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Ford S, Moeskjær S, Young P, Santamaría RI, Harrison E. Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond. Front Microbiol 2021; 12:765271. [PMID: 34858375 PMCID: PMC8631192 DOI: 10.3389/fmicb.2021.765271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 02/01/2023] Open
Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
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Affiliation(s)
- Sam Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sara Moeskjær
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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Abedon ST, Danis-Wlodarczyk KM, Wozniak DJ, Sullivan MB. Improving Phage-Biofilm In Vitro Experimentation. Viruses 2021; 13. [PMID: 34205417 DOI: 10.3390/v13061175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting.
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Chaudhry W, Lee E, Worthy A, Weiss Z, Grabowicz M, Vega N, Levin B. Mucoidy, a general mechanism for maintaining lytic phage in populations of bacteria. FEMS Microbiol Ecol 2021; 96:5897354. [PMID: 32845324 PMCID: PMC7532286 DOI: 10.1093/femsec/fiaa162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
We present evidence that phage resistance resulting from overproduction of exopolysaccharides, mucoidy, provides a general answer to the longstanding question of how lytic viruses are maintained in populations dominated by bacteria upon which they cannot replicate. In serial transfer culture, populations of mucoid Escherichia coli MG1655 that are resistant to lytic phages with different receptors, and thereby requiring independent mutations for surface resistance, are capable of maintaining these phages with little effect on their total density. Based on the results of our analysis of a mathematical model, we postulate that the maintenance of phage in populations dominated by mucoid cells can be attributed primarily to high rates of transition from the resistant mucoid states to susceptible non-mucoid states. Our tests with both population dynamic and single cell experiments as well as genomic analysis are consistent with this hypothesis. We discuss reasons for the generalized resistance of these mucoid E. coli, and the genetic and molecular mechanisms responsible for the high rate of transition from mucoid to sensitive states responsible for the maintenance of lytic phage in mucoid populations of E. coli.
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Affiliation(s)
- Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Esther Lee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrew Worthy
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Weiss
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Marcin Grabowicz
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicole Vega
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Bruce Levin
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
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Abstract
Virus-like particle (VLP) is a term that has been in use for about 80 years. Usually, VLP has meant a particle that is like a virus, generally by appearance, but without either proven or actual virus functionality. Initially VLP referred to particles seen in electron microscope images of tissues. More recently, VLP has come to mean other things to other researchers. A key divergence has been use of VLP in association with vaccine and biotechnology applications versus use of VLP in enumeration of viruses in environmental samples. To these viral ecologists, a VLP is a particle that is virus sized, has nucleic acid, and could be a functional virus. But to vaccine developers and biotechnology researchers a VLP instead is a viral structure that intentionally lacks a viral genome. In this study, we look at the history of use of VLP, following changes in meaning as the technology to study VLPs changed.
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Affiliation(s)
- Paul Hyman
- Department of Biology and Toxicology, Ashland University, Ashland, Ohio, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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Dominguez-Mirazo M, Jin R, Weitz JS. Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in " Candidatus Liberibacter asiaticus". mSphere 2019; 4:e00409-19. [PMID: 31722990 DOI: 10.1128/mSphere.00409-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.” Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”
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Dominguez-Mirazo M, Jin R, Weitz JS. Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in " Candidatus Liberibacter asiaticus". mSphere 2019; 4. [PMID: 31722990 DOI: 10.1101/661967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."
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Affiliation(s)
- Marian Dominguez-Mirazo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rong Jin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
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Abedon ST. Ecology of Anti-Biofilm Agents II: Bacteriophage Exploitation and Biocontrol of Biofilm Bacteria. Pharmaceuticals (Basel) 2015; 8:559-89. [PMID: 26371011 PMCID: PMC4588183 DOI: 10.3390/ph8030559] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 08/30/2015] [Accepted: 09/02/2015] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are the viruses of bacteria. In the guise of phage therapy they have been used for decades to successfully treat what are probable biofilm-containing chronic bacterial infections. More recently, phage treatment or biocontrol of biofilm bacteria has been brought back to the laboratory for more rigorous assessment as well as towards the use of phages to combat environmental biofilms, ones other than those directly associated with bacterial infections. Considered in a companion article is the inherent ecological utility of bacteriophages versus antibiotics as anti-biofilm agents. Discussed here is a model for phage ecological interaction with bacteria as they may occur across biofilm-containing ecosystems. Specifically, to the extent that individual bacterial types are not highly abundant within biofilm-containing environments, then phage exploitation of those bacteria may represent a "Feast-or-famine" existence in which infection of highly localized concentrations of phage-sensitive bacteria alternate with treacherous searches by the resulting phage progeny virions for new concentrations of phage-sensitive bacteria to infect. An updated synopsis of the literature concerning laboratory testing of phage use to combat bacterial biofilms is then provided along with tips on how "Ecologically" such phage-mediated biofilm control can be modified to more reliably achieve anti-biofilm efficacy.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, OH 44906, USA.
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Allen HK, Abedon ST. Virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms. Front Microbiol 2014; 5:700. [PMID: 25566216 PMCID: PMC4264494 DOI: 10.3389/fmicb.2014.00700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/25/2014] [Indexed: 11/24/2022] Open
Affiliation(s)
- Heather K Allen
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture Ames, IA, USA
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University Mansfield, OH, USA
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Kropinski AM, Waddell T, Meng J, Franklin K, Ackermann HW, Ahmed R, Mazzocco A, Yates J, Lingohr EJ, Johnson RP. The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5. Virol J 2013; 10:76. [PMID: 23497209 PMCID: PMC3606486 DOI: 10.1186/1743-422x-10-76] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 02/28/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Bacteriophages (phages) have been used extensively as analytical tools to type bacterial cultures and recently for control of zoonotic foodborne pathogens in foods and in animal reservoirs. METHODS We examined the host range, morphology, genome and proteome of the lytic E. coli O157 phage rV5, derived from phage V5, which is a member of an Escherichia coli O157:H7 phage typing set. RESULTS Phage rV5 is a member of the Myoviridae family possessing an icosahedral head of 91 nm between opposite apices. The extended tail measures 121 x 17 nm and has a sheath of 44 x 20 nm and a 7 nm-wide core in the contracted state. It possesses a 137,947 bp genome (43.6 mol%GC) which encodes 233 ORFs and six tRNAs. Until recently this virus appeared to be phylogenetically isolated with almost 70% of its gene products ORFans. rV5 is closely related to coliphages Delta and vB-EcoM-FY3, and more distantly related to Salmonella phages PVP-SE1 and SSE-121, Cronobacter sakazakii phage vB_CsaM_GAP31, and coliphages phAPEC8 and phi92. A complete shotgun proteomic analysis was carried out on rV5, extending what had been gleaned from the genomic analyses. Host range studies revealed that rV5 is active against several other E. coli.
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Affiliation(s)
- Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tom Waddell
- Abbott Point of Care, 185 Corkstown Road, Ottawa, ON, K2H 8V4, Canada
| | - Juncai Meng
- Merck Research Laboratories, 126E Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Kristyn Franklin
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Hans-Wolfgang Ackermann
- Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, G1K 7P4, Canada
| | - Rafiq Ahmed
- Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Amanda Mazzocco
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - John Yates
- The Scripps Research Institute, Department of Cell Biology, Proteomic Mass Spectrometry Laboratory, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Erika J Lingohr
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Roger P Johnson
- Public Health Agency of Canada, Laboratory for Foodborne Diseases, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
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Kropinski AM, Lingohr EJ, Moyles DM, Ojha S, Mazzocco A, She YM, Bach SJ, Rozema EA, Stanford K, McAllister TA, Johnson RP. Endemic bacteriophages: a cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals. Virol J 2012; 9:207. [PMID: 22985539 PMCID: PMC3496638 DOI: 10.1186/1743-422x-9-207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/31/2012] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND One of the most effective targets for control of zoonotic foodborne pathogens in the farm to fork continuum is their elimination in food animals destined for market. Phage therapy for Escherichia coli O157:H7 in ruminants, the main animal reservoir of this pathogen, is a popular research topic. Since phages active against this pathogen may be endemic in host animals and their environment, they may emerge during trials of phage therapy or other interventions, rendering interpretation of trials problematic. METHODS During separate phage therapy trials, sheep and cattle inoculated with 109 to 1010 CFU of E. coli O157:H7 soon began shedding phages dissimilar in plaque morphology to the administered therapeutic phages. None of the former was previously identified in the animals or in their environment. The dissimilar "rogue" phage was isolated and characterized by host range, ultrastructure, and genomic and proteomic analyses. RESULTS The "rogue" phage (Phage vB_EcoS_Rogue1) is distinctly different from the administered therapeutic Myoviridae phages, being a member of the Siphoviridae (head: 53 nm; striated tail: 152x8 nm). It has a 45.8 kb genome which is most closely related to coliphage JK06, a member of the "T1-like viruses" isolated in Israel. Detailed bioinformatic analysis reveals that the tail of these phages is related to the tail genes of coliphage lambda. The presence of "rogue" phages resulting from natural enrichments can pose problems in the interpretation of phage therapeutic studies. Similarly, evaluation of any interventions for foodborne or other bacterial pathogens in animals may be compromised unless tests for such phages are included to identify their presence and potential impact.
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Affiliation(s)
- Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, N1G 2 W1, Canada
| | - Erika J Lingohr
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Dianne M Moyles
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, N1G 2 W1, Canada
| | - Shivani Ojha
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Amanda Mazzocco
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
| | - Yi-Min She
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, ON, K1A 0 K9, Canada
| | - Susan J Bach
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, BC, V0H 1Z0, Canada
| | - Erica A Rozema
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, AB, T1J 4 V6, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Kim Stanford
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, AB, T1J 4 V6, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Roger P Johnson
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3 W4, Canada
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Kutter EM, Skutt-Kakaria K, Blasdel B, El-Shibiny A, Castano A, Bryan D, Kropinski AM, Villegas A, Ackermann HW, Toribio AL, Pickard D, Anany H, Callaway T, Brabban AD. Characterization of a ViI-like phage specific to Escherichia coli O157:H7. Virol J 2011; 8:430. [PMID: 21899740 PMCID: PMC3184105 DOI: 10.1186/1743-422x-8-430] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/07/2011] [Indexed: 12/16/2022] Open
Abstract
Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).
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Affiliation(s)
| | | | - Bob Blasdel
- The Evergreen State College, Olympia, WA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH
| | - Ayman El-Shibiny
- The Evergreen State College, Olympia, WA, USA
- Faculty of Environmental Agricultural Sciences, Suez Canal University, Egypt
| | - Anna Castano
- The Evergreen State College, Olympia, WA, USA
- Department of Pediatric Neurology, University of Colorado Children's Hospital, Denver, CO
| | | | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Molecular & Cellular Biology, University of Guelph, ON, Canada
| | - Andre Villegas
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Ana L Toribio
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Hany Anany
- Canadian Research Institute for Food Safety, University of Guelph, ON, Canada
- Microbiology Department, Ain Shams University, Cairo, Egypt
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