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Faltus T. The Medicinal Phage-Regulatory Roadmap for Phage Therapy under EU Pharmaceutical Legislation. Viruses 2024; 16:443. [PMID: 38543808 PMCID: PMC10974108 DOI: 10.3390/v16030443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 05/23/2024] Open
Abstract
Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target and kill pathogenic bacteria. The legal handling of this type of therapy raises several questions. These include whether phage therapeutics belong to a specially regulated class of medicinal products, and which legal framework should be followed with regard to the various technical ways in which phage therapeutics can be manufactured and administered. The article shows to which class of medicinal products phage therapeutics from wild type phages and from genetically modified (designer) phages do or do not belong. Furthermore, the article explains which legal framework is relevant for the manufacture and administration of phage therapeutics, which are manufactured in advance in a uniform, patient-independent manner, and for tailor-made patient-specific phage therapeutics. For the systematically coherent, successful translation of phage therapy, the article considers pharmaceutical law and related legal areas, such as genetic engineering law. Finally, the article shows how the planned legislative revisions of Directive 2001/83/EC and Regulation (EC) No 726/2004 may affect the legal future of phage therapy.
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Affiliation(s)
- Timo Faltus
- Chair of Public Law, Law School, Faculty of Law, Economics and Business, Martin-Luther-University Halle-Wittenberg, 06099 Halle an der Saale, Germany
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2
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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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3
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Ali Z, Dishisha T, El-Gendy AO, Azmy AF. Isolation and phenotypic characterization of bacteriophage SA14 with lytic- and anti-biofilm activity against multidrug-resistant Enterococcus faecalis. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2023. [DOI: 10.1186/s43088-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
Abstract
Background
Antimicrobial resistance is a growing global health concern demanding more attention and action at the international-, national- and regional levels. In the present study, bacteriophage was sought as a potential alternative to traditional antibiotics.
Results
Vancomycin-resistant Enterococcus faecalis was isolated from a urine sample. Partial 16S rRNA-gene sequencing and VITEK®2 system were employed for its identification, biochemical characterization, and antibiotic susceptibility testing. The isolate was resistant to eight antibiotics (out of 11): vancomycin, gentamicin (high-level synergy), streptomycin (high-level synergy), ciprofloxacin, levofloxacin, erythromycin, quinupristin/dalfopristin, and tetracycline. Bacteriophage SA14 was isolated from sewage water using the multidrug-resistant isolate as a host. Transmission electron micrographs revealed that phage SA14 is a member of the Siphoviridae family displaying the typical circular head and long non-contractile tail. The phage showed characteristic stability to a wide range of solution pH and temperatures, with optimal stability at pH 7.4 and 4 °C, while showing high specificity toward their host. Based on the one-step growth curve, the phage's latent period was 25 min, and the burst size was 20 PFU/ml. The lytic activity of phage SA14 was evaluated at various multiplicities of infection (MOI), all considerably suppressed the growth of the host organism. Moreover, phage SA14 displayed a characteristic anti-biofilm activity as observed by the reduction in adhered biomass and -viable cells in the pre-formed biofilm by 19.1-fold and 2.5-fold, respectively.
Conclusion
Phage therapy can be a valuable alternative to antibiotics against multi-drug resistant microorganisms.
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4
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Characterization of Stenotrophomonas maltophilia phage AXL1 as a member of the genus Pamexvirus encoding resistance to trimethoprim-sulfamethoxazole. Sci Rep 2022; 12:10299. [PMID: 35717537 PMCID: PMC9206674 DOI: 10.1038/s41598-022-14025-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Stenotrophomonas maltophilia is a ubiquitous environmental bacterium capable of causing disease in humans. Antibiotics are largely ineffective against this pathogen due to numerous chromosomally encoded antibiotic resistance mechanisms. An alternative treatment option is phage therapy, the use of bacteriophages to selectively kill target bacteria that are causing infection. To this aim, we isolated the Siphoviridae bacteriophage AXL1 (vB_SmaS-AXL_1) from soil and herein describe its characterization. Host range analysis on a panel of 30 clinical S. maltophilia strains reveals a moderate tropism that includes cross-species infection of Xanthomonas, with AXL1 using the type IV pilus as its host surface receptor for infection. Complete genome sequencing and analysis revealed a 63,962 bp genome encoding 83 putative proteins. Comparative genomics place AXL1 in the genus Pamexvirus, along with seven other phages that infect one of Stenotrophomonas, Pseudomonas or Xanthomonas species. Functional genomic analyses identified an AXL1-encoded dihydrofolate reductase enzyme that provides additional resistance to the antibiotic combination trimethoprim-sulfamethoxazole, the current recommended treatment option for S. maltophilia infections. This research characterizes the sixth type IV pilus-binding phage of S. maltophilia and is an example of phage-encoded antibiotic resistance.
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Danis-Wlodarczyk KM, Wozniak DJ, Abedon ST. Treating Bacterial Infections with Bacteriophage-Based Enzybiotics: In Vitro, In Vivo and Clinical Application. Antibiotics (Basel) 2021; 10:1497. [PMID: 34943709 PMCID: PMC8698926 DOI: 10.3390/antibiotics10121497] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Over the past few decades, we have witnessed a surge around the world in the emergence of antibiotic-resistant bacteria. This global health threat arose mainly due to the overuse and misuse of antibiotics as well as a relative lack of new drug classes in development pipelines. Innovative antibacterial therapeutics and strategies are, therefore, in grave need. For the last twenty years, antimicrobial enzymes encoded by bacteriophages, viruses that can lyse and kill bacteria, have gained tremendous interest. There are two classes of these phage-derived enzymes, referred to also as enzybiotics: peptidoglycan hydrolases (lysins), which degrade the bacterial peptidoglycan layer, and polysaccharide depolymerases, which target extracellular or surface polysaccharides, i.e., bacterial capsules, slime layers, biofilm matrix, or lipopolysaccharides. Their features include distinctive modes of action, high efficiency, pathogen specificity, diversity in structure and activity, low possibility of bacterial resistance development, and no observed cross-resistance with currently used antibiotics. Additionally, and unlike antibiotics, enzybiotics can target metabolically inactive persister cells. These phage-derived enzymes have been tested in various animal models to combat both Gram-positive and Gram-negative bacteria, and in recent years peptidoglycan hydrolases have entered clinical trials. Here, we review the testing and clinical use of these enzymes.
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Affiliation(s)
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
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6
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Sørensen PE, Ng DYK, Duchateau L, Ingmer H, Garmyn A, Butaye P. Classification of In Vitro Phage-Host Population Growth Dynamics. Microorganisms 2021; 9:2470. [PMID: 34946072 PMCID: PMC8708399 DOI: 10.3390/microorganisms9122470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
The therapeutic use of bacteriophages (phage therapy) represents a promising alternative to antibiotics to control bacterial pathogens. However, the understanding of the phage-bacterium interactions and population dynamics seems essential for successful phage therapy implementation. Here, we investigated the effect of three factors: phage species (18 lytic E. coli-infecting phages); bacterial strain (10 APEC strains); and multiplicity of infection (MOI) (MOI 10, 1, and 0.1) on the bacterial growth dynamics. All factors had a significant effect, but the phage appeared to be the most important. The results showed seven distinct growth patterns. The first pattern corresponded to the normal bacterial growth pattern in the absence of a phage. The second pattern was complete bacterial killing. The remaining patterns were in-between, characterised by delayed growth and/or variable killing of the bacterial cells. In conclusion, this study demonstrates that the phage-host dynamics is an important factor in the capacity of a phage to eliminate bacteria. The classified patterns show that this is an essential factor to consider when developing a phage therapy. This methodology can be used to rapidly screen for novel phage candidates for phage therapy. Accordingly, the most promising candidates were phages found in Group 2, characterised by growth dynamics with high bacterial killing.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
| | - Duncan Y. K. Ng
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Luc Duchateau
- Biometrics Research Center, Ghent University, 9820 Merelbeke, Belgium;
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
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7
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Attrill EL, Claydon R, Łapińska U, Recker M, Meaden S, Brown AT, Westra ER, Harding SV, Pagliara S. Individual bacteria in structured environments rely on phenotypic resistance to phage. PLoS Biol 2021; 19:e3001406. [PMID: 34637438 PMCID: PMC8509860 DOI: 10.1371/journal.pbio.3001406] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria–phage interactions in naturally structured environments. Bacteriophages represent a promising avenue to overcome the current antibiotic resistance crisis, but evolution of phage resistance remains a concern. This study shows that in the presence of spatial refuges, genetic resistance to phage is less of a problem than commonly assumed, but the persistence of genetically susceptible bacteria suggests that eradicating bacterial pathogens from structured environments may require combined phage-antibiotic therapies.
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Affiliation(s)
- Erin L. Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rory Claydon
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Sean Meaden
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Aidan T. Brown
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Edze R. Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
| | - Sarah V. Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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8
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Korf IHE, Kittler S, Bierbrodt A, Mengden R, Rohde C, Rohde M, Kroj A, Lehnherr T, Fruth A, Flieger A, Lehnherr H, Wittmann J. In Vitro Evaluation of a Phage Cocktail Controlling Infections with Escherichia coli. Viruses 2020; 12:v12121470. [PMID: 33352791 PMCID: PMC7768485 DOI: 10.3390/v12121470] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Worldwide, poultry industry suffers from infections caused by avian pathogenic Escherichia coli. Therapeutic failure due to resistant bacteria is of increasing concern and poses a threat to human and animal health. This causes a high demand to find alternatives to fight bacterial infections in animal farming. Bacteriophages are being especially considered for the control of multi-drug resistant bacteria due to their high specificity and lack of serious side effects. Therefore, the study aimed on characterizing phages and composing a phage cocktail suitable for the prevention of infections with E. coli. Six phages were isolated or selected from our collections and characterized individually and in combination with regard to host range, stability, reproduction, and efficacy in vitro. The cocktail consisting of six phages was able to inhibit formation of biofilms by some E. coli strains but not by all. Phage-resistant variants arose when bacterial cells were challenged with a single phage but not when challenged by a combination of four or six phages. Resistant variants arising showed changes in carbon metabolism and/or motility. Genomic comparison of wild type and phage-resistant mutant E28.G28R3 revealed a deletion of several genes putatively involved in phage adsorption and infection.
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Affiliation(s)
- Imke H. E. Korf
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
- Correspondence:
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany;
| | | | - Ruth Mengden
- Food Inspection, Animal Welfare and Veterinary Service of the Land of Bremen, Border Control Post Bremerhaven, Senator-Borttscheller-Straße 8, 27568 Bremerhaven, Germany;
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Andrea Kroj
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Tatiana Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Angelika Fruth
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Antje Flieger
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Hansjörg Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
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9
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Fauconnier A, Nagel TE, Fauconnier C, Verbeken G, De Vos D, Merabishvili M, Pirnay JP. The Unique Role That WHO Could Play in Implementing Phage Therapy to Combat the Global Antibiotic Resistance Crisis. Front Microbiol 2020; 11:1982. [PMID: 33013742 PMCID: PMC7500132 DOI: 10.3389/fmicb.2020.01982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/27/2020] [Indexed: 01/26/2023] Open
Affiliation(s)
| | - Tobi E Nagel
- Phages for Global Health, Oakland, CA, United States
| | | | - Gilbert Verbeken
- 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
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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10
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Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-550. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
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11
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Storms ZJ, Teel MR, Mercurio K, Sauvageau D. The Virulence Index: A Metric for Quantitative Analysis of Phage Virulence. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:27-36. [PMID: 36147620 PMCID: PMC9041455 DOI: 10.1089/phage.2019.0001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background: One of the main challenges in developing phage therapy and manufacturing phage products is the reliable evaluation of their efficacy, performance, and quality. Since phage virulence is intrinsically difficult to fully capture, researchers have turned to rapid but partially inadequate methods for its evaluation. Materials and Methods: This study demonstrates a standardized quantitative method to assess phage virulence based on three parameters: the virulence index (VP )-quantifying the virulence of a phage against a host, the local virulence (vi )-assessing killing potential at given multiplicities of infection (MOIs), and MV50 -the MOI at which the phage achieves 50% of its maximum theoretical virulence. This was shown through comparative analysis of the virulence of phages T4, T5, and T7. Results: Under the conditions tested, phage T7 displayed the highest virulence, followed by phage T4 and, finally, by phage T5. The impact of parameters such as temperature and medium composition on virulence was shown for each phage. The use of the method to evaluate the virulence of combinations of phages-for example, for cocktail formulation-is also shown with phages T5 and T7. Conclusions: The method presented provides a platform for high-throughput quantitative assessment of phage virulence and quality control of phage products. It can also be applied to phage screening, evaluation of phage strains, phage mutants, infection conditions and/or the susceptibility of host strains, and the formulation of phage cocktails.
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Affiliation(s)
- Zachary J. Storms
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Matthew R. Teel
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Kevin Mercurio
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.,Address correspondence to: Dominic Sauvageau, PhD, Department of Chemical and Materials Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
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12
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13
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Duyvejonck H, Merabishvili M, Pirnay JP, De Vos D, Verbeken G, Van Belleghem J, Gryp T, De Leenheer J, Van der Borght K, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Development of a qPCR platform for quantification of the five bacteriophages within bacteriophage cocktail 2 (BFC2). Sci Rep 2019; 9:13893. [PMID: 31554892 PMCID: PMC6761158 DOI: 10.1038/s41598-019-50461-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022] Open
Abstract
To determine phage titers accurately, reproducibly and in a non-laborious and cost-effective manner, we describe the development of a qPCR platform for molecular quantification of five phages present in bacteriophage cocktail 2 (BFC2). We compared the performance of this molecular approach, with regard to quantification and reproducibility, with the standard culture-based double agar overlay method (DAO). We demonstrated that quantification of each of the five phages in BFC2 was possible by means of qPCR, without prior DNA extraction, but yields were significantly higher in comparison to DAO. Although DAO is assumed to provide an indication of the number of infective phage particles, whereas qPCR only provides information on the number of phage genomes, the difference in yield (qPCR/DAO ratio) was observed to be phage-dependent and appeared rather constant for all phages when analyzing different (freshly prepared) stocks of these phages. While DAO is necessary to determine sensitivity of clinical strains against phages in clinical applications, qPCR might be a valid alternative for rapid and reproducible quantification of freshly prepared stocks, after initial establishment of a correction factor towards DAO.
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Affiliation(s)
- Hans Duyvejonck
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium. .,Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium.
| | - Maya Merabishvili
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium.,The Eliava Institute of Bacteriophages, Microbiology and Virology, Gotua 3, Tbilisi, 0160, Georgia
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Jonas Van Belleghem
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Tessa Gryp
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Julie De Leenheer
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Kelly Van der Borght
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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14
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Tayyarcan EK, Acar Soykut E, Menteş Yılmaz O, Boyaci IH, Khaaladi M, Fattouch S. Investigation of different interactions betweenStaphylococcus aureusphages and pomegranate peel, grape seed, and black cumin extracts. J Food Saf 2019. [DOI: 10.1111/jfs.12679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Esra Acar Soykut
- Yeniçağa Yaşar Çelik Vocational SchoolBolu Abant İzzet Baysal University Bolu Turkey
| | | | - Ismail H. Boyaci
- Department of Food EngineeringHacettepe University Ankara Turkey
| | - Maha Khaaladi
- National Institute of Applied Sciences and Technology (INSAT)University of Carthage Tunis Tunisia
| | - Sami Fattouch
- National Institute of Applied Sciences and Technology (INSAT)University of Carthage Tunis Tunisia
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15
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"French Phage Network" Annual Conference 2018-Fourth Meeting Report. Viruses 2019; 11:v11050470. [PMID: 31126089 PMCID: PMC6563222 DOI: 10.3390/v11050470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 05/21/2019] [Indexed: 11/22/2022] Open
Abstract
The present meeting report aims to cover the scientific activities of the 4th French Bacteriophage Network (Phages.fr) symposium which took place during 24th–25th September 2018, at the Agora du Haut-Carré in Talence (France). The hosting institute was University Bordeaux and 72 participants attended the meeting from both public and private sectors, coming from France, Belgium, Ireland, Germany, Portugal and Canada. The scientific program was structured in three themed oral sessions entitled “ecology and evolution”, “bacteriophage-host molecular interaction”, and “therapy and biotechnology applications” consisting of 21 oral presentations, including three keynote lectures, and a presentation of the activities of the Spanish bacteriophage network. A poster session included 22 presentations.
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16
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Fauconnier A. Phage Therapy Regulation: From Night to Dawn. Viruses 2019; 11:v11040352. [PMID: 30999559 PMCID: PMC6521264 DOI: 10.3390/v11040352] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/23/2019] [Accepted: 04/07/2019] [Indexed: 12/18/2022] Open
Abstract
After decades of disregard in the Western world, phage therapy is witnessing a return of interest. However, the pharmaceutical legislation that has since been implemented is basically designed for regulating industrially-made pharmaceuticals, devoid of any patient customization and intended for large-scale distribution. Accordingly, the resulting regulatory framework is hardly reconcilable with the concept of sustainable phage therapy, involving tailor-made medicinal products in the global perspective of both evolutionary and personalized medicine. The repeated appeal for a dedicated regulatory framework has not been heard by the European legislature, which, in this matter, features a strong resistance to change despite the precedent of the unhindered implementation of advanced therapy medicinal product (ATMPs) regulation. It is acknowledged that in many aspects, phage therapy medicinal products are quite unconventional pharmaceuticals and likely this lack of conformity to the canonical model hampered the development of a suitable regulatory pathway. However, the regulatory approaches of countries where phage therapy traditions and practice have never been abandoned are now being revisited by some Western countries, opening new avenues for phage therapy regulation. As a next step, supranational and international organizations are urged to take over the initiatives originally launched by national regulatory authorities.
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Affiliation(s)
- Alan Fauconnier
- Culture In Vivo ASBL, rue du Progrès, 4, boîte 7, 1400 Nivelles, Belgium.
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17
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Engineering Bacteriophages as Versatile Biologics. Trends Microbiol 2019; 27:355-367. [DOI: 10.1016/j.tim.2018.09.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023]
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Geredew Kifelew L, Mitchell JG, Speck P. Mini-review: efficacy of lytic bacteriophages on multispecies biofilms. BIOFOULING 2019; 35:472-481. [PMID: 31144513 DOI: 10.1080/08927014.2019.1613525] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/07/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
There is potential for phages to prevent and control bacterial biofilms, but few studies have examined the effect of phages on the multispecies biofilms that characterize most bacterial infections. This paper reviews the mechanism of action of phages, the evidence supporting the view that phage therapy will be effective against bacterial targets and the opposite viewpoint, phage application approaches, and the comparative advantage of phage therapy in multispecies biofilms. The few reports measuring the actions of lytic phages against multispecies biofilms are also reviewed. The authors are cautiously optimistic about the application of phages against their targets when in multispecies biofilms because some lysis mechanisms do not require species specificity.
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Affiliation(s)
| | - James G Mitchell
- a Flinders University, College of Science and Engineering , Bedford Park , South Australia
| | - Peter Speck
- a Flinders University, College of Science and Engineering , Bedford Park , South Australia
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19
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Protection of Phage Applications in Crop Production: A Patent Landscape. Viruses 2019; 11:v11030277. [PMID: 30893844 PMCID: PMC6466637 DOI: 10.3390/v11030277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 01/21/2023] Open
Abstract
In agriculture, the prevention and treatment of bacterial infections represents an increasing challenge. Traditional (chemical) methods have been restricted to ensure public health and to limit the occurrence of resistant strains. Bacteriophages could be a sustainable alternative. A major hurdle towards the commercial implementation of phage-based biocontrol strategies concerns aspects of regulation and intellectual property protection. Within this study, two datasets have been composed to analyze both scientific publications and patent documents and to get an idea on the focus of research and development (R&D) by means of an abstract and claim analysis. A total of 137 papers and 49 patent families were found from searching public databases, with their numbers increasing over time. Within this dataset, the majority of the patent documents were filed by non-profit organizations in Asia. There seems to be a good correlation between the papers and patent documents in terms of targeted bacterial genera. Furthermore, granted patents seem to claim rather broad and cover methods of treatment. This review shows that there is indeed growing publishing and patenting activity concerning phage biocontrol. Targeted research is needed to further stimulate the exploration of phages within integrated pest management strategies and to deal with bacterial infections in crop production.
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Abdelkader K, Gerstmans H, Saafan A, Dishisha T, Briers Y. The Preclinical and Clinical Progress of Bacteriophages and Their Lytic Enzymes: The Parts are Easier than the Whole. Viruses 2019; 11:v11020096. [PMID: 30678377 PMCID: PMC6409994 DOI: 10.3390/v11020096] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
The therapeutic potential of phages has been considered since their first identification more than a century ago. The evident concept of using a natural predator to treat bacterial infections has, however, since then been challenged considerably. Initially, the vast success of antibiotics almost eliminated the study of phages for therapy. Upon the renaissance of phage therapy research, the most provocative and unique properties of phages such as high specificity, self-replication and co-evolution prohibited a rapid preclinical and clinical development. On the one hand, the typical trajectory followed by small molecule antibiotics could not be simply translated into the preclinical analysis of phages, exemplified by the need for complex broad spectrum or personalized phage cocktails of high purity and the more complex pharmacokinetics. On the other hand, there was no fitting regulatory framework to deal with flexible and sustainable phage therapy approaches, including the setup and approval of adequate clinical trials. While significant advances are incrementally made to eliminate these hurdles, phage-inspired antibacterials have progressed in the slipstream of phage therapy, benefiting from the lack of hurdles that are typically associated with phage therapy. Most advanced are phage lytic enzymes that kill bacteria through peptidoglycan degradation and osmotic lysis. Both phages and their lytic enzymes are now widely considered as safe and have now progressed to clinical phase II to show clinical efficacy as pharmaceutical. Yet, more initiatives are needed to fill the clinical pipeline to beat the typical attrition rates of clinical evaluation and to come to a true evaluation of phages and phage lytic enzymes in the clinic.
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Affiliation(s)
- Karim Abdelkader
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
- MeBioS-Biosensors group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium.
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium.
| | - Amal Saafan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Menoufia University, Shebin ElKoum 51132, Egypt.
| | - Tarek Dishisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
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21
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Pirnay JP, De Vos D, Verbeken G. Clinical application of bacteriophages in Europe. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteriophages could help address the antibiotic resistance crisis that impacts health systems all over the world. In 2011, the European Commission formally confirmed that phage products used as therapeutics are medicinal products and thus manufacturers need to navigate the extremely arduous and enormously expensive medicine development and marketing pathway. However, up until now, not one therapeutic phage product has made it to the European market, and yet clinicians are under increasing pressure to use phages in the treatment of multidrug-resistant bacterial infections. While a handful of small European enterprises are struggling to squeeze therapeutic phage products through the conventional and centralised European medicinal products funnel, some clinicians and academics are exploring (European) national solutions to accelerate the availability of phages for the treatment of an increasing number of desperate patients. This mini-review summarises the actual status and perspectives of clinical phage application in Europe.
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22
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Venturini C, Fabjian AP, Lin RCY. Bacteriophage therapy for severe infections. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The rise of multiple antibiotic resistance in clinically relevant bacteria has created a global crisis with increasing burden on healthcare systems. The need to optimise alternative therapies to antibiotics, particularly in high risk nosocomial settings, is therefore immediate. Bacteriophages are specialised lethal viruses of bacteria, and an underused clinical resource for the treatment of severe infections refractory to antibiotics. Both the gaps in knowledge of bacteriophage biology, particularly the details of host-pathogen dynamic interactions, and legislative hurdles related to the regulation of natural microorganisms for therapy have delayed progress in bacteriophage clinical applications. At the Westmead Institute for Medical Research (WIMR), in collaboration with Westmead Hospital (Western Sydney Local Health District, WSLHD) and the University of Sydney (USyd), we have been investigating rational design protocols for routine bacteriophage application in clinical practice and testing bacteriophage therapeutics on patients suffering from multidrug resistant (MDR) severe infections.
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23
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Chang RYK, Wallin M, Lin Y, Leung SSY, Wang H, Morales S, Chan HK. Phage therapy for respiratory infections. Adv Drug Deliv Rev 2018; 133:76-86. [PMID: 30096336 PMCID: PMC6226339 DOI: 10.1016/j.addr.2018.08.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/06/2018] [Accepted: 08/01/2018] [Indexed: 01/12/2023]
Abstract
A respiratory infection caused by antibiotic-resistant bacteria can be life-threatening. In recent years, there has been tremendous effort put towards therapeutic application of bacteriophages (phages) as an alternative or supplementary treatment option over conventional antibiotics. Phages are natural parasitic viruses of bacteria that can kill the bacterial host, including antibiotic-resistant bacteria. Inhaled phage therapy involves the development of stable phage formulations suitable for inhalation delivery followed by preclinical and clinical studies for assessment of efficacy, pharmacokinetics and safety. We presented an overview of recent advances in phage formulation for inhalation delivery and their efficacy in acute and chronic rodent respiratory infection models. We have reviewed and presented on the prospects of inhaled phage therapy as a complementary treatment option with current antibiotics and as a preventative means. Inhaled phage therapy has the potential to transform the prevention and treatment of bacterial respiratory infections, including those caused by antibiotic-resistant bacteria.
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Affiliation(s)
| | - Martin Wallin
- Faculty of Pharmaceutical Sciences, University of Copenhagen, Denmark
| | - Yu Lin
- Advanced Drug Delivery Group, School of Pharmacy, University of Sydney, Sydney, Australia
| | - Sharon Sui Yee Leung
- Advanced Drug Delivery Group, School of Pharmacy, University of Sydney, Sydney, Australia; Faculty of Pharmacy, The Chinese University of Hong Kong, Hong Kong, China
| | - Hui Wang
- Advanced Drug Delivery Group, School of Pharmacy, University of Sydney, Sydney, Australia
| | - Sandra Morales
- AmpliPhi Biosciences AU, Brookvale, Sydney, NSW, Australia
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, School of Pharmacy, University of Sydney, Sydney, Australia.
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24
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Harada LK, Silva EC, Campos WF, Del Fiol FS, Vila M, Dąbrowska K, Krylov VN, Balcão VM. Biotechnological applications of bacteriophages: State of the art. Microbiol Res 2018; 212-213:38-58. [DOI: 10.1016/j.micres.2018.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 02/06/2023]
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25
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Rossitto M, Fiscarelli EV, Rosati P. Challenges and Promises for Planning Future Clinical Research Into Bacteriophage Therapy Against Pseudomonas aeruginosa in Cystic Fibrosis. An Argumentative Review. Front Microbiol 2018; 9:775. [PMID: 29780361 PMCID: PMC5945972 DOI: 10.3389/fmicb.2018.00775] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 04/05/2018] [Indexed: 01/16/2023] Open
Abstract
Although early aggressive and prolonged treatment with specific antibiotics can extend survival in patients with cystic fibrosis (CF) colonized by opportunistic Pseudomonas aeruginosa (PA), antibiotics fail to eradicate the infecting multidrug-resistant (MDR) PA strains in CF. Century-long research has suggested treating patients with bacteriophages (phages, prokaryotic viruses) naturally hosted by bacteria. Although the only phage types used in therapy, lytic phages, lyse PA aggregated in biofilm matrix by depolymerase degrading enzymes, how they can effectively, safely, and persistently do so in patients with CF is unclear. Even though advanced techniques for formulating phage cocktails, training phages and collecting phage libraries have improved efficacy in vitro, whether personalized or ready-to-use therapeutic approaches or phages and antibiotics combined are effective and safe in vivo, and can reduce PA biofilms, remains debatable. Hence, to advance clinical research on phage therapy in clinical trials, also involving mucoid and non-mucoid multidrug-resistant PA in CF, and overcome problems in Western international regulations, we need reliable and repeatable information from experiments in vitro and in vivo on phage characterization, cocktail selection, personalized approaches, and phages combined with antibiotics. These findings, challenges, and promises prompted us to undertake this argumentative review to seek up-to-date information from papers describing lytic phage activity tested in vitro on PA laboratory strains, and PA strains from chronic infections including CF. We also reviewed in vivo studies on phage activity on pulmonary and non-pulmonary animal host models infected by laboratory or CF PA strains. Our argumentative review provides essential information showing that future phage clinical research in CF should use well-characterized and selected phages isolated against CF PA, tested in vitro under dynamic conditions in cocktails or combined with antibiotics, and in vivo on non-pulmonary and pulmonary host models infected with mucoid and non-mucoid CF MDR PA. Our findings should encourage pharmaceutical industries to conduct clinical trials in vitro and in vivo testing patented genomic engineered phages from phage libraries combined with antibiotics to treat or even prevent multidrug-resistant PA in CF, thus helping international regulatory agencies to plan future clinical research on phage therapy in CF.
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Affiliation(s)
- Martina Rossitto
- Cystic Fibrosis Microbiology, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ersilia V. Fiscarelli
- Cystic Fibrosis Microbiology, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Paola Rosati
- Unit of Clinical Epidemiology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
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26
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Abstract
For phage therapy-the treatment of bacterial infections using bacterial viruses-a key issue is the conflict between apparent ease of clinical application, on the one hand, and on the other hand, numerous difficulties that can be associated with undertaking preclinical development. These conflicts between achieving efficacy in the real world versus rigorously understanding that efficacy should not be surprising because equivalent conflicts have been observed in applied biology for millennia: exploiting the inherent, holistic tendencies of useful systems, e.g., of dairy cows, inevitably is easier than modeling those systems or maintaining effectiveness while reducing such systems to isolated parts. Trial and error alone, in other words, can be a powerful means toward technological development. Undertaking trial and error-based programs, especially in the clinic, nonetheless is highly dependent on those technologies possessing both inherent safety and intrinsic tendencies toward effectiveness, but in this modern era we tend to forget that ideally there would exist antibacterials which could be thus developed, that is, with tendencies toward both safety and effectiveness, and which are even relatively inexpensive. Consequently, we tend to demand rigor as well as expense of development even to the point of potentially squandering such utility, were it to exist. In this review I lay out evidence that in phage therapy such potential, in fact, does exist. Advancement of phage therapy unquestionably requires effective regulation as well as rigorous demonstration of efficacy, but after nearly 100 years of clinical practice, perhaps not as much emphasis on strictly laboratory-based proof of principle.
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27
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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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28
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Torres-Barceló C, Kaltz O, Froissart R, Gandon S, Ginet N, Ansaldi M. "French Phage Network"-Second Meeting Report. Viruses 2017; 9:v9040087. [PMID: 28430166 PMCID: PMC5408693 DOI: 10.3390/v9040087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 03/29/2017] [Accepted: 04/19/2017] [Indexed: 12/22/2022] Open
Abstract
The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the exchange on complementary approaches, but also to engage new collaborations. Here, we provide a summary of the topics presented during the second meeting of the French Phage Network that took place in Marseille in November 2016.
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Affiliation(s)
- Clara Torres-Barceló
- Plant Populations and Bio-aggressors in Tropical Ecosystems (PVBMT) UMR, Pôle de Protection des Plantes, F-97410, Saint-Pierre, Reunion Island, France.
| | - Oliver Kaltz
- Institut des Sciences de l'Evolution, UMR 5554 (CC065), Université de Montpellier, F-34095 Montpellier, France.
| | - Rémy Froissart
- CNRS, IRD, Université de Montpellier, Laboratory «Maladies Infectieuses & Vecteurs : Ecologie, Génétique, Evolution & Contrôle» (MIVEGEC), UMR 5290, F-34394 Montpellier, France.
| | - Sylvain Gandon
- CNRS, Université de Montpellier, Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, F-34293 Montpellier, France.
| | - Nicolas Ginet
- CNRS, Aix-Marseille Université, Laboratoire de chimie bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, F-13402 Marseille, France.
| | - Mireille Ansaldi
- CNRS, Aix-Marseille Université, Laboratoire de chimie bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, F-13402 Marseille, France.
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29
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Purohit HJ, Kapley A, Khardenavis A, Qureshi A, Dafale NA. Insights in Waste Management Bioprocesses Using Genomic Tools. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:121-170. [PMID: 27926430 DOI: 10.1016/bs.aambs.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
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Affiliation(s)
- H J Purohit
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Kapley
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Khardenavis
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Qureshi
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - N A Dafale
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
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30
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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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31
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Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep 2016; 6:26717. [PMID: 27225966 PMCID: PMC4880932 DOI: 10.1038/srep26717] [Citation(s) in RCA: 370] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/05/2016] [Indexed: 02/08/2023] Open
Abstract
Increasing prevalence and severity of multi-drug-resistant (MDR) bacterial infections has necessitated novel antibacterial strategies. Ideally, new approaches would target bacterial pathogens while exerting selection for reduced pathogenesis when these bacteria inevitably evolve resistance to therapeutic intervention. As an example of such a management strategy, we isolated a lytic bacteriophage, OMKO1, (family Myoviridae) of Pseudomonas aeruginosa that utilizes the outer membrane porin M (OprM) of the multidrug efflux systems MexAB and MexXY as a receptor-binding site. Results show that phage selection produces an evolutionary trade-off in MDR P. aeruginosa, whereby the evolution of bacterial resistance to phage attack changes the efflux pump mechanism, causing increased sensitivity to drugs from several antibiotic classes. Although modern phage therapy is still in its infancy, we conclude that phages, such as OMKO1, represent a new approach to phage therapy where bacteriophages exert selection for MDR bacteria to become increasingly sensitive to traditional antibiotics. This approach, using phages as targeted antibacterials, could extend the lifetime of our current antibiotics and potentially reduce the incidence of antibiotic resistant infections.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Mark Sistrom
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - John E Wertz
- E. coli Genetic Stock Center, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Kaitlyn E Kortright
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deepak Narayan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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Rios AC, Moutinho CG, Pinto FC, Del Fiol FS, Jozala A, Chaud MV, Vila MMDC, Teixeira JA, Balcão VM. Alternatives to overcoming bacterial resistances: State-of-the-art. Microbiol Res 2016; 191:51-80. [PMID: 27524653 DOI: 10.1016/j.micres.2016.04.008] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/28/2016] [Accepted: 04/21/2016] [Indexed: 12/23/2022]
Abstract
Worldwide, bacterial resistance to chemical antibiotics has reached such a high level that endangers public health. Presently, the adoption of alternative strategies that promote the elimination of resistant microbial strains from the environment is of utmost importance. This review discusses and analyses several (potential) alternative strategies to current chemical antibiotics. Bacteriophage (or phage) therapy, although not new, makes use of strictly lytic phage particles as an alternative, or a complement, in the antimicrobial treatment of bacterial infections. It is being rediscovered as a safe method, because these biological entities devoid of any metabolic machinery do not possess any affinity whatsoever to eukaryotic cells. Lysin therapy is also recognized as an innovative antimicrobial therapeutic option, since the topical administration of preparations containing purified recombinant lysins with amounts in the order of nanograms, in infections caused by Gram-positive bacteria, demonstrated a high therapeutic potential by causing immediate lysis of the target bacterial cells. Additionally, this therapy exhibits the potential to act synergistically when combined with certain chemical antibiotics already available on the market. Another potential alternative antimicrobial therapy is based on the use of antimicrobial peptides (AMPs), amphiphilic polypeptides that cause disruption of the bacterial membrane and can be used in the treatment of bacterial, fungal and viral infections, in the prevention of biofilm formation, and as antitumoral agents. Interestingly, bacteriocins are a common strategy of bacterial defense against other bacterial agents, eliminating the potential opponents of the former and increasing the number of available nutrients in the environment for their own growth. They can be applied in the food industry as biopreservatives and as probiotics, and also in fighting multi-resistant bacterial strains. The use of antibacterial antibodies promises to be extremely safe and effective. Additionally, vaccination emerges as one of the most promising preventive strategies. All these will be tackled in detail in this review paper.
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Affiliation(s)
- Alessandra C Rios
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil
| | - Carla G Moutinho
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal; University Fernando Pessoa, Porto, Portugal
| | | | - Fernando S Del Fiol
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil
| | - Angela Jozala
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marco V Chaud
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marta M D C Vila
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil
| | - José A Teixeira
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Victor M Balcão
- LaBNUS-Biomaterials and Nanotechnology Laboratory, i(bs)2i(bs)(2)-intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba/SP, Brazil; CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal.
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Vandenheuvel D, Lavigne R, Brüssow H. Bacteriophage Therapy: Advances in Formulation Strategies and Human Clinical Trials. Annu Rev Virol 2016; 2:599-618. [PMID: 26958930 DOI: 10.1146/annurev-virology-100114-054915] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently, a number of phage therapy phase I and II safety trials have been concluded, showing no notable safety concerns associated with the use of phage. Though hurdles for efficient treatment remain, these trials hold promise for future phase III clinical trials. Interestingly, most phage formulations used in these clinical trials are straightforward phage suspensions, and not much research has focused on the processing of phage cocktails in specific pharmaceutical dosage forms. Additional research on formulation strategies and the stability of phage-based drugs will be of key importance, especially with phage therapy advancing toward phase III clinical trials.
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Affiliation(s)
- Dieter Vandenheuvel
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ,
| | - Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ,
| | - Harald Brüssow
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland;
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Storms ZJ, Sauvageau D. Modeling tailed bacteriophage adsorption: Insight into mechanisms. Virology 2015; 485:355-62. [DOI: 10.1016/j.virol.2015.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
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Kutter EM, Kuhl SJ, Abedon ST. Re-establishing a place for phage therapy in western medicine. Future Microbiol 2015; 10:685-8. [DOI: 10.2217/fmb.15.28] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Sarah J Kuhl
- Veteran's Administration, Northern California, Martinez, CA 94553, USA
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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Sarhan WA, Azzazy HME. Phage approved in food, why not as a therapeutic? Expert Rev Anti Infect Ther 2014; 13:91-101. [DOI: 10.1586/14787210.2015.990383] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Torres-Barceló C, Arias-Sánchez FI, Vasse M, Ramsayer J, Kaltz O, Hochberg ME. A window of opportunity to control the bacterial pathogen Pseudomonas aeruginosa combining antibiotics and phages. PLoS One 2014; 9:e106628. [PMID: 25259735 PMCID: PMC4178015 DOI: 10.1371/journal.pone.0106628] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/25/2014] [Indexed: 01/09/2023] Open
Abstract
The evolution of antibiotic resistance in bacteria is a global concern and the use of bacteriophages alone or in combined therapies is attracting increasing attention as an alternative. Evolutionary theory predicts that the probability of bacterial resistance to both phages and antibiotics will be lower than to either separately, due for example to fitness costs or to trade-offs between phage resistance mechanisms and bacterial growth. In this study, we assess the population impacts of either individual or combined treatments of a bacteriophage and streptomycin on the nosocomial pathogen Pseudomonas aeruginosa. We show that combining phage and antibiotics substantially increases bacterial control compared to either separately, and that there is a specific time delay in antibiotic introduction independent of antibiotic dose, that minimizes both bacterial density and resistance to either antibiotics or phage. These results have implications for optimal combined therapeutic approaches.
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Affiliation(s)
- Clara Torres-Barceló
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
- * E-mail: (CTB); (MEH)
| | - Flor I. Arias-Sánchez
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
| | - Marie Vasse
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
| | - Johan Ramsayer
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
| | - Oliver Kaltz
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
| | - Michael E. Hochberg
- Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Wissenshaftskolleg zu Berlin, Berlin, Germany
- * E-mail: (CTB); (MEH)
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Taking bacteriophage therapy seriously: a moral argument. BIOMED RESEARCH INTERNATIONAL 2014; 2014:621316. [PMID: 24868534 PMCID: PMC4020481 DOI: 10.1155/2014/621316] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/14/2014] [Accepted: 04/21/2014] [Indexed: 01/21/2023]
Abstract
The excessive and improper use of antibiotics has led to an increasing incidence of bacterial resistance. In Europe the yearly number of infections caused by multidrug resistant bacteria is more than 400.000, each year resulting in 25.000 attributable deaths. Few new antibiotics are in the pipeline of the pharmaceutical industry. Early in the 20th century, bacteriophages were described as entities that can control bacterial populations. Although bacteriophage therapy was developed and practiced in Europe and the former Soviet republics, the use of bacteriophages in clinical setting was neglected in Western Europe since the introduction of traditional antibiotics. Given the worldwide antibiotic crisis there is now a growing interest in making bacteriophage therapy available for use in modern western medicine. Despite the growing interest, access to bacteriophage therapy remains highly problematic. In this paper, we argue that the current state of affairs is morally unacceptable and that all stakeholders (pharmaceutical industry, competent authorities, lawmakers, regulators, and politicians) have the moral duty and the shared responsibility towards making bacteriophage therapy urgently available for all patients in need.
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Verbeken G, Pirnay JP, Lavigne R, Jennes S, De Vos D, Casteels M, Huys I. Call for a dedicated European legal framework for bacteriophage therapy. Arch Immunol Ther Exp (Warsz) 2014; 62:117-29. [PMID: 24500660 PMCID: PMC3950567 DOI: 10.1007/s00005-014-0269-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 01/21/2023]
Abstract
The worldwide emergence of antibiotic resistances and the drying up of the antibiotic pipeline have spurred a search for alternative or complementary antibacterial therapies. Bacteriophages are bacterial viruses that have been used for almost a century to combat bacterial infections, particularly in Poland and the former Soviet Union. The antibiotic crisis has triggered a renewed clinical and agricultural interest in bacteriophages. This, combined with new scientific insights, has pushed bacteriophages to the forefront of the search for new approaches to fighting bacterial infections. But before bacteriophage therapy can be introduced into clinical practice in the European Union, several challenges must be overcome. One of these is the conceptualization and classification of bacteriophage therapy itself and the extent to which it constitutes a human medicinal product regulated under the European Human Code for Medicines (Directive 2001/83/EC). Can therapeutic products containing natural bacteriophages be categorized under the current European regulatory framework, or should this framework be adapted? Various actors in the field have discussed the need for an adapted (or entirely new) regulatory framework for the reintroduction of bacteriophage therapy in Europe. This led to the identification of several characteristics specific to natural bacteriophages that should be taken into consideration by regulators when evaluating bacteriophage therapy. One important consideration is whether bacteriophage therapy development occurs on an industrial scale or a hospital-based, patient-specific scale. More suitable regulatory standards may create opportunities to improve insights into this promising therapeutic approach. In light of this, we argue for the creation of a new, dedicated European regulatory framework for bacteriophage therapy.
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Affiliation(s)
- Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Burn Wound Centre, Queen Astrid Military Hospital, Brussels, Belgium,
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40
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Affiliation(s)
- Eric C Keen
- Department of Biology, University of Miami, 1211 Dickinson Drive, Coral Gables, FL 33146, USA.
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Wittmann J, Dreiseikelmann B, Rohde C, Rohde M, Sikorski J. Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans. PLoS One 2014; 9:e86935. [PMID: 24466294 PMCID: PMC3899368 DOI: 10.1371/journal.pone.0086935] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 12/19/2013] [Indexed: 11/19/2022] Open
Abstract
The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.
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Affiliation(s)
- Johannes Wittmann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany
- * E-mail:
| | - Brigitte Dreiseikelmann
- Department of Microbiology/Genetechnology, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
| | - Christine Rohde
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Department of Medical Microbiology, Central Facility for Microscopy, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Microbial Ecology and Diversity Research, Braunschweig, Germany
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Lynch KH, Abdu AH, Schobert M, Dennis JJ. Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia. BMC Genomics 2013; 14:574. [PMID: 23978260 PMCID: PMC3765740 DOI: 10.1186/1471-2164-14-574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/09/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND As is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characterization of the novel BCC phage JG068 (vB_BceP_JG068). RESULTS JG068 is a podovirus that forms large, clear plaques on Burkholderia cenocepacia K56-2. Host range analysis indicates that this phage can infect environmental, clinical, and epidemic isolates of Burkholderia multivorans, B. cenocepacia, Burkholderia stabilis, and Burkholderia dolosa, likely through interaction with the host lipopolysaccharide as a receptor. The JG068 chromosome is 41,604 base pairs (bp) in length and is flanked by 216 bp short direct terminal repeats. Gene expression originates from both host and phage promoters and is in the forward direction for all 49 open reading frames. The genome sequence shows similarity to Ralstonia phage ϕRSB1, Caulobacter phage Cd1, and uncharacterized genetic loci of blood disease bacterium R229 and Burkholderia pseudomallei 1710b. CoreGenesUniqueGenes analysis indicates that JG068 belongs to the Autographivirinae subfamily and ϕKMV-like phages genus. Modules within the genome encode proteins involved in DNA-binding, morphogenesis, and lysis, but none associated with pathogenicity or lysogeny. Similar to the signal-arrest-release (SAR) endolysin of ϕKMV, inducible expression of the JG068 SAR endolysin causes lysis of Escherichia coli that is dependent on the presence of an N-terminal signal sequence. In an in vivo assay using the Galleria mellonella infection model, treatment of B. cenocepacia K56-2-infected larvae with JG068 results in a significant increase in larval survival. CONCLUSIONS As JG068 has a broad host range, does not encode virulence factors, is obligately lytic, and has activity against an epidemic B. cenocepacia strain in vivo, this phage is a highly promising candidate for BCC phage therapy development.
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Affiliation(s)
- Karlene H Lynch
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Ashraf H Abdu
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Max Schobert
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jonathan J Dennis
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
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Betts A, Vasse M, Kaltz O, Hochberg ME. Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1. Evol Appl 2013; 6:1054-63. [PMID: 24187587 PMCID: PMC3804238 DOI: 10.1111/eva.12085] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/30/2013] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance is becoming increasingly problematic for the treatment of infectious disease in both humans and livestock. The bacterium Pseudomonas aeruginosa is often found to be resistant to multiple antibiotics and causes high patient mortality in hospitals. Bacteriophages represent a potential option to combat pathogenic bacteria through their application in phage therapy. Here, we capitalize on previous studies showing how evolution may increase phage infection capacity relative to ancestral genotypes. We passaged four different phage isolates (podoviridae, myoviridae) through six serial transfers on the ancestral strain of Pseudomonas aeruginosa PAO1. We first demonstrate that repeated serial passage on ancestral bacteria increases infection capacity of bacteriophage on ancestral hosts and on those evolved for one transfer. This result is confirmed when examining the ability of evolved phage to reduce ancestral host population sizes. Second, through interaction with a single bacteriophage for 24 h, P. aeruginosa can evolve resistance to the ancestor of that bacteriophage; this also provides these evolved bacteria with cross-resistance to the other three bacteriophages. We discuss how the evolutionary training of phages could be employed as effective means of combatting bacterial infections or disinfecting surfaces in hospital settings, with reduced risk of bacterial resistance compared with conventional methods.
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Affiliation(s)
- Alex Betts
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier 2 Montpellier CEDEX 05, France
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Hosseinidoust Z, Tufenkji N, van de Ven TGM. Predation in homogeneous and heterogeneous phage environments affects virulence determinants of Pseudomonas aeruginosa. Appl Environ Microbiol 2013; 79:2862-71. [PMID: 23435883 PMCID: PMC3623153 DOI: 10.1128/aem.03817-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/14/2013] [Indexed: 01/21/2023] Open
Abstract
The rise of bacterial variants in the presence of lytic phages has been one of the basic grounds for evolution studies. However, there are incongruent results among different studies investigating the effect of phage resistance acquisition on bacterial fitness and virulence. We used experimental evolution to generate three classes of Pseudomonas aeruginosa variants under selective pressure from two different homogeneous phage environments and one heterogeneous phage environment. The fitness and virulence determinants of the variants, such as growth, motility, biofilm formation, resistance to oxidative stress, and the production of siderophores and chromophores, changed significantly compared to the control. Variants with similar colony morphology that were developed through different phage treatments have different phenotypic traits. Also, mRNA transcription for genes associated with certain phenotypic traits changed significantly; however, sequencing did not reveal any point mutations in selected gene loci. Furthermore, the appearance of small colony variants and melanogenic variants and the increase in pyocyanin and pyoverdin production for some variants are believed to affect the virulence of the population. The knowledge gained from this study will fundamentally contribute to our understanding of the evolutionary dynamics of bacteria under phage selective pressure which is crucial to the efficient utilization of bacteriophages in medical contexts.
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Affiliation(s)
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
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46
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Huys I, Vaneechoutte M, Verbeken G, Debarbieux L. Key issues in phage therapy: a report of a dedicated workshop at the Viruses of Microbes II meeting. Res Microbiol 2013; 164:806-10. [PMID: 23583722 DOI: 10.1016/j.resmic.2013.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Isabelle Huys
- Centre for Pharmaceutical Care and Pharmaco-Economy, Faculty of Pharmaceutical Sciences, Univ. Leuven, Leuven, Belgium.
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Henein A. What are the limitations on the wider therapeutic use of phage? BACTERIOPHAGE 2013; 3:e24872. [PMID: 24228220 PMCID: PMC3821673 DOI: 10.4161/bact.24872] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 01/13/2013] [Accepted: 04/29/2013] [Indexed: 01/03/2023]
Abstract
Bacterial resistance to antibiotics poses a serious health threat. Since research into new antibiotics is not progressing at the same rate as the development of bacterial resistance, widespread calls for alternatives to antibiotics have been made. Phage therapy is an ideal alternative candidate to be investigated. However the success of phage therapy may be hampered by a lack of investment support from large pharmaceutical companies, due to their narrow spectrum of activity in antibiotics, very large costs associated with clinical trials of the variety of phages needed, and regulatory requirements remaining unclear. Intellectual property is difficult to secure for therapeutic phage products for a variety of reasons, and patenting procedures vary widely between the US and the EU. Consequently, companies are more likely to invest in phage products for decontamination or veterinary use, rather than clinical use in humans. Some still raise questions as to the safety of phage therapy overall, suggesting the possibility of cytotoxicity and immunogenicity, depending on the phage preparation and route. On the other hand, with patients dying because of infections untreatable with conventional antibiotics, the question arises as to whether it is ethical not to pursue phage therapy more diligently. A paradigm shift about how phage therapy is perceived is required, as well as more rigorous proof of efficacy in the form of clinical trials of existing medicinal phage products. Phage therapy potential may be fulfilled in the meantime by allowing individual preparations to be used on a named-patient basis, with extensive monitoring and multidisciplinary team input. The National Health Service and academia have a role in carrying out clinical phage research, which would be beneficial to public health, but not necessarily financially rewarding.
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Merabishvili M, De Vos D, Verbeken G, Kropinski AM, Vandenheuvel D, Lavigne R, Wattiau P, Mast J, Ragimbeau C, Mossong J, Scheres J, Chanishvili N, Vaneechoutte M, Pirnay JP. Selection and characterization of a candidate therapeutic bacteriophage that lyses the Escherichia coli O104:H4 strain from the 2011 outbreak in Germany. PLoS One 2012; 7:e52709. [PMID: 23285164 PMCID: PMC3528706 DOI: 10.1371/journal.pone.0052709] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022] Open
Abstract
In 2011, a novel strain of O104:H4 Escherichia coli caused a serious outbreak of foodborne hemolytic uremic syndrome and bloody diarrhea in Germany. Antibiotics were of questionable use and 54 deaths occurred. Candidate therapeutic bacteriophages that efficiently lyse the E. coli O104:H4 outbreak strain could be selected rather easily from a phage bank or isolated from the environment. It is argued that phage therapy should be more considered as a potential armament against the growing threat of (resistant) bacterial infections.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
- Laboratory of Bacteriology Research, Ghent University, Ghent, 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
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium
| | - Pierre Wattiau
- Unit of Highly Pathogenic & Foodborne Zoonoses, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical 8 Research Centre, Brussels, Belgium
| | - Catherine Ragimbeau
- Surveillance and Epidemiology of Infectious Diseases, Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Joel Mossong
- Surveillance and Epidemiology of Infectious Diseases, Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Jacques Scheres
- Maastricht University Medical Centre, Maastricht, The Netherlands
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Nina Chanishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
| | | | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- * E-mail:
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