr EJ, Masson L, Manges A, Harel J, et al. (2012) Bacteriophages with the ability to degrade uropathogenic Escherichia coli biofilms. Viruses 4: 471–487.
- 57. Wietzorrek A, Schwarz H, Herrmann C, Braun V (2006) The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1. J Bacteriol 188: 1419–1436.
- 58. Battaglioli EJ, Baisa GA, Weeks AE, Schroll RA, Hryckowian AJ, et al. (2011) Isolation of generalized transducing bacteriophages for uropathogenic strains of Escherichia coli. Appl Environ Microbiol 77: 6630–6635.
- 59. Jun JW, Kim JH, Shin SP, Han JE, Chai JY, et al. (2013) Characterization and complete genome sequence of the Shigella bacteriophage pSf-1. Res Microbiol 164: 979–986.
- 60. Lee YD, Kim JY, Park JH, Chang H (2012) Genomic analysis of bacteriophage ESP2949-1, which is virulent for Cronobacter sakazakii. Arch Virol 157: 199–202.
- 61. Krumsiek J, Arnold R, Rattei T (2007) Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23: 1026–1028.
- 62. Darling AE, Mau B, Perna NT (2010) progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: art.no.e11147.
- 63. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.
- 64. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
- 65. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275–282.
- 66. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.