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Pyle JD, Lund SR, O'Toole KH, Saleh L. Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans. Cell Rep 2024; 43:114631. [PMID: 39154342 DOI: 10.1016/j.celrep.2024.114631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection, or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX-associated glycosyltransferases (GTs) that catalyze linkage of diverse sugars to 5hmC nucleobase substrates. Metavirome mining revealed thousands of biosynthetic gene clusters containing enzymes with predicted roles in cytosine sugar hypermodification. We developed a platform for high-throughput screening of GT-containing pathways, relying on the Escherichia coli metabolome as a substrate pool. We successfully reconstituted several pathways and isolated diverse sugar modifications appended to cytosine, including mono-, di-, or tri-saccharides comprised of hexoses, N-acetylhexosamines, or heptose. These findings expand our knowledge of hypermodifications on nucleic acids and the origins of corresponding sugar-installing enzymes.
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Affiliation(s)
- Jesse D Pyle
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Sean R Lund
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Katherine H O'Toole
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Lana Saleh
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
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2
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Phenotypic and genotypic characterization of the new Bacillus cereus phage SWEP1. Arch Virol 2021; 166:3183-3188. [PMID: 34505918 DOI: 10.1007/s00705-021-05222-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
A new Bacillus cereus phage, SWEP1, was isolated from black soil. The host lysis activity of phage SWEP1 has a relatively short latent time (20 min) and a small burst size of 83 PFU. The genome of SWEP1 consists of 162,461 bp with 37.77% G+C content. The phage encodes 278 predicted proteins, 103 of which were assigned functionally. No tRNA genes were found. Comparative genomics analysis indicated that SWEP1 is related to Bacillus phage B4 (86.91% identity, 90% query coverage). Phenotypic and genotypic characterization suggested that SWEP1 is a new member of a new species in the genus Bequatrovirus, family Herelleviridae.
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3
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Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. J Virol 2021; 95:e0239120. [PMID: 34287047 DOI: 10.1128/jvi.02391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.
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Hassim A, Lekota KE, van Dyk DS, Dekker EH, van Heerden H. A Unique Isolation of a Lytic Bacteriophage Infected Bacillus anthracis Isolate from Pafuri, South Africa. Microorganisms 2020; 8:microorganisms8060932. [PMID: 32575780 PMCID: PMC7356010 DOI: 10.3390/microorganisms8060932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/11/2020] [Indexed: 11/24/2022] Open
Abstract
Bacillus anthracis is a soil-borne, Gram-positive endospore-forming bacterium and the causative agent of anthrax. It is enzootic in Pafuri, Kruger National Park in South Africa. The bacterium is amplified in a wild ungulate host, which then becomes a source of infection to the next host upon its death. The exact mechanisms involving the onset (index case) and termination of an outbreak are poorly understood, in part due to a paucity of information about the soil-based component of the bacterium’s lifecycle. In this study, we present the unique isolation of a dsDNA bacteriophage from a wildebeest carcass site suspected of having succumbed to anthrax. The aggressively lytic bacteriophage hampered the initial isolation of B. anthracis from samples collected at the carcass site. Classic bacteriologic methods were used to test the isolated phage on B. anthracis under different conditions to simulate deteriorating carcass conditions. Whole genome sequencing was employed to determine the relationship between the bacterium isolated on site and the bacteriophage-dubbed Bacillus phage Crookii. The 154,012 bp phage belongs to Myoviridae and groups closely with another African anthrax carcass-associated Bacillus phage WPh. Bacillus phage Crookii was lytic against B. cereus sensu lato group members but demonstrated a greater affinity for encapsulated B. anthracis at lower concentrations (<1 × 108 pfu) of bacteriophage. The unusual isolation of this bacteriophage demonstrates the phage’s role in decreasing the inoculum in the environment and impact on the life cycle of B. anthracis at a carcass site.
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Affiliation(s)
- Ayesha Hassim
- Department of Veterinary Tropical diseases, University of Pretoria, Faculty of Veterinary Science, Pretoria 0110, South Africa; (K.E.L); (H.v.H.)
- Correspondence: ; Tel.: +27-125-298-339
| | - Kgaugelo Edward Lekota
- Department of Veterinary Tropical diseases, University of Pretoria, Faculty of Veterinary Science, Pretoria 0110, South Africa; (K.E.L); (H.v.H.)
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - David Schalk van Dyk
- Department of Agriculture Fisheries and Forestry, Office of the State Veterinarian, Skukuza 1350, South Africa; (D.S.v.D.); (E.H.D.)
| | - Edgar Henry Dekker
- Department of Agriculture Fisheries and Forestry, Office of the State Veterinarian, Skukuza 1350, South Africa; (D.S.v.D.); (E.H.D.)
| | - Henriette van Heerden
- Department of Veterinary Tropical diseases, University of Pretoria, Faculty of Veterinary Science, Pretoria 0110, South Africa; (K.E.L); (H.v.H.)
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5
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Akhwale JK, Rohde M, Rohde C, Bunk B, Spröer C, Klenk HP, Boga HI, Wittmann J. Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya. PLoS One 2019; 14:e0212102. [PMID: 30763364 PMCID: PMC6375668 DOI: 10.1371/journal.pone.0212102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/28/2019] [Indexed: 12/17/2022] Open
Abstract
We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.
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Affiliation(s)
- Juliah Khayeli Akhwale
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Central Facility for Microscopy, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Christine Rohde
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Johannes Wittmann
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
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6
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Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proc Natl Acad Sci U S A 2018; 115:567-572. [PMID: 29298913 DOI: 10.1073/pnas.1714658115] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Engineered bacteriophages provide powerful tools for biotechnology, diagnostics, pathogen control, and therapy. However, current techniques for phage editing are experimentally challenging and limited to few phages and host organisms. Viruses that target Gram-positive bacteria are particularly difficult to modify. Here, we present a platform technology that enables rapid, accurate, and selection-free construction of synthetic, tailor-made phages that infect Gram-positive bacteria. To this end, custom-designed, synthetic phage genomes were assembled in vitro from smaller DNA fragments. We show that replicating, cell wall-deficient Listeria monocytogenes L-form bacteria can reboot synthetic phage genomes upon transfection, i.e., produce virus particles from naked, synthetic DNA. Surprisingly, Listeria L-form cells not only support rebooting of native and synthetic Listeria phage genomes but also enable cross-genus reactivation of Bacillus and Staphylococcus phages from their DNA, thereby broadening the approach to phages that infect other important Gram-positive pathogens. We then used this platform to generate virulent phages by targeted modification of temperate phage genomes and demonstrated their superior killing efficacy. These synthetic, virulent phages were further armed by incorporation of enzybiotics into their genomes as a genetic payload, which allowed targeting of phage-resistant bystander cells. In conclusion, this straightforward and robust synthetic biology approach redefines the possibilities for the development of improved and completely new phage applications, including phage therapy.
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7
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Willms IM, Hoppert M, Hertel R. Characterization of Bacillus Subtilis Viruses vB_BsuM-Goe2 and vB_BsuM-Goe3. Viruses 2017; 9:E146. [PMID: 28604650 PMCID: PMC5490822 DOI: 10.3390/v9060146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
The Spounavirinae viruses are ubiquitous in nature and have an obligatory virulent lifestyle. They infect Firmicutes, a bacterial phylum containing an array of environmental non-pathogenic and pathogenic organisms. To expand the knowledge of this viral subfamily, new strains were isolated and investigated in this study. Here we present two new viruses, vB_BsuM-Goe2 and vB_BsuM-Goe3, isolated from raw sewage and infecting Bacillus species. Both were morphologically classified via transmission electron microscopy (TEM) as members of the Spounavirinae subfamily belonging to the Myoviridae family. Genomic sequencing and analyses allowed further affiliation of vB_BsuM-Goe2 to the SPO1-like virus group and vB_BsuM-Goe3 to the Bastille-like virus group. Experimentally determined adsorption constant, latency period, burst size and host range for both viruses revealed different survival strategies. Thus vB_BsuM-Goe2 seemed to rely on fewer host species compared to vB_BsuM-Goe3, but efficiently recruits those. Stability tests pointed out that both viruses are best preserved in LB-medium or TMK-buffer at 4 or 21 °C, whereas cryopreservation strongly reduced viability.
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Affiliation(s)
- Inka M Willms
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, University of Goettingen, 37077 Goettingen, Germany.
| | - Robert Hertel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
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8
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Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MRC, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 162:1153-1157. [PMID: 28040838 DOI: 10.1007/s00705-016-3173-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Hans-Wolfgang Ackermann
- L'Institut de biologie intégrative et des systems, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec, QC, G1V 0A6, Canada
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznan, Poland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Robert A Edwards
- Departments of Computer Science and Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Francois Enault
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biologyand PathobiologyUniversity of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001, Leuven, Belgium
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, LV-1067, Latvia
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124, Braunschweig, Germany
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
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9
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Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis. Virology 2016; 489:243-51. [DOI: 10.1016/j.virol.2015.12.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/02/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022]
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10
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Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP. Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae. BMC Genomics 2015; 16:582. [PMID: 26250905 PMCID: PMC4528723 DOI: 10.1186/s12864-015-1757-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
Background Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea. .,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea. .,Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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Abstract
Phage therapy has been proven to be more effective, in some cases, than conventional antibiotics, especially regarding multidrug-resistant biofilm infections. The objective here was to isolate an anti-Enterococcus faecalis bacteriophage and to evaluate its efficacy against planktonic and biofilm cultures. E. faecalis is an important pathogen found in many infections, including endocarditis and persistent infections associated with root canal treatment failure. The difficulty in E. faecalis treatment has been attributed to the lack of anti-infective strategies to eradicate its biofilm and to the frequent emergence of multidrug-resistant strains. To this end, an anti-E. faecalis and E. faecium phage, termed EFDG1, was isolated from sewage effluents. The phage was visualized by electron microscopy. EFDG1 coding sequences and phylogeny were determined by whole genome sequencing (GenBank accession number KP339049), revealing it belongs to the Spounavirinae subfamily of the Myoviridae phages, which includes promising candidates for therapy against Gram-positive pathogens. This analysis also showed that the EFDG1 genome does not contain apparent harmful genes. EFDG1 antibacterial efficacy was evaluated in vitro against planktonic and biofilm cultures, showing effective lytic activity against various E. faecalis and E. faecium isolates, regardless of their antibiotic resistance profile. In addition, EFDG1 efficiently prevented ex vivo E. faecalis root canal infection. These findings suggest that phage therapy using EFDG1 might be efficacious to prevent E. faecalis infection after root canal treatment.
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12
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Bacteriophage PBC1 and its endolysin as an antimicrobial agent against Bacillus cereus. Appl Environ Microbiol 2015; 81:2274-83. [PMID: 25595773 DOI: 10.1128/aem.03485-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus is an opportunistic human pathogen responsible for food poisoning and other, nongastrointestinal infections. Due to the emergence of multidrug-resistant B. cereus strains, the demand for alternative therapeutic options is increasing. To address these problems, we isolated and characterized a Siphoviridae virulent phage, PBC1, and its lytic enzymes. PBC1 showed a very narrow host range, infecting only 1 of 22 B. cereus strains. Phylogenetic analysis based on the major capsid protein revealed that PBC1 is more closely related to the Bacillus clarkii phage BCJA1c and phages of lactic acid bacteria than to the phages infecting B. cereus. Whole-genome comparison showed that the late-gene region, including the terminase gene, structural genes, and holin gene of PBC1, is similar to that from B. cereus temperate phage 250, whereas their endolysins are different. Compared to the extreme host specificity of PBC1, its endolysin, LysPBC1, showed a much broader lytic spectrum, albeit limited to the genus Bacillus. The catalytic domain of LysPBC1 when expressed alone also showed Bacillus-specific lytic activity, which was lower against the B. cereus group but higher against the Bacillus subtilis group than the full-length protein. Taken together, these results suggest that the virulent phage PBC1 is a useful component of a phage cocktail to control B. cereus, even with its exceptionally narrow host range, as it can kill a strain of B. cereus that is not killed by other phages, and that LysPBC1 is an alternative biocontrol agent against B. cereus.
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