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Pirnay JP, Merabishvili M, De Vos D, Verbeken G. Bacteriophage Production in Compliance with Regulatory Requirements. Methods Mol Biol 2024; 2734:89-115. [PMID: 38066364 DOI: 10.1007/978-1-0716-3523-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
In this chapter, we discuss production requirements for therapeutic bacteriophage preparations. We review the current regulatory expectancies and focus on pragmatic production processes, implementing relevant controls to ensure the quality, safety, and efficacy of the final products. The information disclosed in this chapter can also serve as a basis for discussions with competent authorities regarding the implementation of expedited bacteriophage product development and licensing pathways, taking into account some peculiarities of bacteriophages (as compared to conventional medicines), such as their specificity for, and co-evolution with, their bacterial hosts. To maximize the potential of bacteriophages as natural controllers of bacterial populations, the implemented regulatory frameworks and manufacturing processes should not only cater to defined bacteriophage products. But, they should also facilitate personalized approaches in which bacteriophages are selected ad hoc and even trained to target the patient's infecting bacterial strain(s), whether or not in combination with other antimicrobials such as antibiotics.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium.
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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2
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Peters DL, Davis CM, Harris G, Zhou H, Rather PN, Hrapovic S, Lam E, Dennis JJ, Chen W. Characterization of Virulent T4-Like Acinetobacter baumannii Bacteriophages DLP1 and DLP2. Viruses 2023; 15:v15030739. [PMID: 36992448 PMCID: PMC10051250 DOI: 10.3390/v15030739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
The world is currently facing a global health crisis due to the rapid increase in antimicrobial-resistant bacterial infections. One of the most concerning pathogens is Acinetobacter baumannii, which is listed as a Priority 1 pathogen by the World Health Organization. This Gram-negative bacterium has many intrinsic antibiotic resistance mechanisms and the ability to quickly acquire new resistance determinants from its environment. A limited number of effective antibiotics against this pathogen complicates the treatment of A. baumannii infections. A potential treatment option that is rapidly gaining interest is “phage therapy”, or the clinical application of bacteriophages to selectively kill bacteria. The myoviruses DLP1 and DLP2 (vB_AbaM-DLP_1 and vB_AbaM-DLP_2, respectively) were isolated from sewage samples using a capsule minus variant of A. baumannii strain AB5075. Host range analysis of these phages against 107 A. baumannii strains shows a limited host range, infecting 15 and 21 for phages DLP1 and DLP2, respectively. Phage DLP1 has a large burst size of 239 PFU/cell, a latency period of 20 min, and virulence index of 0.93. In contrast, DLP2 has a smaller burst size of 24 PFU/cell, a latency period of 20 min, and virulence index of 0.86. Both phages show potential for use as therapeutics to combat A. baumannii infections.
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Affiliation(s)
- Danielle L. Peters
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Correspondence:
| | - Carly M. Davis
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Greg Harris
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Hongyan Zhou
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Philip N. Rather
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
- Research Service, Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Sabahudin Hrapovic
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Edmond Lam
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Wangxue Chen
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biology, Brock University, St. Catharines, ON L2S 3A1, Canada
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3
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Successful case of adjunctive intravenous bacteriophage therapy to treat left ventricular assist device infection. J Infect 2021; 83:e1-e3. [PMID: 34058260 DOI: 10.1016/j.jinf.2021.05.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 11/22/2022]
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4
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João J, Lampreia J, Prazeres DMF, Azevedo AM. Manufacturing of bacteriophages for therapeutic applications. Biotechnol Adv 2021; 49:107758. [PMID: 33895333 DOI: 10.1016/j.biotechadv.2021.107758] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/14/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022]
Abstract
Bacteriophages, or simply phages, are the most abundant biological entities on Earth. One of the most interesting characteristics of these viruses, which infect and use bacteria as their host organisms, is their high level of specificity. Since their discovery, phages became a tool for the comprehension of basic molecular biology and originated applications in a variety of areas such as agriculture, biotechnology, food safety, veterinary, pollution remediation and wastewater treatment. In particular, phages offer a solution to one of the major problems in public health nowadays, i.e. the emergence of multidrug-resistant bacteria. In these situations, the use of virulent phages as therapeutic agents offers an alternative to the classic, antibiotic-based strategies. The development of phage therapies should be accompanied by the improvement of phage biomanufacturing processes, both at laboratory and industrial scales. In this review, we first present some historical and general aspects related with the discovery, usage and biology of phages and provide a brief overview of the most relevant phage therapy applications. Then, we showcase current processes used for the production and purification of phages and future alternatives in development. On the production side, key factors such as the bacterial physiological state, the conditions of phage infection and the operation parameters are described alongside with the different operation modes, from batch to semi-continuous and continuous. Traditional purification methods used in the initial phage isolation steps are then described followed by the presentation of current state-of-the-art purification approaches. Continuous purification of phages is finally presented as a future biomanufacturing trend.
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Affiliation(s)
- Jorge João
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - João Lampreia
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Duarte Miguel F Prazeres
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Ana M Azevedo
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
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5
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Jagdale S, Ahiwale S, Gajbhiye M, Kapadnis B. Green approach to phytopathogen: Characterization of lytic bacteriophages of Pseudomonas sp., an etiology of the bacterial blight of pomegranate. Microbiol Res 2019; 228:126300. [PMID: 31422230 DOI: 10.1016/j.micres.2019.126300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/07/2019] [Accepted: 07/12/2019] [Indexed: 11/17/2022]
Abstract
Two morphologically different bacteriophages were isolated from the river and soil samples from various locations of Maharashtra, India against the phytopathogen Pseudomonas sp. that was recently reported to cause a new bacterial blight of pomegranate. Both the phages belonged to the order Caudovirales representing the families Siphoviridae (vB_Psp.S_PRɸL2) and Myoviridae (vB_Psp.M_SSɸL8). The multiplicity of infection ranged from 0.01 to 0.1, phage adsorption rate from 39% to 66%, latent period from 10 to 20 min with a burst size of 24-85 phage particles per infected host cell. The genome size of phages PRɸL2 and SSɸL8 was approximately 25.403 kb and 29.877 kb respectively. Restriction digestion pattern of phage genomic DNA was carried out for phage PRɸL2, Eco RI resulted in two bands and Hind III resulted in three bands while for phage SSɸL8, both Eco RI and Hind III each resulted in three bands. SDS-PAGE protein profile showed six bands for PRɸL2 and nine bands for SSɸL8 of different proteins. Phages showed high pH stability over a range of 4-9, temperature stability over a range of 4-50 °C and UV radiation showed a reduction up to 89.36% for PRɸL2 and 96% for SSɸL8. In short, the present research work discusses for the first time in-detailed characterization of phages of a phytopathogen Pseudomonas sp. from Maharashtra, India, which can be further efficiently used for biological control of the causative agent of a new bacterial blight disease of pomegranate.
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Affiliation(s)
- Smita Jagdale
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India
| | - Sangeeta Ahiwale
- Department of Microbiology, Mahatma Phule Mahavidyalaya, Pimpri, 411017, Pune, Maharashtra, India
| | - Milind Gajbhiye
- Department of Microbiology, Tuljaram Chaturchand College of Arts, Science and Commerce, Baramati, 413102, Maharashtra, India
| | - Balu Kapadnis
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India.
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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Cross-resistance is modular in bacteria-phage interactions. PLoS Biol 2018; 16:e2006057. [PMID: 30281587 PMCID: PMC6188897 DOI: 10.1371/journal.pbio.2006057] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/15/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023] Open
Abstract
Phages shape the structure of natural bacterial communities and can be effective therapeutic agents. Bacterial resistance to phage infection, however, limits the usefulness of phage therapies and could destabilise community structures, especially if individual resistance mutations provide cross-resistance against multiple phages. We currently understand very little about the evolution of cross-resistance in bacteria–phage interactions. Here we show that the network structure of cross-resistance among spontaneous resistance mutants of Pseudomonas aeruginosa evolved against each of 27 phages is highly modular. The cross-resistance network contained both symmetric (reciprocal) and asymmetric (nonreciprocal) cross-resistance, forming two cross-resistance modules defined by high within- but low between-module cross-resistance. Mutations conferring cross-resistance within modules targeted either lipopolysaccharide or type IV pilus biosynthesis, suggesting that the modularity of cross-resistance was structured by distinct phage receptors. In contrast, between-module cross-resistance was provided by mutations affecting the alternative sigma factor, RpoN, which controls many lifestyle-associated functions, including motility, biofilm formation, and quorum sensing. Broader cross-resistance range was not associated with higher fitness costs or weaker resistance against the focal phage used to select resistance. However, mutations in rpoN, providing between-module cross-resistance, were associated with higher fitness costs than mutations associated with within-module cross-resistance, i.e., in genes encoding either lipopolysaccharide or type IV pilus biosynthesis. The observed structure of cross-resistance predicted both the frequency of resistance mutations and the ability of phage combinations to suppress bacterial growth. These findings suggest that the evolution of cross-resistance is common, is likely to play an important role in the dynamic structure of bacteria–phage communities, and could inform the design principles for phage therapy treatments. Phage therapy is a promising alternative to antibiotics for treating bacterial infections. Yet as with antibiotics, bacteria readily evolve resistance to phage attack, including cross-resistance that protects against multiple phages at once and so limits the usefulness of phage cocktails. Here we show, using laboratory experimental evolution of resistance against 27 phages in P. aeruginosa, that cross-resistance is common and determines the ability of phage combinations to suppress bacterial growth. Using whole-genome sequencing, we show that cross-resistance is most common against multiple phages that use the same receptor but that global regulator mutations provide generalist resistance, probably by simultaneously affecting the expression of multiple different phage receptors. Future trials should test if these features of cross-resistance evolution translate to more complex in vivo environments and can therefore be exploited to design more effective phage therapies for the clinic.
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Affiliation(s)
- Rosanna C. T. Wright
- Department of Biology, University of York, York, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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7
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Moulton‐Brown CE, Friman V. Rapid evolution of generalized resistance mechanisms can constrain the efficacy of phage-antibiotic treatments. Evol Appl 2018; 11:1630-1641. [PMID: 30344632 PMCID: PMC6183449 DOI: 10.1111/eva.12653] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance has been estimated to be responsible for over 700,000 deaths per year; therefore, new antimicrobial therapies are urgently needed. One way to increase the efficiency of antibiotics is to use them in combination with bacteria-specific parasitic viruses, phages, which have been shown to exert additive or synergistic effects in controlling bacteria. However, it is still unclear to what extent these combinatory effects are limited by rapid evolution of resistance, especially when the pathogen grows as biofilm on surfaces typical for many persistent and chronic infections. To study this, we used a microcosm system, where genetically isogenic populations of Pseudomonas aeruginosa PAO1 bacterial pathogen were exposed to a phage 14/1, gentamycin or a combination of them both in a spatially structured environment. We found that even though antibiotic and phage-antibiotic treatments were equally effective at controlling bacteria in the beginning of the experiment, combination treatment rapidly lost its efficacy in both planktonic and biofilm populations. In a mechanistic manner, this was due to rapid resistance evolution: While both antibiotic and phage selected for increased resistance on their own, phage selection correlated positively with increase in antibiotic resistance, while biofilm growth, which provided generalized resistance mechanism, was favoured most in the combination treatment. Only relatively small cost of resistance and weak evidence for coevolutionary dynamics were observed. Together, these results suggest that spatial heterogeneity can promote rapid evolution of generalized resistance mechanisms without corresponding increase in phage infectivity, which could potentially limit the effectiveness of phage-antibiotic treatments in the evolutionary timescale.
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8
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Pirnay JP, Merabishvili M, Van Raemdonck H, De Vos D, Verbeken G. Bacteriophage Production in Compliance with Regulatory Requirements. Methods Mol Biol 2018; 1693:233-252. [PMID: 29119444 DOI: 10.1007/978-1-4939-7395-8_18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this chapter we review bacteriophage production requirements to help institutions, which wish to manufacture bacteriophage products for human use in compliance with the applicable regulatory expectancies, defining production processes and implementing relevant controls ensuring quality, safety, and efficacy of the final products. The information disclosed in this chapter can also serve as a basis for discussions with competent authorities regarding the development of expedited bacteriophage product development and licensing pathways, including relevant and pragmatic requirements, and allowing for the full exploitation of bacteriophages as natural controllers of bacterial populations.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium.
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Hilde Van Raemdonck
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
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9
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Moreau P, Diggle SP, Friman VP. Bacterial cell-to-cell signaling promotes the evolution of resistance to parasitic bacteriophages. Ecol Evol 2017; 7:1936-1941. [PMID: 28331600 PMCID: PMC5355186 DOI: 10.1002/ece3.2818] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/19/2016] [Accepted: 01/28/2017] [Indexed: 12/21/2022] Open
Abstract
The evolution of host–parasite interactions could be affected by intraspecies variation between different host and parasite genotypes. Here we studied how bacterial host cell‐to‐cell signaling affects the interaction with parasites using two bacteria‐specific viruses (bacteriophages) and the host bacterium Pseudomonas aeruginosa that communicates by secreting and responding to quorum sensing (QS) signal molecules. We found that a QS‐signaling proficient strain was able to evolve higher levels of resistance to phages during a short‐term selection experiment. This was unlikely driven by demographic effects (mutation supply and encounter rates), as nonsignaling strains reached higher population densities in the absence of phages in our selective environment. Instead, the evolved nonsignaling strains suffered relatively higher growth reduction in the absence of the phage, which could have constrained the phage resistance evolution. Complementation experiments with synthetic signal molecules showed that the Pseudomonas quinolone signal (PQS) improved the growth of nonsignaling bacteria in the presence of a phage, while the activation of las and rhl quorum sensing systems had no effect. Together, these results suggest that QS‐signaling can promote the evolution of phage resistance and that the loss of QS‐signaling could be costly in the presence of phages. Phage–bacteria interactions could therefore indirectly shape the evolution of intraspecies social interactions and PQS‐mediated virulence in P. aeruginosa.
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Affiliation(s)
- Pierre Moreau
- Imperial College London, Silwood Park Campus Ascot Berkshire UK
| | - Stephen P Diggle
- School of Life Sciences Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Ville-Petri Friman
- Imperial College London, Silwood Park Campus Ascot Berkshire UK; Department of Biology The University of York York UK
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10
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Mumford R, Friman VP. Bacterial competition and quorum-sensing signalling shape the eco-evolutionary outcomes of model in vitro phage therapy. Evol Appl 2016; 10:161-169. [PMID: 28127392 PMCID: PMC5253424 DOI: 10.1111/eva.12435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022] Open
Abstract
The rapid rise of antibiotic resistance has renewed interest in phage therapy – the use of bacteria‐specific viruses (phages) to treat bacterial infections. Even though phages are often pathogen‐specific, little is known about the efficiency and eco‐evolutionary outcomes of phage therapy in polymicrobial infections. We studied this experimentally by exposing both quorum‐sensing (QS) signalling PAO1 and QS‐deficient lasR Pseudomonas aeruginosa genotypes (differing in their ability to signal intraspecifically) to lytic PT7 phage in the presence and absence of two bacterial competitors: Staphylococcus aureus and Stenotrophomonas maltophilia–two bacteria commonly associated with P. aeruginosa in polymicrobial cystic fibrosis lung infections. Both the P. aeruginosa genotype and the presence of competitors had profound effects on bacteria and phage densities and bacterial resistance evolution. In general, competition reduced the P. aeruginosa frequencies leading to a lower rate of resistance evolution. This effect was clearer with QS signalling PAO1 strain due to lower bacteria and phage densities and relatively larger pleiotropic growth cost imposed by both phages and competitors. Unexpectedly, phage selection decreased the total bacterial densities in the QS‐deficient lasR pathogen communities, while an increase was observed in the QS signalling PAO1 pathogen communities. Together these results suggest that bacterial competition can shape the eco‐evolutionary outcomes of phage therapy.
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Affiliation(s)
- Rachel Mumford
- Silwood Park Campus Imperial College London Ascot Berkshire UK
| | - Ville-Petri Friman
- Silwood Park Campus Imperial College London Ascot Berkshire UK; Department of Biology University of York York UK
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11
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Friman VP, Soanes-Brown D, Sierocinski P, Molin S, Johansen HK, Merabishvili M, Pirnay JP, De Vos D, Buckling A. Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates. J Evol Biol 2015; 29:188-98. [PMID: 26476097 DOI: 10.1111/jeb.12774] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/12/2015] [Indexed: 12/17/2022]
Abstract
Recent years have seen renewed interest in phage therapy--the use of viruses to specifically kill disease-causing bacteria--because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here, we determined whether in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains and then compared the efficacy of pre-adapted and nonadapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages, whereas all bacteria were able to evolve some level of resistance to ancestral phages. Although the rate of resistance evolution did not differ between intermittent and chronic isolates, it incurred a relatively higher growth cost for chronic isolates when measured in the absence of phages. This is likely to explain why evolved phages were more effective in reducing the densities of chronic isolates. Our data show that pathogen genotypes respond differently to phage pre-adaptation, and as a result, phage therapies might need to be individually adjusted for different patients.
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Affiliation(s)
- V-P Friman
- Biosciences, University of Exeter, Penryn, UK.,Department of Biology, University of York, York, UK
| | | | - P Sierocinski
- Biosciences, University of Exeter, Penryn, UK.,European Centre for Environment and Human Health in Cornwall, University of Exeter, Penryn, UK
| | - S Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - H K Johansen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Department of Clinical Microbiology 9301, Rigshospitalet, København Ø, Denmark
| | - M Merabishvili
- Burn Wound Center, Queen Astrid Military Hospital, Brussel, Belgium.,Research and Development Department, George Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.,Laboratory for Bacteriology Research, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - J-P Pirnay
- Burn Wound Center, Queen Astrid Military Hospital, Brussel, Belgium
| | - D De Vos
- Burn Wound Center, Queen Astrid Military Hospital, Brussel, Belgium
| | - A Buckling
- Biosciences, University of Exeter, Penryn, UK
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12
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Didamony GE, Askora A, Shehata AA. Isolation and Characterization of T7-Like Lytic Bacteriophages Infecting Multidrug Resistant Pseudomonas aeruginosa Isolated from Egypt. Curr Microbiol 2015; 70:786-91. [DOI: 10.1007/s00284-015-0788-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
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13
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Pirnay JP, Blasdel BG, Bretaudeau L, Buckling A, Chanishvili N, Clark JR, Corte-Real S, Debarbieux L, Dublanchet A, De Vos D, Gabard J, Garcia M, Goderdzishvili M, Górski A, Hardcastle J, Huys I, Kutter E, Lavigne R, Merabishvili M, Olchawa E, Parikka KJ, Patey O, Pouilot F, Resch G, Rohde C, Scheres J, Skurnik M, Vaneechoutte M, Van Parys L, Verbeken G, Zizi M, Van den Eede G. Quality and safety requirements for sustainable phage therapy products. Pharm Res 2015; 32:2173-9. [PMID: 25585954 PMCID: PMC4452253 DOI: 10.1007/s11095-014-1617-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/30/2014] [Indexed: 12/11/2022]
Abstract
The worldwide antibiotic crisis has led to a renewed interest in phage therapy. Since time immemorial phages control bacterial populations on Earth. Potent lytic phages against bacterial pathogens can be isolated from the environment or selected from a collection in a matter of days. In addition, phages have the capacity to rapidly overcome bacterial resistances, which will inevitably emerge. To maximally exploit these advantage phages have over conventional drugs such as antibiotics, it is important that sustainable phage products are not submitted to the conventional long medicinal product development and licensing pathway. There is a need for an adapted framework, including realistic production and quality and safety requirements, that allowsa timely supplying of phage therapy products for ‘personalized therapy’ or for public health or medical emergencies. This paper enumerates all phage therapy product related quality and safety risks known to the authors, as well as the tests that can be performed to minimize these risks, only to the extent needed to protect the patients and to allow and advance responsible phage therapy and research.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussel, Belgium,
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14
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Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D, Verbeken G, Noben JP, Lavigne R, Vaneechoutte M, Pirnay JP. Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii. PLoS One 2014; 9:e104853. [PMID: 25111143 PMCID: PMC4128745 DOI: 10.1371/journal.pone.0104853] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/18/2014] [Indexed: 12/24/2022] Open
Abstract
Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Dieter Vandenheuvel
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Noben
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
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15
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Abstract
Bacteria Pseudomonas aeruginosa, being opportunistic pathogens, are the major cause of nosocomial infections and, in some cases, the primary cause of death. They are virtually untreatable with currently known antibiotics. Phage therapy is considered as one of the possible approaches to the treatment of P. aeruginosa infections. Difficulties in the implementation of phage therapy in medical practice are related, for example, to the insufficient number and diversity of virulent phages that are active against P. aeruginosa. Results of interaction of therapeutic phages with bacteria in different conditions and environments are studied insufficiently. A little is known about possible interactions of therapeutic phages with resident prophages and plasmids in clinical strains in the foci of infections. This chapter highlights the different approaches to solving these problems and possible ways to expand the diversity of therapeutic P. aeruginosa phages and organizational arrangements (as banks of phages) to ensure long-term use of phages in the treatment of P. aeruginosa infections.
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Affiliation(s)
- Victor N Krylov
- Mechnikov Research Institute for Vaccines & Sera, Russian Academy of Medical Sciences, Moscow, Russia.
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16
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Phages can constrain protist predation-driven attenuation of Pseudomonas aeruginosa virulence in multienemy communities. ISME JOURNAL 2014; 8:1820-30. [PMID: 24671085 DOI: 10.1038/ismej.2014.40] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 02/18/2014] [Accepted: 02/23/2014] [Indexed: 11/08/2022]
Abstract
The coincidental theory of virulence predicts that bacterial pathogenicity could be a by-product of selection by natural enemies in environmental reservoirs. However, current results are ambiguous and the simultaneous impact of multiple ubiquitous enemies, protists and phages on virulence evolution has not been investigated previously. Here we tested experimentally how Tetrahymena thermophila protist predation and PNM phage parasitism (bacteria-specific virus) alone and together affect the evolution of Pseudomonas aeruginosa PAO1 virulence, measured in wax moth larvae. Protist predation selected for small colony types, both in the absence and presence of phage, which showed decreased edibility to protists, reduced growth in the absence of enemies and attenuated virulence. Although phage selection alone did not affect the bacterial phenotype, it weakened protist-driven antipredatory defence (biofilm formation), its associated pleiotropic growth cost and the correlated reduction in virulence. These results suggest that protist selection can be a strong coincidental driver of attenuated bacterial virulence, and that phages can constrain this effect owing to effects on population dynamics and conflicting selection pressures. Attempting to define causal links such as these might help us to predict the cold and hot spots of coincidental virulence evolution on the basis of microbial community composition of environmental reservoirs.
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17
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Krylov SV, Kropinski AM, Pleteneva EA, Shaburova OV, Burkal’tseva MV, Mirosnnikov KA, Krylov VN. Properties of the new D3-like Pseudomonas aeruginosa bacteriophage phiPMG1: Genome structure and prospects for the use in phage therapy. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412060087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Saussereau E, Debarbieux L. Bacteriophages in the experimental treatment of Pseudomonas aeruginosa infections in mice. Adv Virus Res 2012; 83:123-41. [PMID: 22748810 DOI: 10.1016/b978-0-12-394438-2.00004-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The regular increase of drug-resistant pathogens has been a major force in the renewed interest in the use of bacteriophages as therapeutics. In addition to experience acquired in eastern Europe where bacteriophages have been used to treat bacterial infections in humans, in Western countries only experimental models have been developed until recently. The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen causing particularly severe infections in cystic fibrosis patients. Several experimental models in mice have yielded encouraging results for the use of bacteriophages to treat or prevent septicemia, skin and lungs infections caused by P. aeruginosa. Now, a phase II clinical trial conducted in the United Kingdom provides evidence for the efficacy of bacteriophage treatments in chronic otitis due to antibiotic-resistant P. aeruginosa strains. Together with experimental models, these results provide an incentive to develop more research and clinical studies to fully appreciate the benefits of the use of bacteriophages in medicine.
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Affiliation(s)
- Emilie Saussereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
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19
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Effects of sequential and simultaneous applications of bacteriophages on populations of Pseudomonas aeruginosa in vitro and in wax moth larvae. Appl Environ Microbiol 2012; 78:5646-52. [PMID: 22660719 DOI: 10.1128/aem.00757-12] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Interest in using bacteriophages to treat bacterial infections (phage therapy) is growing, but there have been few experiments comparing the effects of different treatment strategies on both bacterial densities and resistance evolution. While it is established that multiphage therapy is typically more effective than the application of a single phage type, it is not clear if it is best to apply phages simultaneously or sequentially. We tried single- and multiphage therapy against Pseudomonas aeruginosa PAO1 in vitro, using different combinations of phages either simultaneously or sequentially. Across different phage combinations, simultaneous application was consistently equal or superior to sequential application in terms of reducing bacterial population density, and there was no difference (on average) in terms of minimizing resistance. Phage-resistant bacteria emerged in all experimental treatments and incurred significant fitness costs, expressed as reduced growth rate in the absence of phages. Finally, phage therapy increased the life span of wax moth larvae infected with P. aeruginosa, and a phage cocktail was the most effective short-term treatment. When the ratio of phages to bacteria was very high, phage cocktails cured otherwise lethal infections. These results suggest that while adding all available phages simultaneously tends to be the most successful short-term strategy, there are sequential strategies that are equally effective and potentially better over longer time scales.
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20
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High diversity and novel species of Pseudomonas aeruginosa bacteriophages. Appl Environ Microbiol 2012; 78:4510-5. [PMID: 22504803 DOI: 10.1128/aem.00065-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The diversity of Pseudomonas aeruginosa bacteriophages was investigated using a collection of 68 phages isolated from Central Mexico. Most of the phages carried double-stranded DNA (dsDNA) genomes and were classified into 12 species. Comparison of the genomes of selected archetypal phages with extant sequences in GenBank resulted in the identification of six novel species. This finding increased the group diversity by ~30%. The great diversity of phage species could be related to the ubiquitous nature of P. aeruginosa.
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21
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Krylov VN, Miroshnikov KA, Krylov SV, Veyko VP, Pleteneva EA, Shaburova OV, Bourkal’tseva MV. Interspecies migration and evolution of bacteriophages of the genus phiKZ: The purpose and criteria of the search for new phiKZ-like bacteriophages. RUSS J GENET+ 2010. [DOI: 10.1134/s102279541002002x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Glonti T, Chanishvili N, Taylor P. Bacteriophage-derived enzyme that depolymerizes the alginic acid capsule associated with cystic fibrosis isolates ofPseudomonas aeruginosa. J Appl Microbiol 2010; 108:695-702. [DOI: 10.1111/j.1365-2672.2009.04469.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Ceyssens PJ, Noben JP, Ackermann HW, Verhaegen J, De Vos D, Pirnay JP, Merabishvili M, Vaneechoutte M, Chibeu A, Volckaert G, Lavigne R. Survey ofPseudomonas aeruginosaand its phages:de novopeptide sequencing as a novel tool to assess the diversity of worldwide collected viruses. Environ Microbiol 2009; 11:1303-13. [DOI: 10.1111/j.1462-2920.2008.01862.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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24
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Merabishvili M, Pirnay JP, Verbeken G, Chanishvili N, Tediashvili M, Lashkhi N, Glonti T, Krylov V, Mast J, Van Parys L, Lavigne R, Volckaert G, Mattheus W, Verween G, De Corte P, Rose T, Jennes S, Zizi M, De Vos D, Vaneechoutte M. Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. PLoS One 2009; 4:e4944. [PMID: 19300511 PMCID: PMC2654153 DOI: 10.1371/journal.pone.0004944] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 02/13/2009] [Indexed: 12/16/2022] Open
Abstract
We describe the small-scale, laboratory-based, production and quality control of a cocktail, consisting of exclusively lytic bacteriophages, designed for the treatment of Pseudomonas aeruginosa and Staphylococcus aureus infections in burn wound patients. Based on succesive selection rounds three bacteriophages were retained from an initial pool of 82 P. aeruginosa and 8 S. aureus bacteriophages, specific for prevalent P. aeruginosa and S. aureus strains in the Burn Centre of the Queen Astrid Military Hospital in Brussels, Belgium. This cocktail, consisting of P. aeruginosa phages 14/1 (Myoviridae) and PNM (Podoviridae) and S. aureus phage ISP (Myoviridae) was produced and purified of endotoxin. Quality control included Stability (shelf life), determination of pyrogenicity, sterility and cytotoxicity, confirmation of the absence of temperate bacteriophages and transmission electron microscopy-based confirmation of the presence of the expected virion morphologic particles as well as of their specific interaction with the target bacteria. Bacteriophage genome and proteome analysis confirmed the lytic nature of the bacteriophages, the absence of toxin-coding genes and showed that the selected phages 14/1, PNM and ISP are close relatives of respectively F8, φKMV and phage G1. The bacteriophage cocktail is currently being evaluated in a pilot clinical study cleared by a leading Medical Ethical Committee.
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Affiliation(s)
- Maya Merabishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology (EIBMV), Tbilisi, Georgia
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
- Laboratory of Bacteriology Research (LBR), Ghent University Hospital, Ghent, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
- * E-mail:
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Nina Chanishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology (EIBMV), Tbilisi, Georgia
| | - Marina Tediashvili
- Eliava Institute of Bacteriophage, Microbiology and Virology (EIBMV), Tbilisi, Georgia
| | - Nino Lashkhi
- Eliava Institute of Bacteriophage, Microbiology and Virology (EIBMV), Tbilisi, Georgia
| | - Thea Glonti
- Eliava Institute of Bacteriophage, Microbiology and Virology (EIBMV), Tbilisi, Georgia
| | - Victor Krylov
- Laboratory of Bacteriophage Genetics, State Institute for Genetics and Selection of Industrial Microorganisms (SIGSIM), Moscow, Russia
| | - Jan Mast
- Unit Electron Microscopy, Veterinary and Agricultural Research Centre (VAR), Ukkel, Brussels, Belgium
| | - Luc Van Parys
- Section Health of the Division Well-Being (Belgian Defence Staff), Queen Astrid Military Hospital, Neder-over-Heembeek, Brussels, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology (LoGT), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Guido Volckaert
- Laboratory of Gene Technology (LoGT), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Wesley Mattheus
- Laboratory of Gene Technology (LoGT), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gunther Verween
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Peter De Corte
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Thomas Rose
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Serge Jennes
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Martin Zizi
- Section Health of the Division Well-Being (Belgian Defence Staff), Queen Astrid Military Hospital, Neder-over-Heembeek, Brussels, Belgium
- Department of Physiology (FYSP), Vrije Universiteit Brussel, Jette Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Centre, Queen Astrid Military Hospital, Bruynstraat, Neder-over-Heembeek, Brussels, Belgium
| | - Mario Vaneechoutte
- Laboratory of Bacteriology Research (LBR), Ghent University Hospital, Ghent, Belgium
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