101
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Cha K, Oh HK, Jang JY, Jo Y, Kim WK, Ha GU, Ko KS, Myung H. Characterization of Two Novel Bacteriophages Infecting Multidrug-Resistant (MDR) Acinetobacter baumannii and Evaluation of Their Therapeutic Efficacy in Vivo. Front Microbiol 2018; 9:696. [PMID: 29755420 PMCID: PMC5932359 DOI: 10.3389/fmicb.2018.00696] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/26/2018] [Indexed: 01/03/2023] Open
Abstract
Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of Caudovirales as their morphology observed under an electron microscope. Their genomes were double stranded linear DNAs of 42,312 base pairs and 40,260 base pairs, respectively. The two phages were distinct from known Acinetobacter phages when whole genome sequences were compared. PBAB08 showed a 99% similarity with 57% sequence coverage to phage AB1 and PBAB25 showed a 97% similarity with 78% sequence coverage to phage IME_AB3. BLASTN significant alignment coverage of all other known phages were <30%. Seventy six and seventy genes encoding putative phage proteins were found in the genomes of PBAB08 and PBAB25, respectively. Their genomic organizations and sequence similarities were consistent with the modular theory of phage evolution. Therapeutic efficacy of a phage cocktail containing the two and other phages were evaluated in a mice model with nasal infection of MDR A. baumannii. Mice treated with the phage cocktail showed a 2.3-fold higher survival rate than those untreated in 7 days post infection. In addition, 1/100 reduction of the number of A. baumannii in the lung of the mice treated with the phage cocktail was observed. Also, inflammatory responses of mice which were injected with the phage cocktail by intraperitoneal, intranasal, or oral route was investigated. Increase in serum cytokine was minimal regardless of the injection route. A 20% increase in IgE production was seen in intraperitoneal injection route, but not in other routes. Thus, the cocktail containing the two newly isolated phages could serve as a potential candidate for therapeutic interventions to treat A. baummannii infections.
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Affiliation(s)
- Kyoungeun Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea.,The Bacteriophage Bank of Korea, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Hynu K Oh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Jae Y Jang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Yunyeol Jo
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Won K Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Geon U Ha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea
| | - Kwan S Ko
- Samsung Medical Center, Sungkyukwan University School of Medicine, Suwon, South Korea
| | - Heejoon Myung
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, South Korea.,The Bacteriophage Bank of Korea, Hankuk University of Foreign Studies, Yong-In, South Korea
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102
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Optimizing Propagation of Staphylococcus aureus Infecting Bacteriophage vB_SauM-phiIPLA-RODI on Staphylococcus xylosus Using Response Surface Methodology. Viruses 2018; 10:v10040153. [PMID: 29584701 PMCID: PMC5923447 DOI: 10.3390/v10040153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 01/13/2023] Open
Abstract
The use of bacteriophages for killing pathogenic bacteria is a feasible alternative to antibiotics and disinfectants. To obtain the large quantities of phages required for this application, large-scale production of bacteriophages must be optimized. This study aims to define conditions that maximize the phage yield of the virulent and polyvalent staphylococcal bacteriophage vB_SauM-phiIPLA-RODI in broth culture, using the food-grade species Staphylococcus xylosus as the host strain to reduce the risk of growing massive quantities of pathogenic bacteria and therefore, to ensure the safety of the final phage stock. The effect of four variables, namely initial bacterial concentration (5.66–8.40 log10 colony-forming unit (CFU)/mL), initial phage concentration (5–8 log10 plaque-forming unit (PFU)/mL), temperature (21–40 °C) and agitation (20–250 rpm), on phage yield (response) was studied by using response surface methodology (RSM). Successive experimental designs showed that agitation did not significantly impact phage yield, while temperature did have a significant effect, with 38 °C being the optimum for phage propagation. The results allowed the design of a model to describe phage yield as a function of the initial bacterial and phage concentrations at fixed agitation (135 rpm), and optimum temperature (38 °C). The maximum experimental phage yield obtained was 9.3 log10 PFU/mL, while that predicted by the model under the optimized conditions (7.07 log10 CFU/mL initial bacterial population and 6.00 log10 PFU/mL initial phage titer) was 9.25 ± 0.30 log10 PFU/mL, with the desirability of 0.96. This yield is comparable to that obtained when the phage was propagated on the original host, Staphylococcus aureus. Bacteriophage phiIPLA-RODI showed the same host range and very similar biofilm removal ability regardless of the staphylococcal species used for its propagation. The results presented in this study show the suitability of using a food-grade strain of S. xylosus for the propagation of S. aureus infecting phages and the application of RSM to define the optimal propagation conditions.
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103
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Le TS, Nguyen TH, Vo HP, Doan VC, Nguyen HL, Tran MT, Tran TT, Southgate PC, Kurtböke Dİ. Protective Effects of Bacteriophages against Aeromonas hydrophila Species Causing Motile Aeromonas Septicemia (MAS) in Striped Catfish. Antibiotics (Basel) 2018; 7:antibiotics7010016. [PMID: 29495337 PMCID: PMC5872127 DOI: 10.3390/antibiotics7010016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/30/2018] [Accepted: 02/23/2018] [Indexed: 12/04/2022] Open
Abstract
To determine the effectivity of bacteriophages in controlling the mass mortality of striped catfish (Pangasianodon hypophthalmus) due to infections caused by Aeromonas spp. in Vietnamese fish farms, bacteriophages against pathogenic Aeromonas hydrophila were isolated. A. hydrophila-phage 2 and A. hydrophila-phage 5 were successfully isolated from water samples from the Saigon River of Ho Chi Minh City, Vietnam. These phages, belonging to the Myoviridae family, were found to have broad activity spectra, even against the tested multiple-antibiotic-resistant Aeromonas isolates. The latent periods and burst size of phage 2 were 10 min and 213 PFU per infected host cell, respectively. The bacteriophages proved to be effective in inhibiting the growth of the Aeromonas spp. under laboratory conditions. Phage treatments applied to the pathogenic strains during infestation of catfish resulted in a significant improvement in the survival rates of the tested fishes, with up to 100% survival with MOI 100, compared to 18.3% survival observed in control experiments. These findings illustrate the potential for using phages as an effective bio-treatment method to control Motile Aeromonas Septicemia (MAS) in fish farms. This study provides further evidence towards the use of bacteriophages to effectively control disease in aquaculture operations.
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Affiliation(s)
- Tuan Son Le
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland 4556, Australia.
- Research Institute for Marine Fisheries, 224 Le Lai, Ngo Quyen, Hai Phong 180000, Vietnam.
| | - Thi Hien Nguyen
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Hong Phuong Vo
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Van Cuong Doan
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Hong Loc Nguyen
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Minh Trung Tran
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Trong Tuan Tran
- Research Institute for Aquaculture No. 2, 116 Nguyen Dinh Chieu, District 1, Ho Chi Minh 700000, Vietnam.
| | - Paul C Southgate
- Australian Centre for Pacific Islands Research and Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia.
| | - D İpek Kurtböke
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland 4556, Australia.
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104
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Abstract
In a view of growing interest in bacteriophages as the most abundant members of microbial communities and as antibacterial agents, reliable methods for bacteriophage long-term preservation, that warrant the access to original or mutant stocks of unchanged properties, have become of crucial importance. A storage method that retains the infectivity of any kind of bacteriophage virions, either in a cell lysate or in a purified suspension, does not exist, due to the enormous diversity of bacteriophages and hence the differentiation of their sensitivity to various storage conditions. Here, we describe a method of long-term bacteriophage preservation, which is based on freezing of freshly infected susceptible bacteria at early stages of bacteriophage development. The infected bacteria release mature bacteriophages upon melting enabling the recovery of bacteriophage virions with high efficiency. The only limitation of this method is the sensitivity of bacteriophage host to deep-freezing, and thus it can be used for the long-term preservation of the vast majority of bacteriophages.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland.
- Faculty of Agriculture and Biology, Autonomous Department of Microbial Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, Warsaw, 02-776, Poland.
| | - Aleksandra Głowacka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Piotr Golec
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Gdańsk, 02-106, Poland
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105
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Abstract
Basic mathematical descriptions are useful in phage ecology, applied phage ecology such as in the course of phage therapy, and also toward keeping track of expected phage-bacterial interactions as seen during laboratory manipulation of phages. The most basic mathematical descriptor of phages is their titer, that is, their concentration within stocks, experimental vessels, or other environments. Various phenomena can serve to modify phage titers, and indeed phage titers can vary as a function of how they are measured. An important aspect of how changes in titers can occur results from phage interactions with bacteria. These changes tend to vary in degree as a function of bacterial densities within environments, and particularly densities of those bacteria that are susceptible to or at least adsorbable by a given phage type. Using simple mathematical models one can describe phage-bacterial interactions that give rise particularly to phage adsorption events. With elaboration one can consider changes in both phage and bacterial densities as a function of both time and these interactions. In addition, phages along with their impact on bacteria can be considered as spatially constrained processes. In this chapter we consider the simpler of these concepts, providing in particular detailed verbal explanations toward facile mathematical insight. The primary goal is to stimulate a more informed use and manipulation of phages and phage populations within the laboratory as well as toward more effective phage application outside of the laboratory, such as during phage therapy. More generally, numerous issues and approaches to the quantification of phages are considered along with the quantification of individual, ecological, and applied properties of phages.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, 299 Bromfield, Columbus, OH, 43210, USA.
| | - Tena I Katsaounis
- Department of Mathematics, The Ohio State University, Columbus, OH, USA
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106
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Abstract
The one-step growth experiment is fundamental to the description of a new bacteriophage. The following protocol is optimized for those working with rapidly growing bacterial cultures.
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Affiliation(s)
- Andrew M Kropinski
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
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107
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The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses. Cell Host Microbe 2017; 22:801-808.e3. [PMID: 29174401 DOI: 10.1016/j.chom.2017.10.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 01/12/2023]
Abstract
The intestinal microbiota and human health are intimately linked, but interactions between bacteria and bacteriophages in the context of the mammalian intestine remain largely unexplored. We used comparative population genomics to study a tripartite network consisting of a virulent bacteriophage, its bacterial host, and a phage-insensitive bacterial strain both in vitro and within the murine gut. The bacteriophage adapted to infect the insensitive strain when the three partners co-existed in the gut of conventional mice, but not in dixenic mice or in planktonic cultures. The molecular changes associated with modifications in the bacteriophage host spectrum included single amino acid substitutions and an unusual homologous intragenomic recombination event within the genome of the bacteriophage. An intermediate bacterial host isolated from the murine microbiota mediated bacteriophage adaptation. Our data indicate that by offering access to new hosts, the microbiota shifts the genetic diversity of bacteriophages, thereby promoting long-term persistence of bacteriophage populations.
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108
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Strotskaya A, Savitskaya E, Metlitskaya A, Morozova N, Datsenko KA, Semenova E, Severinov K. The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies. Nucleic Acids Res 2017; 45:1946-1957. [PMID: 28130424 PMCID: PMC5389539 DOI: 10.1093/nar/gkx042] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/17/2017] [Indexed: 12/22/2022] Open
Abstract
CRISPR-Cas systems provide prokaryotes with adaptive defense against bacteriophage infections. Given an enormous variety of strategies used by phages to overcome their hosts, one can expect that the efficiency of protective action of CRISPR-Cas systems against different viruses should vary. Here, we created a collection of Escherichia coli strains with type I-E CRISPR-Cas system targeting various positions in the genomes of bacteriophages λ, T5, T7, T4 and R1-37 and investigated the ability of these strains to resist the infection and acquire additional CRISPR spacers from the infecting phage. We find that the efficiency of CRISPR-Cas targeting by the host is determined by phage life style, the positions of the targeted protospacer within the genome, and the state of phage DNA. The results also suggest that during infection by lytic phages that are susceptible to CRISPR interference, CRISPR-Cas does not act as a true immunity system that saves the infected cell but rather enforces an abortive infection pathway leading to infected cell death with no phage progeny release.
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Affiliation(s)
- Alexandra Strotskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Waksman Institute of Microbiology, Piscataway, NJ, USA
| | - Ekaterina Savitskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Natalia Morozova
- Peter the Great St. Petersburg State Polytechnic University, St. Petersburg, Russia
| | | | | | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Waksman Institute of Microbiology, Piscataway, NJ, USA.,Peter the Great St. Petersburg State Polytechnic University, St. Petersburg, Russia
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109
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Baig A, Colom J, Barrow P, Schouler C, Moodley A, Lavigne R, Atterbury R. Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection. Front Microbiol 2017; 8:1652. [PMID: 28912765 PMCID: PMC5582158 DOI: 10.3389/fmicb.2017.01652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/15/2017] [Indexed: 11/29/2022] Open
Abstract
We have performed microbiological and genomic characterization of an historic collection of nine bacteriophages, specifically infecting a K1 E. coli O18:K1:H7 ColV+ strain. These phages were isolated from sewage and tested for their efficacy in vivo for the treatment of systemic E. coli infection in a mouse infection model by Smith and Huggins (1982). The aim of the study was to identify common microbiological and genomic characteristics, which co-relate to the performance of these phages in in vivo study. These features will allow an informed selection of phages for use as therapeutic agents. Transmission electron microscopy showed that six of the nine phages were Podoviridae and the remaining three were Siphoviridae. The four best performing phages in vivo belonged to the Podoviridae family. In vitro, these phages exhibited very short latent and rise periods in our study. In agreement with their microbiological profiles, characterization by genome sequencing showed that all six podoviruses belong to the Autographivirinae subfamily. Of these, four were isolates of the same species (99% identity), whereas two had divergent genomes compared to other podoviruses. The Siphoviridae phages, which were moderate to poor performers in vivo, exhibited longer latent and rise periods in vitro. Two of the three siphoviruses were closely related to each other (99% identity), but all can be associated with the Guernseyvirinae subfamily. Genome sequence comparison of both types of phages showed that a gene encoding for DNA-dependent RNA polymerase was only present in phages with faster replication cycle, which may account for their better performance in vivo. These data define a combination of microbiological, genomic and in vivo characteristics which allow a more rational evaluation of the original in vivo data and pave the way for the selection of phages for future phage therapy trails.
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Affiliation(s)
- Abiyad Baig
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington CampusSutton Bonington, United Kingdom
| | - Joan Colom
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington CampusSutton Bonington, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington CampusSutton Bonington, United Kingdom
| | - Catherine Schouler
- Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, Université François Rabelais de ToursNouzilly, France
| | - Arshnee Moodley
- Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, Université François Rabelais de ToursNouzilly, France.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Rob Lavigne
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark.,Laboratory of Gene Technology, Department of Biosystems, KU LeuvenLeuven, Belgium
| | - Robert Atterbury
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington CampusSutton Bonington, United Kingdom
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110
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Pourcel C, Midoux C, Vergnaud G, Latino L. A carrier state is established in Pseudomonas aeruginosa by phage LeviOr01, a newly isolated ssRNA levivirus. J Gen Virol 2017; 98:2181-2189. [PMID: 28771128 DOI: 10.1099/jgv.0.000883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
ssRNA bacteriophages are very abundant but poorly studied, particularly in relation to their effect on bacterial evolution. We isolated a new Pseudomonas aeruginosa levivirus, vB_PaeL_PcyII-10_LeviOr01, from hospital waste water. Its genome comprises 3669 nucleotides and encodes four putative proteins. Following bacterial infection, a carrier state is established in a fraction of the cells, conferring superinfection immunity. Such cells also resist other phages that use type IV pili as a receptor. The carrier population is composed of a mixture of cells producing phage, and susceptible cells that are non-carriers. Carrier cells accumulate phage until they burst, releasing large quantities of virions. The continuous presence of phage favours the emergence of host variants bearing mutations in genes involved in type IV pilus biogenesis, but also in genes affecting lipopolysaccharide (LPS) synthesis. The establishment of a carrier state in which phage particles are continuously released was previously reported for some dsRNA phages, but has not previously been described for a levivirus. The present results highlight the importance of the carrier state, an association that benefits both phages and bacteria and plays a role in bacterial evolution.
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Affiliation(s)
- Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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111
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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: 20] [Impact Index Per Article: 2.9] [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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112
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A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome. PLoS Genet 2017; 13:e1006838. [PMID: 28594826 PMCID: PMC5481146 DOI: 10.1371/journal.pgen.1006838] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 06/22/2017] [Accepted: 05/23/2017] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans. Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts. The mechanisms allowing virulent V. cholerae strains to defend against the ubiquitous threat of predatory phages have not been established. Here, we show that V. cholerae PLEs (phage-inducible chromosomal island-like elements) are widespread genomic islands dedicated to phage defense. Analysis of V. cholerae isolates spanning a 60-year collection period identified five unique PLEs. Remarkably, we found that all PLEs (regardless of geographic or temporal origin) respond to infection by a myovirus called ICP1, the most prominent V. cholerae phage found in cholera patient stool samples from Bangladesh. We found that PLE activity reduces phage genome replication and accelerates cell lysis following ICP1 infection, killing infected host cells and preventing the production of progeny phage. PLEs are mobilized by ICP1 infection and can spread to neighboring cells such that protection from phage predation can be horizontally acquired. Our results reveal that PLEs are a persistent feature of the V. cholerae mobilome that are adapted to providing protection from a single predatory phage and advance our understanding of how phages influence pathogen evolution. Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. V. cholerae is commonly recovered from patient samples with predatory bacteriophages (phages), which impose strong selective pressure favoring phage resistant strains over their vulnerable counterparts. Here, we investigated the activity of PLEs (phage-inducible chromosomal island-like elements), a novel group of mobile genetic elements that have contributed to phage resistance in V. cholerae over the last 60 years. Surprisingly, we found that PLEs are protective against a single, prevalent phage type. We found that PLE activity reduces phage genome replication and accelerates the kinetics of bacterial cell lysis. Our study shows that mobile genetic elements play a key role in phage resistance in successful epidemic V. cholerae.
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113
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Abedon ST. Phage "delay" towards enhancing bacterial escape from biofilms: a more comprehensive way of viewing resistance to bacteriophages. AIMS Microbiol 2017; 3:186-226. [PMID: 31294157 PMCID: PMC6605007 DOI: 10.3934/microbiol.2017.2.186] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
In exploring bacterial resistance to bacteriophages, emphasis typically is placed on those mechanisms which completely prevent phage replication. Such resistance can be detected as extensive reductions in phage ability to form plaques, that is, reduced efficiency of plating. Mechanisms include restriction-modification systems, CRISPR/Cas systems, and abortive infection systems. Alternatively, phages may be reduced in their “vigor” when infecting certain bacterial hosts, that is, with phages displaying smaller burst sizes or extended latent periods rather than being outright inactivated. It is well known, as well, that most phages poorly infect bacteria that are less metabolically active. Extracellular polymers such as biofilm matrix material also may at least slow phage penetration to bacterial surfaces. Here I suggest that such “less-robust” mechanisms of resistance to bacteriophages could serve bacteria by slowing phage propagation within bacterial biofilms, that is, delaying phage impact on multiple bacteria rather than necessarily outright preventing such impact. Related bacteria, ones that are relatively near to infected bacteria, e.g., roughly 10+ µm away, consequently may be able to escape from biofilms with greater likelihood via standard dissemination-initiating mechanisms including erosion from biofilm surfaces or seeding dispersal/central hollowing. That is, given localized areas of phage infection, so long as phage spread can be reduced in rate from initial points of contact with susceptible bacteria, then bacterial survival may be enhanced due to bacteria metaphorically “running away” to more phage-free locations. Delay mechanisms—to the extent that they are less specific in terms of what phages are targeted—collectively could represent broader bacterial strategies of phage resistance versus outright phage killing, the latter especially as require specific, evolved molecular recognition of phage presence. The potential for phage delay should be taken into account when developing protocols of phage-mediated biocontrol of biofilm bacteria, e.g., as during phage therapy of chronic bacterial infections.
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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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114
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Isolation and Characterization of a Shewanella Phage-Host System from the Gut of the Tunicate, Ciona intestinalis. Viruses 2017; 9:v9030060. [PMID: 28327522 PMCID: PMC5371815 DOI: 10.3390/v9030060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/08/2017] [Accepted: 03/17/2017] [Indexed: 01/16/2023] Open
Abstract
Outnumbering all other biological entities on earth, bacteriophages (phages) play critical roles in structuring microbial communities through bacterial infection and subsequent lysis, as well as through horizontal gene transfer. While numerous studies have examined the effects of phages on free-living bacterial cells, much less is known regarding the role of phage infection in host-associated biofilms, which help to stabilize adherent microbial communities. Here we report the cultivation and characterization of a novel strain of Shewanella fidelis from the gut of the marine tunicate Ciona intestinalis, inducible prophages from the S. fidelis genome, and a strain-specific lytic phage recovered from surrounding seawater. In vitro biofilm assays demonstrated that lytic phage infection affects biofilm formation in a process likely influenced by the accumulation and integration of the extracellular DNA released during cell lysis, similar to the mechanism that has been previously shown for prophage induction.
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115
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Lal TM, Sano M, Ransangan J. Isolation and Characterization of Large Marine Bacteriophage (Myoviridae), VhKM4 Infecting Vibrio harveyi. JOURNAL OF AQUATIC ANIMAL HEALTH 2017; 29:26-30. [PMID: 28166465 DOI: 10.1080/08997659.2016.1249578] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The causative agent responsible for vibriosis in tropical fish aquaculture, Vibrio harveyi, has become a major bacterial pathogen. Studies suggest that this bacterium has developed resistance to antibiotics commonly used in aquaculture. In view of this situation and the requirement for the proposed postantibiotic era, bacteriophage therapy seems to be a promising control strategy for fish vibriosis. In this study, a lytic Vibrio phage VhKM4 belonging to a member of large, marine Myoviridae was successfully isolated. It exhibited bacteriolysis to both V. harveyi VHJR7 and V. parahaemolyticus ATCC 17802. The latent period of the VhKM4 phage was recorded at 60 min. It also recorded average burst size of approximately 52 plaque-forming units per infected cell. A strong bacteriolytic activity at low multiplicity of infection of 0.01 indicates the effectiveness of this large marine myovirid against fish pathogenic strain of V. harveyi VHJR7. Received June 16, 2016; accepted October 7, 2016.
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Affiliation(s)
- Tamrin M Lal
- a Borneo Marine Research Institute , Universiti Malaysia Sabah , Jalan UMS, 88400 Kota Kinabalu , Sabah , Malaysia
| | - Motohiko Sano
- b Laboratory of Fish Pathology, Department of Marine Biosciences , Tokyo University of Marine Science and Technology , Room 223, Building 2 2F, Konan 4-5-7, Minato-ku , Tokyo 108-8477 , Japan
| | - Julian Ransangan
- a Borneo Marine Research Institute , Universiti Malaysia Sabah , Jalan UMS, 88400 Kota Kinabalu , Sabah , Malaysia
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116
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Owen SV, Wenner N, Canals R, Makumi A, Hammarlöf DL, Gordon MA, Aertsen A, Feasey NA, Hinton JCD. Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1. Front Microbiol 2017; 8:235. [PMID: 28280485 PMCID: PMC5322425 DOI: 10.3389/fmicb.2017.00235] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/02/2017] [Indexed: 01/30/2023] Open
Abstract
In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580, and BTP5. We show that common S. Typhimurium prophages Gifsy-2, Gifsy-1, and ST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species "Salmonella virus BTP1", belonging to the P22virus genus. Surprisingly, ∼109 BTP1 virus particles per ml were detected in the supernatant of non-induced, stationary-phase cultures of strain D23580, representing the highest spontaneously induced phage titer so far reported for a bacterial prophage. High spontaneous induction is shown to be an intrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around 0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.
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Affiliation(s)
- Siân V Owen
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Nicolas Wenner
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Angela Makumi
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven Leuven, Belgium
| | - Disa L Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University Uppsala, Sweden
| | - Melita A Gordon
- Institute of Infection and Global Health, University of LiverpoolLiverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research ProgrammeBlantyre, Malawi
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven Leuven, Belgium
| | | | - Jay C D Hinton
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
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117
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Castillo D, Middelboe M. Genomic diversity of bacteriophages infecting the fish pathogenFlavobacterium psychrophilum. FEMS Microbiol Lett 2016; 363:fnw272. [DOI: 10.1093/femsle/fnw272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/05/2016] [Accepted: 11/29/2016] [Indexed: 01/21/2023] Open
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118
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Weber-Dąbrowska B, Jończyk-Matysiak E, Żaczek M, Łobocka M, Łusiak-Szelachowska M, Górski A. Bacteriophage Procurement for Therapeutic Purposes. Front Microbiol 2016; 7:1177. [PMID: 27570518 PMCID: PMC4981656 DOI: 10.3389/fmicb.2016.01177] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023] Open
Abstract
Bacteriophages (phages), discovered 100 years ago, are able to infect and destroy only bacterial cells. In the current crisis of antibiotic efficacy, phage therapy is considered as a supplementary or even alternative therapeutic approach. Evolution of multidrug-resistant and pandrug-resistant bacterial strains poses a real threat, so it is extremely important to have the possibility to isolate new phages for therapeutic purposes. Our phage laboratory and therapy center has extensive experience with phage isolation, characterization, and therapeutic application. In this article we present current progress in bacteriophages isolation and use for therapeutic purposes, our experience in this field and its practical implications for phage therapy. We attempt to summarize the state of the art: properties of phages, the methods for their isolation, criteria of phage selection for therapeutic purposes and limitations of their use. Perspectives for the use of genetically engineered phages to specifically target bacterial virulence-associated genes are also briefly presented.
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Affiliation(s)
- Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland; Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life SciencesWarsaw, Poland
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
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119
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Abedon ST. Phage therapy dosing: The problem(s) with multiplicity of infection (MOI). BACTERIOPHAGE 2016; 6:e1220348. [PMID: 27738558 PMCID: PMC5056779 DOI: 10.1080/21597081.2016.1220348] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 11/19/2022]
Abstract
The concept of bacteriophage multiplicity of infection (MOI) – ratios of phages to bacteria – historically has been less easily applied than many phage workers would prefer or, perhaps, may be aware. Here, toward clarification of the concept, I discuss multiplicity of infection in terms of semantics, history, mathematics, pharmacology, and actual practice. For phage therapy and other biocontrol purposes it is desirable, especially, not to solely employ MOI to describe what phage quantities have been applied during dosing. Why? Bacterial densities can change between bacterial challenge and phage application, may not be easily determined immediately prior to phage dosing, and/or target bacterial populations may not be homogeneous with regard to phage access and thereby inconsistent in terms of what MOI individual bacteria experience. Toward experiment reproducibility and as practiced generally for antibacterial application, phage dosing instead should be described in terms of concentrations of formulations (phage titers) as well as volumes applied and, in many cases, absolute numbers of phages delivered. Such an approach typically will be far more desirable from a pharmacological perspective than solely indicating ratios of agents to bacteria. This essay was adapted, with permission, from an appendix of the 2011 monograph, Bacteriophages and Biofilms, Nova Science Publishers.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University , Mansfield, OH, USA
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120
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A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. Sci Rep 2016; 6:30372. [PMID: 27460944 PMCID: PMC4961962 DOI: 10.1038/srep30372] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 11/09/2022] Open
Abstract
Bacteria in the Roseobacter lineage have been studied extensively due to their significant biogeochemical roles in the marine ecosystem. However, our knowledge on bacteriophage which infects the Roseobacter clade is still very limited. Here, we report a new bacteriophage, phage DSS3Φ8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3Φ8 is a lytic siphovirus. Genomic analysis showed that DSS3Φ8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3Φ8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205-279 kb). DSS3Φ8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3Φ8 also contains the integrase and repressor genes, indicating its potential to involve in lysogenic cycle. In addition, four GTA (gene transfer agent) genes were identified in the DSS3Φ8 genome. Genomic analysis suggests that DSS3Φ8 is a highly mosaic phage that inherits the genetic features from siphoviruses, podoviruses, prophages and GTAs. This is the first report of CbK-like phages infecting marine bacteria. We believe phage isolation is still a powerful tool that can lead to discovery of new phages and help interpret the overwhelming unknown sequences in the viral metagenomics.
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121
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Experimental Phage Therapy for Burkholderia pseudomallei Infection. PLoS One 2016; 11:e0158213. [PMID: 27387381 PMCID: PMC4936672 DOI: 10.1371/journal.pone.0158213] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 06/13/2016] [Indexed: 12/19/2022] Open
Abstract
Burkholderia pseudomallei is an intracellular Gram-negative bacterial pathogen intrinsically resistant to a variety of antibiotics. Phages have been developed for use as an alternative treatment therapy, particularly for bacterial infections that do not respond to conventional antibiotics. In this study, we investigated the use of phages to treat cells infected with B. pseudomallei. Phage C34 isolated from seawater was purified and characterised on the basis of its host range and morphology using transmission electron microscopy (TEM). Phage C34 was able to lyse 39.5% of B. pseudomallei clinical strains. Due to the presence of contractile tail, phage C34 is classified as a member of the family Myoviridae, a tailed double-stranded DNA virus. When 2 × 105 A549 cells were exposed to 2 × 107 PFU of phage C34, 24 hours prior to infection with 2 × 106 CFU of B. pseudomallei, it was found that the survivability of the cells increased to 41.6 ± 6.8% as compared to 22.8 ± 6.0% in untreated control. Additionally, application of phage successfully rescued 33.3% of mice infected with B. pseudomallei and significantly reduced the bacterial load in the spleen of the phage-treated mice. These findings indicate that phage can be a potential antimicrobial agent for B. pseudomallei infections.
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122
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Dufour N, Clermont O, La Combe B, Messika J, Dion S, Khanna V, Denamur E, Ricard JD, Debarbieux L. Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4 Escherichia coli clonal complex. J Antimicrob Chemother 2016; 71:3072-3080. [PMID: 27387322 DOI: 10.1093/jac/dkw253] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/02/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Amongst the highly diverse Escherichia coli population, the ST131-O25b:H4 clonal complex is particularly worrisome as it is associated with a high level of antibiotic resistance. The lack of new antibiotics, the worldwide continuous increase of infections caused by MDR bacteria and the need for narrow-spectrum antimicrobial agents have revived interest in phage therapy. In this article, we describe a virulent bacteriophage, LM33_P1, which specifically infects O25b strains, and provide data related to its therapeutic potential. METHODS A large panel of E. coli strains (n = 283) was used to assess both the specificity and the activity of bacteriophage LM33_P1. Immunology, biochemistry and genetics-based methods confirmed this specificity. Virology methods and sequencing were used to characterize this bacteriophage in vitro, while three relevant mouse models were employed to show its in vivo efficacy. RESULTS Bacteriophage LM33_P1 exclusively infects O25b E. coli strains with a 70% coverage on sequence types associated with high antibiotic resistance (ST131 and ST69). This specificity is due to an interaction with the LPS mediated by an original tail fibre. LM33_P1 also has exceptional intrinsic properties with a high adsorption constant and produces over 300 virions per cell in <10 min. Using animal pneumonia, septicaemia and urinary tract infection models, we showed the in vivo efficacy of LM33_P1 to reduce the bacterial load in several organs. CONCLUSIONS Bacteriophage LM33_P1 represents the first weapon that specifically and quickly kills O25b E. coli strains. Therapeutic approaches derived from this bacteriophage could be developed to stop or slow down the spread of the ST131-O25b:H4 drug-resistant clonal complex in humans.
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Affiliation(s)
- Nicolas Dufour
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,Institut Pasteur, Department of Microbiology, Molecular Biology of Gene in Extremophiles, F-75015 Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Béatrice La Combe
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Jonathan Messika
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Varun Khanna
- Institut Pasteur, Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,AP-HP, Hôpitaux Universitaires Paris Nord Val-de-Seine, Laboratoire de Génétique Moléculaire, Site Bichat, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Jean-Damien Ricard
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Department of Microbiology, Molecular Biology of Gene in Extremophiles, F-75015 Paris, France
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123
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Chevallereau A, Blasdel BG, De Smet J, Monot M, Zimmermann M, Kogadeeva M, Sauer U, Jorth P, Whiteley M, Debarbieux L, Lavigne R. Next-Generation "-omics" Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006134. [PMID: 27380413 PMCID: PMC4933390 DOI: 10.1371/journal.pgen.1006134] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/31/2016] [Indexed: 01/08/2023] Open
Abstract
As interest in the therapeutic and biotechnological potentials of bacteriophages has grown, so has value in understanding their basic biology. However, detailed knowledge of infection cycles has been limited to a small number of model bacteriophages, mostly infecting Escherichia coli. We present here the first analysis coupling data obtained from global next-generation approaches, RNA-Sequencing and metabolomics, to characterize interactions between the virulent bacteriophage PAK_P3 and its host Pseudomonas aeruginosa. We detected a dramatic global depletion of bacterial transcripts coupled with their replacement by viral RNAs over the course of infection, eventually leading to drastic changes in pyrimidine metabolism. This process relies on host machinery hijacking as suggested by the strong up-regulation of one bacterial operon involved in RNA processing. Moreover, we found that RNA-based regulation plays a central role in PAK_P3 lifecycle as antisense transcripts are produced mainly during the early stage of infection and viral small non coding RNAs are massively expressed at the end of infection. This work highlights the prominent role of RNA metabolism in the infection strategy of a bacteriophage belonging to a new characterized sub-family of viruses with promising therapeutic potential.
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Affiliation(s)
- Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Bob G. Blasdel
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Maria Kogadeeva
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Peter Jorth
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas, Austin, Texas, United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas, Austin, Texas, United States of America
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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124
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Jeon J, D'Souza R, Pinto N, Ryu C, Park J, Yong D, Lee K. Characterization and complete genome sequence analysis of two
Myoviral
bacteriophages infecting clinical carbapenem‐resistant
Acinetobacter baumannii
isolates. J Appl Microbiol 2016; 121:68-77. [DOI: 10.1111/jam.13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/16/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- J. Jeon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - R. D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - N. Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - C.‐M. Ryu
- Molecular Phytobacteriology Laboratory KRIBB Daejeon Korea
- Biosystems and Bioengineering Program School of Science University of Science and Technology (UST) Daejeon Korea
| | - J. Park
- Laboratory Animal Medicine College of Veterinary Medicine Chonnam National University Gwang‐ju Korea
| | - D. Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - K. Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
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125
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Xu Y, Ma Y, Yao S, Jiang Z, Pei J, Cheng C. Characterization, Genome Sequence, and Analysis of Escherichia Phage CICC 80001, a Bacteriophage Infecting an Efficient L-Aspartic Acid Producing Escherichia coli. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:18-26. [PMID: 26501200 DOI: 10.1007/s12560-015-9218-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Escherichia phage CICC 80001 was isolated from the bacteriophage contaminated medium of an Escherichia coli strain HY-05C (CICC 11022S) which could produce L-aspartic acid. The phage had a head diameter of 45-50 nm and a tail of about 10 nm. The one-step growth curve showed a latent period of 10 min and a rise period of about 20 min. The average burst size was about 198 phage particles per infected cell. Tests were conducted on the plaques, multiplicity of infection, and host range. The genome of CICC 80001 was sequenced with a length of 38,810 bp, and annotated. The key proteins leading to host-cell lysis were phylogenetically analyzed. One protein belonged to class II holin, and the other two belonged to the endopeptidase family and N-acetylmuramoyl-L-alanine amidase family, respectively. The genome showed the sequence identity of 82.7% with that of Enterobacteria phage T7, and carried ten unique open reading frames. The bacteriophage resistant E. coli strain designated CICC 11021S was breeding and its L-aspartase activity was 84.4% of that of CICC 11022S.
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Affiliation(s)
- Youqiang Xu
- China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, 100015, People's Republic of China.
- Engineering Technology Research Center of Fumaric Acid Biotransformation in Shandong Province, Yantai, Shandong Province, 265709, People's Republic of China.
| | - Yuyue Ma
- Engineering Technology Research Center of Fumaric Acid Biotransformation in Shandong Province, Yantai, Shandong Province, 265709, People's Republic of China
| | - Su Yao
- China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, 100015, People's Republic of China
| | - Zengyan Jiang
- Engineering Technology Research Center of Fumaric Acid Biotransformation in Shandong Province, Yantai, Shandong Province, 265709, People's Republic of China
| | - Jiangsen Pei
- China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, 100015, People's Republic of China
- Engineering Technology Research Center of Fumaric Acid Biotransformation in Shandong Province, Yantai, Shandong Province, 265709, People's Republic of China
| | - Chi Cheng
- China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, 100015, People's Republic of China.
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126
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Yu P, Mathieu J, Li M, Dai Z, Alvarez PJJ. Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches. Appl Environ Microbiol 2016; 82:808-15. [PMID: 26590277 PMCID: PMC4725286 DOI: 10.1128/aem.02382-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/13/2015] [Indexed: 11/20/2022] Open
Abstract
Many studies on phage biology are based on isolation methods that may inadvertently select for narrow-host-range phages. Consequently, broad-host-range phages, whose ecological significance is largely unexplored, are consistently overlooked. To enhance research on such polyvalent phages, we developed two sequential multihost isolation methods and tested both culture-dependent and culture-independent phage libraries for broad infectivity. Lytic phages isolated from activated sludge were capable of interspecies or even interorder infectivity without a significant reduction in the efficiency of plating (0.45 to 1.15). Two polyvalent phages (PX1 of the Podoviridae family and PEf1 of the Siphoviridae family) were characterized in terms of adsorption rate (3.54 × 10(-10) to 8.53 × 10(-10) ml/min), latent time (40 to 55 min), and burst size (45 to 99 PFU/cell), using different hosts. These phages were enriched with a nonpathogenic host (Pseudomonas putida F1 or Escherichia coli K-12) and subsequently used to infect model problematic bacteria. By using a multiplicity of infection of 10 in bacterial challenge tests, >60% lethality was observed for Pseudomonas aeruginosa relative to uninfected controls. The corresponding lethality for Pseudomonas syringae was ∼ 50%. Overall, this work suggests that polyvalent phages may be readily isolated from the environment by using different sequential hosts, and this approach should facilitate the study of their ecological significance as well as enable novel applications.
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Affiliation(s)
- Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Mengyan Li
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Zhaoyi Dai
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
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127
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Barr JJ, Auro R, Sam-Soon N, Kassegne S, Peters G, Bonilla N, Hatay M, Mourtada S, Bailey B, Youle M, Felts B, Baljon A, Nulton J, Salamon P, Rohwer F. Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters. Proc Natl Acad Sci U S A 2015; 112:13675-80. [PMID: 26483471 PMCID: PMC4640763 DOI: 10.1073/pnas.1508355112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4∆hoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4∆hoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4∆hoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage-host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.
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Affiliation(s)
- Jeremy J Barr
- Department of Biology, San Diego State University, San Diego, CA 92182;
| | - Rita Auro
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Nicholas Sam-Soon
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182
| | - Sam Kassegne
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182
| | - Gregory Peters
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Natasha Bonilla
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Mark Hatay
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Sarah Mourtada
- Department of Mathematics, San Diego State University, San Diego, CA 92182
| | - Barbara Bailey
- Department of Mathematics, San Diego State University, San Diego, CA 92182
| | | | - Ben Felts
- Department of Mathematics, San Diego State University, San Diego, CA 92182
| | - Arlette Baljon
- Department of Physics, San Diego State University, San Diego, CA 92182
| | - Jim Nulton
- Department of Mathematics, San Diego State University, San Diego, CA 92182
| | - Peter Salamon
- Department of Mathematics, San Diego State University, San Diego, CA 92182
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182
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128
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Lu Y, Shi H, Zhang Z, Han F, Li J, Sun Y. Isolation and characterization of a lytic bacteriophage φKp-lyy15 of Klebsiella pneumoniae. Virol Sin 2015; 30:66-8. [PMID: 25648354 DOI: 10.1007/s12250-014-3523-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yinyin Lu
- Department of Pathogenobiology, Basic Medical School, Jilin University, Changchun, 130021, China
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129
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Sekulovic O, Ospina Bedoya M, Fivian-Hughes AS, Fairweather NF, Fortier LC. The Clostridium difficile cell wall protein CwpV confers phase-variable phage resistance. Mol Microbiol 2015; 98:329-42. [PMID: 26179020 PMCID: PMC4737114 DOI: 10.1111/mmi.13121] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 01/21/2023]
Abstract
Bacteriophages are present in virtually all ecosystems, and bacteria have developed multiple antiphage strategies to counter their attacks. Clostridium difficile is an important pathogen causing severe intestinal infections in humans and animals. Here we show that the conserved cell-surface protein CwpV provides antiphage protection in C. difficile. This protein, for which the expression is phase-variable, is classified into five types, each differing in their repeat-containing C-terminal domain. When expressed constitutively from a plasmid or the chromosome of locked 'ON' cells of C. difficile R20291, CwpV conferred antiphage protection. Differences in the level of phage protection were observed depending on the phage morphological group, siphophages being the most sensitive with efficiency of plaquing (EOP) values of < 5 × 10(-7) for phages ϕCD38-2, ϕCD111 and ϕCD146. Protection against the myophages ϕMMP01 and ϕCD52 was weaker, with EOP values between 9.0 × 10(-3) and 1.1 × 10(-1). The C-terminal domain of CwpV carries the antiphage activity and its deletion, or part of it, significantly reduced the antiphage protection. CwpV does not affect phage adsorption, but phage DNA replication is prevented, suggesting a mechanism reminiscent of superinfection exclusion systems normally encoded on prophages. CwpV thus represents a novel ubiquitous host-encoded and phase-variable antiphage system in C. difficile.
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Affiliation(s)
- Ognjen Sekulovic
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Maicol Ospina Bedoya
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Amanda S Fivian-Hughes
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Neil F Fairweather
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Louis-Charles Fortier
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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130
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Denes T, den Bakker HC, Tokman JI, Guldimann C, Wiedmann M. Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption. Appl Environ Microbiol 2015; 81:4295-305. [PMID: 25888172 PMCID: PMC4475870 DOI: 10.1128/aem.00087-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/12/2015] [Indexed: 02/06/2023] Open
Abstract
Listeria-infecting phages are readily isolated from Listeria-containing environments, yet little is known about the selective forces they exert on their host. Here, we identified that two virulent phages, LP-048 and LP-125, adsorb to the surface of Listeria monocytogenes strain 10403S through different mechanisms. We isolated and sequenced, using whole-genome sequencing, 69 spontaneous mutant strains of 10403S that were resistant to either one or both phages. Mutations from 56 phage-resistant mutant strains with only a single mutation mapped to 10 genes representing five loci on the 10403S chromosome. An additional 12 mutant strains showed two mutations, and one mutant strain showed three mutations. Two of the loci, containing seven of the genes, accumulated the majority (n = 64) of the mutations. A representative mutant strain for each of the 10 genes was shown to resist phage infection through mechanisms of adsorption inhibition. Complementation of mutant strains with the associated wild-type allele was able to rescue phage susceptibility for 6 out of the 10 representative mutant strains. Wheat germ agglutinin, which specifically binds to N-acetylglucosamine, bound to 10403S and mutant strains resistant to LP-048 but did not bind to mutant strains resistant to only LP-125. We conclude that mutant strains resistant to only LP-125 lack terminal N-acetylglucosamine in their wall teichoic acid (WTA), whereas mutant strains resistant to both phages have disruptive mutations in their rhamnose biosynthesis operon but still possess N-acetylglucosamine in their WTA.
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Affiliation(s)
- Thomas Denes
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Henk C den Bakker
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jeffrey I Tokman
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Claudia Guldimann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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131
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Abedon ST. Phage therapy of pulmonary infections. BACTERIOPHAGE 2015; 5:e1020260. [PMID: 26442188 PMCID: PMC4422798 DOI: 10.1080/21597081.2015.1020260] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 11/01/2022]
Abstract
It is generally agreed that a bacteriophage-associated phenomenon was first unambiguously observed one-hundred years ago with the findings of Twort in 1915. This was independently followed by complementary observations by d'Hérelle in 1917. D'Hérelle's appreciation of the bacteriophage phenomenon appears to have directly led to the development of phages as antibacterial agents within a variety of contexts, including medical and agricultural. Phage use to combat nuisance bacteria appears to be especially useful where targets are sufficiently problematic, suitably bactericidal phages exist, and alternative approaches are lacking in effectiveness, availability, safety, or cost effectiveness, etc. Phage development as antibacterial agents has been strongest particularly when antibiotics have been less available or useful, e.g., such as in the treatment of chronic infections by antibiotic-resistant bacteria. One relatively under-explored or at least not highly reported use of phages as therapeutic agents has been to combat bacterial infections of the lungs and associated tissues. These infections are diverse in terms of their etiologies, manifestations, and also in terms of potential strategies of phage delivery. Here I review the literature considering the phage therapy of pulmonary and pulmonary-related infections, with emphasis on reports of clinical treatment along with experimental treatment of pulmonary infections using animal models.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology; The Ohio State University ; Mansfield, OH USA
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132
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Lv M, Wang S, Yan G, Sun C, Feng X, Gu J, Han W, Lei L. Genome sequencing and analysis of an Escherichia coli phage vB_EcoM-ep3 with a novel lysin, Lysep3. Virus Genes 2015; 50:487-97. [PMID: 25842152 DOI: 10.1007/s11262-015-1195-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/28/2015] [Indexed: 02/05/2023]
Abstract
Bacteriophages represent one prospect for preventing and treating multi-drug-resistant Escherichia coli. In this study, we have isolated a novel E. coli-specific bacteriophage and characterised its biological properties. vB_EcoM-ep3 has a broad host range and was able to lyse 9 out of 15 clinical isolates of multi-drug-resistant pathogenic E. coli from chickens. The optimal multiplicity of infection for vB_EcoM-ep3 in host bacteria was 0.01. vB_EcoM-ep3 was thermostable at temperatures below 50 °C for up to 60 min. Electron microscopy demonstrated that vB_EcoM-ep3 belongs to Myoviridae. The vB_EcoM-ep3 genome contained 42,351 pairs of nucleotides with a GC content of 53.35 %. There were 52 predicted open reading frames that appeared to overlap and have a modular structure. Phylogenetic analysis indicates that the closest evolutionary relative to vB_EcoM-ep3 is the previously reported E. coli phage vB_EcoM_ECO1230-10. However, there was no homology between reported E. coli phage lysins and the vB_EcoM-ep3 lysin gene. Lysep3 was 58 % similar to the Pseudomonas phage PPpW-3 lysin despite showing no similarities at the gene sequence level. And Lysep3 has good lysis activity.
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Affiliation(s)
- Meng Lv
- College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, People's Republic of China,
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133
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Khan Mirzaei M, Nilsson AS. Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS One 2015; 10:e0118557. [PMID: 25761060 PMCID: PMC4356574 DOI: 10.1371/journal.pone.0118557] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
Phage therapy, treating bacterial infections with bacteriophages, could be a future alternative to antibiotic treatment of bacterial infections. There are, however, several problems to be solved, mainly associated to the biology of phages, the interaction between phages and their bacterial hosts, but also to the vast variation of pathogenic bacteria which implies that large numbers of different phages are going to be needed. All of these phages must under present regulation of medical products undergo extensive clinical testing before they can be applied. It will consequently be of great economic importance that effective and versatile phages are selected and collected into phage libraries, i.e., the selection must be carried out in a way that it results in highly virulent phages with broad host ranges. We have isolated phages using the Escherichia coli reference (ECOR) collection and compared two methods, spot testing and efficiency of plating (EOP), which are frequently used to identify phages suitable for phage therapy. The analyses of the differences between the two methods show that spot tests often overestimate both the overall virulence and the host range and that the results are not correlated to the results of EOP assays. The conclusion is that single dilution spot tests cannot be used for identification and selection of phages to a phage library and should be replaced by EOP assays. The difference between the two methods can be caused by many factors. We have analysed if the differences and lack of correlation could be caused by lysis from without, bacteriocins in the phage lysate, or by the presence of prophages harbouring genes coding for phage resistance systems in the genomes of the bacteria in the ECOR collection.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
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134
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Henry M, Biswas B, Vincent L, Mokashi V, Schuch R, Bishop-Lilly KA, Sozhamannan S. Development of a high throughput assay for indirectly measuring phage growth using the OmniLog(TM) system. BACTERIOPHAGE 2014; 2:159-167. [PMID: 23275867 PMCID: PMC3530525 DOI: 10.4161/bact.21440] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The conventional and most accepted method of measuring the lytic activity of a phage against its bacterial host is the plaque assay. This method is laborious, time consuming and expensive, especially in high throughput analyses where multiple phage-bacterial interactions are required to be monitored simultaneously. It can also vary considerably with the experimenter and by the growth and plating conditions. Alternatively, the lytic activity can be measured indirectly by following the decrease in optical density of the bacterial cultures owing to lysis. Here we describe an automated, high throughput, indirect liquid lysis assay to evaluate phage growth using the OmniLogTM system. The OmniLogTM system uses redox chemistry, employing cell respiration as a universal reporter. During active growth of bacteria, cellular respiration reduces a tetrazolium dye and produces a color change that is measured in an automated fashion. On the other hand, successful phage infection and subsequent growth of the phage in its host bacterium results in reduced bacterial growth and respiration and a concomitant reduction in color. Here we show that microtiter plate wells inoculated with Bacillus anthracis and phage show decreased or no growth, compared with the wells containing bacteria only or phage resistant bacteria plus phage. Also, we show differences in the kinetics of bacterial growth and the timing of appearance of phage resistant bacteria in the presence of individual phages or a cocktail of B. anthracis specific phages. The results of these experiments indicate that the OmniLogTM system could be used reliably for indirectly measuring phage growth in high throughput host range and phage and antibiotics combination studies.
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Affiliation(s)
- Matthew Henry
- Henry M. Jackson Foundation; Bethesda, MD USA ; Naval Medical Research Center; Biological Defense Research Directorate; Navy Medical Research Center-Frederick; Fort Detrick, MD USA
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135
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Abedon ST. Phage therapy: eco-physiological pharmacology. SCIENTIFICA 2014; 2014:581639. [PMID: 25031881 PMCID: PMC4054669 DOI: 10.1155/2014/581639] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Bacterial virus use as antibacterial agents, in the guise of what is commonly known as phage therapy, is an inherently physiological, ecological, and also pharmacological process. Physiologically we can consider metabolic properties of phage infections of bacteria and variation in those properties as a function of preexisting bacterial states. In addition, there are patient responses to pathogenesis, patient responses to phage infections of pathogens, and also patient responses to phage virions alone. Ecologically, we can consider phage propagation, densities, distribution (within bodies), impact on body-associated microbiota (as ecological communities), and modification of the functioning of body "ecosystems" more generally. These ecological and physiological components in many ways represent different perspectives on otherwise equivalent phenomena. Comparable to drugs, one also can view phages during phage therapy in pharmacological terms. The relatively unique status of phages within the context of phage therapy as essentially replicating antimicrobials can therefore result in a confluence of perspectives, many of which can be useful towards gaining a better mechanistic appreciation of phage therapy, as I consider here. Pharmacology more generally may be viewed as a discipline that lies at an interface between organism-associated phenomena, as considered by physiology, and environmental interactions as considered by ecology.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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136
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Watkins SC, Smith JR, Hayes PK, Watts JEM. Characterisation of host growth after infection with a broad-range freshwater cyanopodophage. PLoS One 2014; 9:e87339. [PMID: 24489900 PMCID: PMC3906167 DOI: 10.1371/journal.pone.0087339] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Freshwater cyanophages are poorly characterised in comparison to their marine counterparts, however, the level of genetic diversity that exists in freshwater cyanophage communities is likely to exceed that found in marine environments, due to the habitat heterogeneity within freshwater systems. Many cyanophages are specialists, infecting a single host species or strain; however, some are less fastidious and infect a number of different host genotypes within the same species or even hosts from different genera. Few instances of host growth characterisation after infection by broad host-range phages have been described. Here we provide an initial characterisation of interactions between a cyanophage isolated from a freshwater fishing lake in the south of England and its hosts. Designated ΦMHI42, the phage is able to infect isolates from two genera of freshwater cyanobacteria, Planktothrix and Microcystis. Transmission Electron Microscopy and Atomic Force Microscopy indicate that ΦMHI42 is a member of the Podoviridae, albeit with a larger than expected capsid. The kinetics of host growth after infection with ΦMHI42 differed across host genera, species and strains in a way that was not related to the growth rate of the uninfected host. To our knowledge, this is the first characterisation of the growth of cyanobacteria in the presence of a broad host-range freshwater cyanophage.
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Affiliation(s)
- Siobhan C. Watkins
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - James R. Smith
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Paul K. Hayes
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Joy E. M. Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
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137
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Genetic evidence for the involvement of the S-layer protein gene sap and the sporulation genes spo0A, spo0B, and spo0F in Phage AP50c infection of Bacillus anthracis. J Bacteriol 2013; 196:1143-54. [PMID: 24363347 DOI: 10.1128/jb.00739-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In order to better characterize the Bacillus anthracis typing phage AP50c, we designed a genetic screen to identify its bacterial receptor. Insertions of the transposon mariner or targeted deletions of the structural gene for the S-layer protein Sap and the sporulation genes spo0A, spo0B, and spo0F in B. anthracis Sterne resulted in phage resistance with concomitant defects in phage adsorption and infectivity. Electron microscopy of bacteria incubated with AP50c revealed phage particles associated with the surface of bacilli of the Sterne strain but not with the surfaces of Δsap, Δspo0A, Δspo0B, or Δspo0F mutants. The amount of Sap in the S layer of each of the spo0 mutant strains was substantially reduced compared to that of the parent strain, and incubation of AP50c with purified recombinant Sap led to a substantial reduction in phage activity. Phylogenetic analysis based on whole-genome sequences of B. cereus sensu lato strains revealed several closely related B. cereus and B. thuringiensis strains that carry sap genes with very high similarities to the sap gene of B. anthracis. Complementation of the Δsap mutant in trans with the wild-type B. anthracis sap or the sap gene from either of two different B. cereus strains that are sensitive to AP50c infection restored phage sensitivity, and electron microscopy confirmed attachment of phage particles to the surface of each of the complemented strains. Based on these data, we postulate that Sap is involved in AP50c infectivity, most likely acting as the phage receptor, and that the spo0 genes may regulate synthesis of Sap and/or formation of the S layer.
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138
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Arachchi GJG, Cruz CD, Dias-Wanigasekera BM, McIntyre L, Billington C, Hudson A, Flint SH, Mutukumira AN. Host range and in vitro lysis of Listeria monocytogenes seafood isolates by bacteriophages. FOOD SCI TECHNOL INT 2013; 20:591-603. [DOI: 10.1177/1082013213497211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Listeria-infecting bacteriophages (listeriaphages) can be used to control Listeria monocytogenes in the food industry. However, the sensitivity of many of seafood-borne Listeria strains to phages has not been reported. This research investigated the host ranges of three listeriaphages (FWLLm1, FWLLm3 and FWLLm5) by the formation of lytic zones and plaques on host lawns and in vitro lysis kinetics of listeriaphage FWLLm3. The study also predicted the phage titres required to lyse host cells. The host ranges of the phages were determined using 50 L. monocytogenes strains, of which 48 were isolated from the seafood industry and two from clinical cases. Of the 50 strains, 36 were tested at 25 and 30 ℃ and the remainder (14) at 15 and 25 ℃. Based on the formation of either discrete plaques or lytic zones (host kill zones), the host ranges of FWLLm1, FWLLm3 and FWLLm5 were about 87%, 81% and 87%, respectively, at 25 ℃. Six L. monocytogenes strains from the seafood environment were insensitive to all three phages, while the other seafood strains (42) were phage-sensitive. The adsorption rate constant ( k value) of listeriaphage FWLLm3 was between 1.2 × 10−9 and 1.6 × 10−9 ml/min across four host strains in tryptic soy broth at 25 ℃. The cultures (at 3–4 log colony-forming unit (CFU/ml) were completely lysed (<1 log CFU/ml) when cultures were infected with FWLLm3 at > 8.7 log phage-forming units (PFU/ml) for 30 min. Re-growth of phage-infected cultures was not detected after 24 h. The effective empirical phage titre was similar to the calculated titre using a kinetic model. Results indicate the potential use of the three phages for controlling L. monocytogenes strains in seafood processing environments.
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Affiliation(s)
- Geevika J Ganegama Arachchi
- Institute of Food, Nutrition and Human Health, Massey University, Albany Campus, North Shore City, Auckland, New Zealand
| | - Cristina D Cruz
- The New Zealand Institute for Plant & Food Research (PFR) Limited, Mt Albert, Auckland, New Zealand
| | | | - Lynn McIntyre
- Department of Food Science and Agri-Food Supply Chain Management, Harper Adams University, Edgmond, Newport, Shropshire, United Kingdom
| | - Craig Billington
- Food Programme, Institute of Environmental Science and Research (ESR) Limited, Christchurch Science Centre (CSC), Ilam, Christchurch, New Zealand
| | - Andrew Hudson
- Food Programme, Institute of Environmental Science and Research (ESR) Limited, Christchurch Science Centre (CSC), Ilam, Christchurch, New Zealand
| | - Steve H Flint
- Institute of Food, Nutrition and Human Health, Massey University, Albany Campus, North Shore City, Auckland, New Zealand
| | - Anthony N Mutukumira
- Institute of Food, Nutrition and Human Health, Massey University, Albany Campus, North Shore City, Auckland, New Zealand
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139
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Hardies SC, Hwang YJ, Hwang CY, Jang GI, Cho BC. Morphology, physiological characteristics, and complete sequence of marine bacteriophage ϕRIO-1 infecting Pseudoalteromonas marina. J Virol 2013; 87:9189-98. [PMID: 23760254 PMCID: PMC3754069 DOI: 10.1128/jvi.01521-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 06/06/2013] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the genus Pseudoalteromonas are ubiquitous in the world's oceans. Marine bacteria have been posited to be associated with a major ancient branch of podoviruses related to T7. Yet, although Pseudoalteromonas phages belonging to the Corticoviridae and the Siphoviridae and prophages belonging to the Myoviridae have been reported, no Pseudoalteromonas podovirus was previously known. Here, a new lytic Pseudoalteromonas marina phage, ϕRIO-1, belonging to the Podoviridae was isolated and characterized with respect to morphology, genomic sequence, and biological properties. Its major encoded proteins were distantly similar to those of T7. The most similar previously sequenced viruses were Pseudomonas phage PA11 and Salinivibrio phage CW02. Whereas many elements of the morphology and gene organization of ϕRIO-1 are similar to those of podoviruses broadly related to T7, ϕRIO-1 conspicuously lacked an RNA polymerase gene. Since definitions of a T7 supergroup have included similarity in the DNA polymerase gene, a detailed phylogenetic analysis was conducted, and two major DNA polymerase clades in Autographivirinae and several structural variants of the polA family represented in podoviruses were found. ϕRIO-1 carries an operon similar to that in a few other podoviruses predicted to specify activities related to γ-glutamyl amide linkages and/or unusual peptide bonds. Most growth properties of ϕRIO-1 were typical of T7-like phages, except for a long latent period.
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Affiliation(s)
- Stephen C. Hardies
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yeon J. Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences, and Research Institute of Oceanography (RIO), Seoul National University, Seoul, South Korea
| | - Chung Y. Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Gwang I. Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences, and Research Institute of Oceanography (RIO), Seoul National University, Seoul, South Korea
| | - Byung C. Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences, and Research Institute of Oceanography (RIO), Seoul National University, Seoul, South Korea
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140
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Fouts DE, Klumpp J, Bishop-Lilly KA, Rajavel M, Willner KM, Butani A, Henry M, Biswas B, Li M, Albert MJ, Loessner MJ, Calendar R, Sozhamannan S. Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity. Virol J 2013; 10:165. [PMID: 23714204 PMCID: PMC3670811 DOI: 10.1186/1743-422x-10-165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/21/2013] [Indexed: 11/23/2022] Open
Abstract
Background Vibrio cholerae O139 Bengal is the only serogroup other than O1 implicated in cholera epidemics. We describe the isolation and characterization of an O139 serogroup-specific phage, vB_VchP_VchO139-I (ϕVchO139-I) that has similar host range and virion morphology as phage vB_VchP_JA1 (ϕJA1) described previously. We aimed at a complete molecular characterization of both phages and elucidation of their genetic and structural differences and assessment of their genetic relatedness to the N4-like phage group. Methods Host-range analysis and plaque morphology screening were done for both ϕJA1 and ϕVchO139-I. Both phage genomes were sequenced by a 454 and Sanger hybrid approach. Genomes were annotated and protein homologies were determined by Blast and HHPred. Restriction profiles, PFGE patterns and data on the physical genome structure were acquired and phylogenetic analyses were performed. Results The host specificity of ϕJA1 has been attributed to the unique capsular O-antigen produced by O139 strains. Plaque morphologies of the two phages were different; ϕVchO139-I produced a larger halo around the plaques than ϕJA1. Restriction profiles of ϕJA1 and ϕVchO139-I genomes were also different. The genomes of ϕJA1 and ϕVchO139-I consisted of linear double-stranded DNA of 71,252 and 70,938 base pairs. The presence of direct terminal repeats of around 1974 base pairs was demonstrated. Whole genome comparison revealed single nucleotide polymorphisms, small insertions/deletions and differences in gene content. Both genomes had 79 predicted protein encoding sequences, of which only 59 were identical between the two closely related phages. They also encoded one tRNA-Arg gene, an intein within the large terminase gene, and four homing endonuclease genes. Whole genome phylogenetic analyses of ϕJA1 and ϕVchO139-I against other sequenced N4-like phages delineate three novel subgroups or clades within this phage family. Conclusions The closely related phages feature significant genetic differences, in spite of being morphologically identical. The phage morphology, genetic organization, genomic content and large terminase protein based phylogeny support the placement of these two phages in the Podoviridae family, more specifically within the N4-like phage group. The physical genome structure of ϕJA1 could be demonstrated experimentally. Our data pave the way for potential use of ϕJA1 and ϕVchO139-I in Vibrio cholerae typing and control.
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141
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Synergistic action of gentamicin and bacteriophage in a continuous culture population of Staphylococcus aureus. PLoS One 2012; 7:e51017. [PMID: 23226451 PMCID: PMC3511404 DOI: 10.1371/journal.pone.0051017] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
With the increasing frequency of antibiotic resistance and the decreasing frequency of new antibiotics entering the market, interest has returned to developing bacteriophage as a therapeutic agent. Acceptance of phage therapy, however, is limited by the unknown pharmacodynamics of a replicating agent, as well as the potential for the evolution of resistant bacteria. One way to overcome some of these limitations is to incorporate phage and antibiotics into a dual therapy regimen; however, this increases the complexity of the pharmacodynamics. The aim of this study is to develop an experimental system to evaluate the pharmacodynamics of dual phage-drug therapy. A continuous culture system for Staphylococcus aureus is used to simulate the pharmacokinetics of periodic antibiotic dosing alone and in combination with lytic phage. A computer model representation of the system allows further evaluation of the conditions governing the observed pharmacodynamics. The results of this experimental/modeling approach suggest that dual therapy can be more efficacious than single therapies, particularly if there is an overlap in the physiological pathways targeted by the individual agents. In this case, treatment with gentamicin induces a population of cells with a strong aggregation phenotype. These aggregators also have an increased ability to form biofilm, which is a well-known, non-genetic mechanism of drug resistance. However, the aggregators are also more susceptible than the parental strain to the action of the phage. Thus, dual treatment with gentamicin and phage resulted in lower final cell densities than either treatment alone. Unlike in the phage-only treatment, phage-resistant isolates were not detected in the dual treatment.
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142
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Isolation and characterisation of lytic bacteriophages of Klebsiella pneumoniae and Klebsiella oxytoca. Curr Microbiol 2012; 66:251-8. [PMID: 23143289 DOI: 10.1007/s00284-012-0264-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
Abstract
Klebsiella bacteria have emerged as an increasingly important cause of community-acquired nosocomial infections. Extensive use of broad-spectrum antibiotics in hospitalised patients has led to both increased carriage of Klebsiella and the development of multidrug-resistant strains that frequently produce extended-spectrum β-lactamases and/or other defences against antibiotics. Many of these strains are highly virulent and exhibit a strong propensity to spread. In this study, six lytic Klebsiella bacteriophages were isolated from sewage-contaminated river water in Georgia and characterised as phage therapy candidates. Two of the phages were investigated in greater detail. Biological properties, including phage morphology, nucleic acid composition, host range, growth phenotype, and thermal and pH stability were studied for all six phages. Limited sample sequencing was performed to define the phylogeny of the K. pneumoniae- and K. oxytoca-specific bacteriophages vB_Klp_5 and vB_Klox_2, respectively. Both of the latter phages had large burst sizes, efficient rates of adsorption and were stable under different adverse conditions. Phages reported in this study are double-stranded DNA bacterial viruses belonging to the families Podoviridae and Siphoviridae. One or more of the six phages was capable of efficiently lysing ~63 % of Klebsiella strains comprising a collection of 123 clinical isolates from Georgia and the United Kingdom. These phages exhibit a number of properties indicative of potential utility in phage therapy cocktails.
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143
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Novel Podoviridae family bacteriophage infecting Weissella cibaria isolated from Kimchi. Appl Environ Microbiol 2012; 78:7299-308. [PMID: 22885743 DOI: 10.1128/aem.00031-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first complete genome sequence of a phage infecting Weissella cibaria (Weissella kimchii) is presented. The bacteriophage YS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, YS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that YS61 resembles Podoviridae of the subfamily Picovirinae. Within the subfamily Picovirinae, the 29-like phages have been extensively studied, and their terminal protein-primed DNA replication is well characterized. Our data strongly suggest that YS61 also replicates by a protein-primed mechanism. Weissella phage YS61 is, however, markedly different from members of the Picovirinae with respect to genome size and morphology. Picovirinae are characterized by small (approximately 20-kb) genomes which contrasts with the 33,594-bp genome of YS61. Based on electron microscopy analysis, YS61 was classified as a member of the Podoviridae of morphotype C2, similar to the 29-like phages, but its capsid dimensions are significantly larger than those reported for these phages. The novelty of YS61 was also emphasized by the low number of open reading frames (ORFs) showing significant similarity to database sequences. We propose that the bacteriophage YS61 should represent a new subfamily within the family Podoviridae.
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144
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Characterization of a Leuconostoc bacteriophage infecting flavor producers of cheese starter cultures. Appl Environ Microbiol 2012; 78:6769-72. [PMID: 22798359 DOI: 10.1128/aem.00562-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dairy siphovirus φLmd1, which infects starter culture isolate Leuconostoc mesenteroides subsp. dextranicum A1, showed resistance to pasteurization and was able to grow on 3 of the 4 commercial starter cultures tested. Its 26,201-bp genome was similar to that of Leuconostoc phage of vegetable origin but not to those of dairy phages infecting Lactococcus.
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145
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Karumidze N, Thomas JA, Kvatadze N, Goderdzishvili M, Hakala KW, Weintraub ST, Alavidze Z, Hardies SC. Characterization of lytic Pseudomonas aeruginosa bacteriophages via biological properties and genomic sequences. Appl Microbiol Biotechnol 2012; 94:1609-17. [PMID: 22562168 DOI: 10.1007/s00253-012-4119-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
Abstract
Pseudomonas aeruginosa is an important cause of infections, especially in patients with immunodeficiency or diabetes. Antibiotics are effective in preventing morbidity and mortality from Pseudomonas infection, but because of spreading multidrug-resistant bacterial strains, bacteriophages are being explored as an alternative therapy. Two newly purified broad host range Pseudomonas phages, named vB_Pae-Kakheti25 and vB_Pae-TbilisiM32, were characterized as candidates for use in phage therapy. Morphology, host range, growth properties, thermal stability, serology, genomic sequence, and virion composition are reported. When phages are used as bactericides, they are used in mixtures to overcome the development of resistance in the targeted bacterial population. These two phages are representative of diverse siphoviral and podoviral phage families, respectively, and hence have unrelated mechanisms of infection and no cross-antigenicity. Composing bactericidal phage mixtures with members of different phage families may decrease the incidence of developing resistance through a common mechanism.
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Affiliation(s)
- Natia Karumidze
- Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
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146
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Abstract
Phage therapy is the clinical or veterinary application of bacterial viruses (bacteriophages) as antibacterial "drugs." More generally, phages can be used as biocontrol agents against plant as well as foodborne pathogens. In this chapter, we consider the therapeutic use of phage cocktails, which is the combining of two or more phage types to produce more pharmacologically diverse formulations. The primary motivation for the use of cocktails is their broader spectra of activity in comparison to individual phage isolates: they can impact either more bacterial types or achieve effectiveness under a greater diversity of conditions. The combining of phages can also facilitate better targeting of multiple strains making up individual bacterial species or covering multiple species that might be responsible for similar disease states, in general providing, relative to individual phage isolates, a greater potential for presumptive or empirical treatment. Contrasting the use of phage banks, or even phage isolation against specific etiologies that have been obtained directly from patients under treatment, here we consider the utility as well as potential shortcomings associated with the use of phage cocktails as therapeutic antibacterial agents.
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Affiliation(s)
- Benjamin K Chan
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
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147
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Abedon S. Phage therapy pharmacology: calculating phage dosing. ADVANCES IN APPLIED MICROBIOLOGY 2011; 77:1-40. [PMID: 22050820 DOI: 10.1016/b978-0-12-387044-5.00001-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phage therapy, which can be described as a phage-mediated biocontrol of bacteria (or, simply, biocontrol), is the application of bacterial viruses-also bacteriophages or phages-to reduce densities of nuisance or pathogenic bacteria. Predictive calculations for phage therapy dosing should be useful toward rational development of therapeutic as well as biocontrol products. Here, I consider the theoretical basis of a number of concepts relevant to phage dosing for phage therapy including minimum inhibitory concentration (but also "inundation threshold"), minimum bactericidal concentration (but also "clearance threshold"), decimal reduction time (D value), time until bacterial eradication, threshold bacterial density necessary to support phage population growth ("proliferation threshold"), and bacterial density supporting half-maximal phage population growth rates (K(B)). I also address the concepts of phage killing titers, multiplicity of infection, and phage peak densities. Though many of the presented ideas are not unique to this chapter, I nonetheless provide variations on derivations and resulting formulae, plus as appropriate discuss relative importance. The overriding goal is to present a variety of calculations that are useful toward phage therapy dosing so that they may be found in one location and presented in a manner that allows facile appreciation, comparison, and implementation. The importance of phage density as a key determinant of the phage potential to eradicate bacterial targets is stressed throughout the chapter.
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148
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149
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Abedon ST. Kinetics of phage-mediated biocontrol of bacteria. Foodborne Pathog Dis 2009; 6:807-15. [PMID: 19459758 DOI: 10.1089/fpd.2008.0242] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriophages (phages) are the viruses of bacteria. One subset of phages, those that can be described as obligately lytic, can effect an active phage therapy because their population growth occurs at the expense of bacterial survival. That is, phages can be employed to reduce bacterial loads--such as in animals preslaughter, in foods postharvest, or in humans postinfection--and in the process can actually increase what in pharmacological terms would be their antibacterial dose. This self-amplification may provide advantages if either antibacterial dosing or penetration to target bacteria is otherwise constrained. One situation in which these kinetic aspects of drug delivery may be constrained is in preslaughter treatment of food animals toward control of zoonotic pathogens (e.g., Escherichia coli O157:H7 in cattle). In such treatment, the self-amplifying nature of phages may be harnessed, though potentially under time constraints. In this discursive I cover three areas. The first is semantic, where I contrast the terms phage therapy and phage-mediated biocontrol of bacteria, both of which are employed to describe similar but perhaps not identical procedures. Second, I consider the importance of time in therapy or biocontrol procedures while contrasting passive versus active therapies. Third, I discuss conceptually how to go about modifying phage characteristics to increase rates of phage population growth and do so explicitly by casting phage infection in terms of Michaelis-Menten saturation kinetics. I conclude suggesting that phage therapy ultimately may be rationally guided by theoretical considerations of the impact of phage properties on rates of phage population growth.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio 44906, USA.
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150
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Santos SB, Carvalho CM, Sillankorva S, Nicolau A, Ferreira EC, Azeredo J. The use of antibiotics to improve phage detection and enumeration by the double-layer agar technique. BMC Microbiol 2009; 9:148. [PMID: 19627589 PMCID: PMC2728735 DOI: 10.1186/1471-2180-9-148] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 07/23/2009] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The Double-Layer Agar (DLA) technique is extensively used in phage research to enumerate and identify phages and to isolate mutants and new phages. Many phages form large and well-defined plaques that are easily observed so that they can be enumerated when plated by the DLA technique. However, some give rise to small and turbid plaques that are very difficult to detect and count. To overcome these problems, some authors have suggested the use of dyes to improve the contrast between the plaques and the turbid host lawns. It has been reported that some antibiotics stimulate bacteria to produce phages, resulting in an increase in final titer. Thus, antibiotics might contribute to increasing plaque size in solid media. RESULTS Antibiotics with different mechanisms of action were tested for their ability to enhance plaque morphology without suppressing phage development. Some antibiotics increased the phage plaque surface by up to 50-fold. CONCLUSION This work presents a modification of the DLA technique that can be used routinely in the laboratory, leading to a more accurate enumeration of phages that would be difficult or even impossible otherwise.
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Affiliation(s)
- Sílvio B Santos
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
| | - Carla M Carvalho
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
| | - Sanna Sillankorva
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
| | - Ana Nicolau
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
| | - Eugénio C Ferreira
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
| | - Joana Azeredo
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700-057 Braga, Portugal
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