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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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2
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Kumar A, Yadav A. Synthetic phage and its application in phage therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:61-89. [PMID: 37739560 DOI: 10.1016/bs.pmbts.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Synthetic phage analysis has been implemented in progressive various areas of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been altered for developing gene circuits to program biological systems. Due to their extremely potent potency, phages also provide greater medical availability against bacterial agents and bacterial diagnostic agents. Its host specificity and our growing ability to manipulate, them further expand its possibility. New Phages also genetically redesign programmable biomaterials with highly tunable properties. Moreover, new phages are central to powerful directed evolution platforms. It is used to enhance existing biological, functions to create new phages. In other sites, the mining of antibiotics, and the emergence and dissemination of more than one type of drug-resistant microbe, a human health concerns. The major point in controlling and treating microbial infections. At present, genetic modifications and biochemical treatments are used to modify phages. Among these, genetic engineering involves the identification of defective proteins, modification of host bodies, recognized receptors, and disruption of bacterial phage resistance signaling gateways.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
| | - Anuj Yadav
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
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3
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Baral B. Phages against killer superbugs: An enticing strategy against antibiotics-resistant pathogens. Front Pharmacol 2023; 14:1036051. [PMID: 36762109 PMCID: PMC9902939 DOI: 10.3389/fphar.2023.1036051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
The emerging resistivity of antibiotic resistance superbugs desire the need to resolve the global problem of antibiotic resistance. Among several other methods currently being adopted, one possible solution may be the development of supplemental therapies for antibiotics. The use of the normal and advanced bactericidal properties of bacteriophages (bacteriophage therapy) may be one of the viable infection control options. It is evident, however, that the safe and regulated application of phage treatment will need extensive knowledge of the characteristics and behaviour of certain phage-bacterium systems. This mini review offers an overview of the potential for phage therapy as well as the constraints and obstacles it faces in becoming a commonly accepted infection management strategy.
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Ababi M, Tridgett M, Osgerby A, Jaramillo A. Scarless Recombineering of Phage in Lysogenic State. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2479:1-9. [PMID: 35583728 DOI: 10.1007/978-1-0716-2233-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We present a scarless recombineering-based method for introducing multiple point mutations into the genome of a temperate phage. The method uses the λ Red recombineering system to promote exogenous ssDNA oligos to anneal on the prophage lagging strand during host genome replication. DNA repair is suppressed by inducing the expression of a dominant-negative mutant protein of the methyl-directed mismatch repair system. Screening for recombinant cells without a selection marker is feasible due to its high recombination frequency, estimated as more than 40% after six cycles. The method enables scarless editing of the genome of a bacteriophage in 4-5 days.
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Affiliation(s)
- Maria Ababi
- Warwick Medical School, University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Alexander Osgerby
- School of Life Sciences, University of Warwick, Coventry, UK.,Chemical Engineering, University of Birmingham, Birmingham, UK
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry, UK. .,De novo Synthetic Biology Lab, I2SysBio, CSIC-University of Valencia, Paterna, Spain.
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5
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Abstract
Increasing antimicrobial resistance and medical device-related infections have led to a renewed interest in phage therapy as an alternative or adjunct to conventional antimicrobials. Expanded access and compassionate use cases have risen exponentially but have varied widely in approach, methodology, and clinical situations in which phage therapy might be considered. Large gaps in knowledge contribute to heterogeneity in approach and lack of consensus in many important clinical areas. The Antibacterial Resistance Leadership Group (ARLG) has convened a panel of experts in phage therapy, clinical microbiology, infectious diseases, and pharmacology, who worked with regulatory experts and a funding agency to identify questions based on a clinical framework and divided them into three themes: potential clinical situations in which phage therapy might be considered, laboratory testing, and pharmacokinetic considerations. Suggestions are provided as answers to a series of questions intended to inform clinicians considering experimental phage therapy for patients in their clinical practices.
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6
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Liu P, Arsuaga J, Calderer MC, Golovaty D, Vazquez M, Walker S. Ion-dependent DNA configuration in bacteriophage capsids. Biophys J 2021; 120:3292-3302. [PMID: 34265262 DOI: 10.1016/j.bpj.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/01/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.
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Affiliation(s)
- Pei Liu
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California Davis, Davis, California; Department of Molecular and Cellular Biology, University of California Davis, Davis, California.
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Dmitry Golovaty
- Department of Mathematics, The University of Akron, Akron, Ohio.
| | - Mariel Vazquez
- Department of Mathematics, University of California Davis, Davis, California; Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California
| | - Shawn Walker
- Department of Mathematics, Louisiana State University, Baton Rouge, Louisiana
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Kazantseva OA, Piligrimova EG, Shadrin AM. vB_BcM_Sam46 and vB_BcM_Sam112, members of a new bacteriophage genus with unusual small terminase structure. Sci Rep 2021; 11:12173. [PMID: 34108535 PMCID: PMC8190038 DOI: 10.1038/s41598-021-91289-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
One of the serious public health concerns is food contaminated with pathogens and their vital activity products such as toxins. Bacillus cereus group of bacteria includes well-known pathogenic species such as B. anthracis, B. cereus sensu stricto (ss), B. cytotoxicus and B. thuringiensis. In this report, we describe the Bacillus phages vB_BcM_Sam46 and vB_BcM_Sam112 infecting species of this group. Electron microscopic analyses indicated that phages Sam46 and Sam112 have the myovirus morphotype. The genomes of Sam46 and Sam112 comprise double-stranded DNA of 45,419 bp and 45,037 bp in length, respectively, and have the same GC-content. The genome identity of Sam46 and Sam112 is 96.0%, indicating that they belong to the same phage species. According to the phylogenetic analysis, these phages form a distinct clade and may be members of a new phage genus, for which we propose the name 'Samaravirus'. In addition, an interesting feature of the Sam46 and Sam112 phages is the unusual structure of their small terminase subunit containing N-terminal FtsK_gamma domain.
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Affiliation(s)
- Olesya A Kazantseva
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
| | - Emma G Piligrimova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey M Shadrin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
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8
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Francius G, Cervulle M, Clément E, Bellanger X, Ekrami S, Gantzer C, Duval JFL. Impacts of Mechanical Stiffness of Bacteriophage-Loaded Hydrogels on Their Antibacterial Activity. ACS APPLIED BIO MATERIALS 2021; 4:2614-2627. [PMID: 35014378 DOI: 10.1021/acsabm.0c01595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The elaboration of efficient hydrogel-based materials with antimicrobial properties requires a refined control of defining their physicochemical features, which includes mechanical stiffness, so as to properly mediate their antibacterial activity. In this work, we design hydrogels consisting of polyelectrolyte multilayer films for the loading of T4 and φX174 bacteria-killing viruses, also called bacteriophages. We investigate the antiadhesion and bactericidal performances of this biomaterial against Escherichia coli, with a specific focus on the effects of chemical cross-linking of the hydrogel matrix, which, in turn, mediates the hydrogel stiffness. Depending on the latter and on phage replication features, it is found that the hydrogels loaded with the bacteria-killing viruses make both contact killing (targeted bacteria are those adhered at the hydrogel surface) and release killing (planktonic bacteria are the targets) possible with ca. 20-80% efficiency after only 4 h of incubation at 25 °C as compared to cases where hydrogels are free of viruses. We further demonstrate the lack of dependence of virus diffusion within the hydrogel and of the maximal viral storage capacity on the hydrogel mechanical properties. In addition to the evidenced bacteriolytic activity of the phages loaded in the hydrogels, the antimicrobial property of the phage-loaded materials is shown to be partly controlled by the chemistry of the hydrogel skeleton and, more specifically, by the mobility of the peripheral free polycationic components, known for their ability to weaken and permeabilize membranes of bacteria, the latter then becoming "easier" targets for the viruses.
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Affiliation(s)
| | - Manon Cervulle
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Eloïse Clément
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | | | - Saeid Ekrami
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community. Biochem Soc Trans 2021; 48:399-409. [PMID: 32159213 DOI: 10.1042/bst20190172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/09/2020] [Accepted: 02/13/2020] [Indexed: 12/27/2022]
Abstract
Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to 'knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.
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10
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Paczesny J, Bielec K. Application of Bacteriophages in Nanotechnology. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1944. [PMID: 33003494 PMCID: PMC7601235 DOI: 10.3390/nano10101944] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
Bacteriophages (phages for short) are viruses, which have bacteria as hosts. The single phage body virion, is a colloidal particle, often possessing a dipole moment. As such, phages were used as perfectly monodisperse systems to study various physicochemical phenomena (e.g., transport or sedimentation in complex fluids), or in the material science (e.g., as scaffolds). Nevertheless, phages also execute the life cycle to multiply and produce progeny virions. Upon completion of the life cycle of phages, the host cells are usually destroyed. Natural abilities to bind to and kill bacteria were a starting point for utilizing phages in phage therapies (i.e., medical treatments that use phages to fight bacterial infections) and for bacteria detection. Numerous applications of phages became possible thanks to phage display-a method connecting the phenotype and genotype, which allows for selecting specific peptides or proteins with affinity to a given target. Here, we review the application of bacteriophages in nanoscience, emphasizing bio-related applications, material science, soft matter research, and physical chemistry.
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Affiliation(s)
- Jan Paczesny
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
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11
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Refining the Galleria mellonella Model by Using Stress Marker Genes to Assess Clostridioides difficile Infection and Recuperation during Phage Therapy. Microorganisms 2020; 8:microorganisms8091306. [PMID: 32867060 PMCID: PMC7564439 DOI: 10.3390/microorganisms8091306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
The Galleria mellonella is an effective model for probing Clostridioides difficile interactions with phages. Despite valuable insights from this model, the larvae are not easily amenable to assessing detailed clinical responses to either bacteria or phages. Here, larval survival, colonisation and toxin levels were compared to expression profiles of 17 G. mellonella stress genes to monitor Clostridiodes difficile infection (CDI), and recuperation during phage therapy. The larvae were infected with a ribotype 014/020 isolate and treated with an optimised phage cocktail. Larvae treated prophylactically with phages and the phage-control larval group were protected, showing the highest survival, and low C. difficile colonisation and toxin rates, compared to co-infection, remedial and bacterial-control larval groups. Expression of growth (9) and reproduction (2) genes were enhanced within prophylaxis and phage-control larval groups compared to the co-infection, remedial and bacterial control groups. In contrast, expression of infection (2), humoral (1) and cellular (3) immunity genes declined in the prophylactic and phage-control groups but increased in the co-infection, remedial and bacterial control larvae. The molecular markers augment the survival, colonisation and toxin data and allow detailed monitoring of CDI and recovery. This data support the use of stress marker genes as tools to analyse clinical symptoms in this model.
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Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
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Abstract
Antibiotic resistance is arguably the biggest current threat to global health. An increasing number of infections are becoming harder or almost impossible to treat, carrying high morbidity, mortality, and financial cost. The therapeutic use of bacteriophages, viruses that infect and kill bacteria, is well suited to be part of the multidimensional strategies to combat antibiotic resistance. Although phage therapy was first implemented almost a century ago, it was brought to a standstill after the successful introduction of antibiotics. Now, with the rise of antibiotic resistance, phage therapy is experiencing a well-deserved rebirth. Among the admittedly vast literature recently published on this topic, this review aims to provide a forward-looking perspective on phage therapy and its role in modern society. We cover the key points of the antibiotic resistance crisis and then explain the biological and evolutionary principles that support the use of phages, their interaction with the immune system, and a comparison with antibiotic therapy. By going through up-to-date reports and, whenever possible, human clinical trials, we examine the versatility of phage therapy. We discuss conventional approaches as well as novel strategies, including the use of phage-antibiotic combinations, phage-derived enzymes, exploitation of phage resistance mechanisms, and phage bioengineering. Finally, we discuss the benefits of phage therapy beyond the clinical perspective, including opportunities for scientific outreach and effective education, interdisciplinary collaboration, cultural and economic growth, and even innovative use of social media, making the case that phage therapy is more than just an alternative to antibiotics.
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14
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Chanishvili N, Aminov R. Bacteriophage therapy: coping with the growing antibiotic resistance problem. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The global problem of multidrug-resistant bacterial pathogens requires urgent actions, including the development of therapies supplementary or alternative to antibiotics. One of the infection control options could be phage therapy. This article gives a brief overview of phage therapy potentials as well as the challenges it faces in order to become a widely accepted form of infection treatment.
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15
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Bacharouche J, Erdemli O, Rivet R, Doucouré B, Caillet C, Mutschler A, Lavalle P, Duval JFL, Gantzer C, Francius G. On the Infectivity of Bacteriophages in Polyelectrolyte Multilayer Films: Inhibition or Preservation of Their Bacteriolytic Activity? ACS APPLIED MATERIALS & INTERFACES 2018; 10:33545-33555. [PMID: 30192508 DOI: 10.1021/acsami.8b10424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Antibiotic resistance in bacterial cells has motivated the scientific community to design new and efficient (bio)materials with targeted bacteriostatic and/or bactericide properties. In this work, a series of polyelectrolyte multilayer films differing in terms of polycation-polyanion combinations are constructed according to the layer-by-layer deposition method. Their capacities to host T4 and φx174 phage particles and maintain their infectivity and bacteriolytic activity are thoroughly examined. It is found that the macroscopic physicochemical properties of the films, which includes film thickness, swelling ratio, or mechanical stiffness (as derived by atomic force microscopy and spectroscopy measurements), do not predominantly control the selectivity of the films for hosting infective phages. Instead, it is evidenced that the intimate electrostatic interactions locally operational between the loaded phages and the polycationic and polyanionic PEM components may lead to phage activity reduction and preservation/enhancement, respectively. It is argued that the underlying mechanism involves the screening of the phage capsid receptors (operational in cell recognition/infection processes) because of the formation of either polymer-phage hetero-assemblies or polymer coating surrounding the bioactive phage surface.
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Affiliation(s)
- Jalal Bacharouche
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
| | - Ozge Erdemli
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann , 67085 Strasbourg Cedex , France
- Université de Strasbourg , Faculté de Chirurgie Dentaire , 8 rue Sainte Elisabeth , 67000 Strasbourg , France
| | - Romain Rivet
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
| | - Balla Doucouré
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
| | - Céline Caillet
- Université de Lorraine, Laboratoire Interdisciplinaire des Environnements Continentaux, UMR 7360 , 54501 Vandœuvre-lès-Nancy , France
- CNRS, Laboratoire Interdisciplinaire des Environnements Continentaux, UMR 7360 , 54501 Vandœuvre-lès-Nancy , France
| | - Angela Mutschler
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann , 67085 Strasbourg Cedex , France
- Université de Strasbourg , Faculté de Chirurgie Dentaire , 8 rue Sainte Elisabeth , 67000 Strasbourg , France
| | - Philippe Lavalle
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann , 67085 Strasbourg Cedex , France
- Université de Strasbourg , Faculté de Chirurgie Dentaire , 8 rue Sainte Elisabeth , 67000 Strasbourg , France
| | - Jérôme F L Duval
- Université de Lorraine, Laboratoire Interdisciplinaire des Environnements Continentaux, UMR 7360 , 54501 Vandœuvre-lès-Nancy , France
- CNRS, Laboratoire Interdisciplinaire des Environnements Continentaux, UMR 7360 , 54501 Vandœuvre-lès-Nancy , France
| | - Christophe Gantzer
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
| | - Grégory Francius
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564 , Villers-lès-Nancy F-54600 , France
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16
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Dunne M, Denyes JM, Arndt H, Loessner MJ, Leiman PG, Klumpp J. Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition. Structure 2018; 26:1573-1582.e4. [PMID: 30244968 DOI: 10.1016/j.str.2018.07.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/11/2018] [Accepted: 07/27/2018] [Indexed: 11/15/2022]
Abstract
The ability of phages to infect specific bacteria has led to their exploitation as bio-tools for bacterial remediation and detection. Many phages recognize bacterial hosts via adhesin tips of their long tail fibers (LTFs). Adhesin sequence plasticity modulates receptor specificity, and thus primarily defines a phage's host range. Here we present the crystal structure of an adhesin (gp38) attached to a trimeric β-helical tip (gp37) from the Salmonella phage S16 LTF. Gp38 contains rare polyglycine type II helices folded into a packed lattice, herein designated "PGII sandwich." Sequence variability within the domain is limited to surface-exposed helices and distal loops that form putative receptor-binding sites. In silico analyses revealed a prevalence of the adhesin architecture among T-even phages, excluding the archetypal T4 phage. Overall, S16 LTF provides a valuable model for understanding binding mechanisms of phage adhesins, and for engineering of phage adhesins with expandable or modulated host ranges.
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Affiliation(s)
- Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
| | - Jenna M Denyes
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Helena Arndt
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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17
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Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis. BMC Genomics 2018; 19:685. [PMID: 30227847 PMCID: PMC6145125 DOI: 10.1186/s12864-018-5056-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/06/2018] [Indexed: 01/05/2023] Open
Abstract
Background In the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Georgia. We report here major trends in the molecular evolution of these phages, which we designate as “Basilisk-Like-Phages” (BLPs), and illustrate patterns in their evolution, genomic plasticity and core genome architecture. Results Comparative whole genome sequence analysis revealed a close evolutionary relationship between our phages and two unclassified Bacillus cereus group phages, phage Basilisk, a broad host range phage (Grose JH et al., J Vir. 2014;88(20):11846-11860) and phage PBC4, a highly host-restricted phage and close relative of Basilisk (Na H. et al. FEMS Microbiol. letters. 2016;363(12)). Genome comparisons of phages v_B-Bak1, v_B-Bak6, and v_B-Bak10 revealed significant similarity in sequence, gene content, and synteny with both Basilisk and PBC4. Transmission electron microscopy (TEM) confirmed the three phages belong to the Siphoviridae family. In contrast to the broad host range of phage Basilisk and the single-strain specificity of PBC4, our three phages displayed host specificity for Bacillus anthracis. Bacillus species including Bacillus cereus, Bacillus subtilis, Bacillus anthracoides, and Bacillus megaterium were refractory to infection. Conclusions Data reported here provide further insight into the shared genomic architecture, host range specificity, and molecular evolution of these rare B. cereus group phages. To date, the three phages represent the only known close relatives of the Basilisk and PBC4 phages and their shared genetic attributes and unique host specificity for B. anthracis provides additional insight into candidate host range determinants. Electronic supplementary material The online version of this article (10.1186/s12864-018-5056-4) contains supplementary material, which is available to authorized users.
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18
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de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends Microbiol 2018; 27:51-63. [PMID: 30181062 DOI: 10.1016/j.tim.2018.08.006] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/07/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023]
Abstract
The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands; Laboratory for Microbiology, Wageningen University, Stippeneng 4 6708 WE, Wageningen, The Netherlands; These authors made equal contributions
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions.
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19
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Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. THE ISME JOURNAL 2018; 12:1605-1618. [PMID: 29568113 PMCID: PMC5955906 DOI: 10.1038/s41396-018-0099-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 01/08/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022]
Abstract
Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.
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Affiliation(s)
| | | | | | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
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20
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Nabergoj D, Kuzmić N, Drakslar B, Podgornik A. Effect of dilution rate on productivity of continuous bacteriophage production in cellstat. Appl Microbiol Biotechnol 2018. [DOI: 10.1007/s00253-018-8893-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Kłopot A, Zakrzewska A, Lecion D, Majewska JM, Harhala MA, Lahutta K, Kaźmierczak Z, Łaczmański Ł, Kłak M, Dąbrowska K. Real-Time qPCR as a Method for Detection of Antibody-Neutralized Phage Particles. Front Microbiol 2017; 8:2170. [PMID: 29163448 PMCID: PMC5672142 DOI: 10.3389/fmicb.2017.02170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/23/2017] [Indexed: 01/08/2023] Open
Abstract
The most common method for phage quantitation is the plaque assay, which relies on phage ability to infect bacteria. However, non-infective phage particles may preserve other biological properties; specifically, they may enter interactions with the immune system of animals and humans. Here, we demonstrate real-time quantitative polymerase chain reaction (qPCR) detection of bacteriophages as an alternative to the plaque assay. The closely related staphylococcal bacteriophages A3R and 676Z and the coliphage T4 were used as model phages. They were tested in vivo in mice, ex vivo in human sera, and on plastic surfaces designed for ELISAs. T4 phage was injected intravenously into pre-immunized mice. The phage was completely neutralized by specific antibodies within 5 h (0 pfu/ml of serum, as determined by the plaque assay), but it was still detected by qPCR in the amount of approximately 107 pfu/ml of serum. This demonstrates a substantial timelapse between "microbiological disappearance" and true clearance of phage particles from the circulation. In human sera ex vivo, qPCR was also able to detect neutralized phage particles that were not detected by the standard plaque assay. The investigated bacteriophages differed considerably in their ability to immobilize on plastic surfaces: this difference was greater than one order of magnitude, as shown by qPCR of phage recovered from plastic plates. The ELISA did not detect differences in phage binding to plates. Major limitations of qPCR are possible inhibitors of the PCR reaction or free phage DNA, which need to be considered in procedures of phage sample preparation for qPCR testing. We propose that phage pharmacokinetic and pharmacodynamic studies should not rely merely on detection of antibacterial activity of a phage. Real-time qPCR can be an alternative for phage detection, especially in immunological studies of bacteriophages. It can also be useful for studies of phage-based drug nanocarriers or biosensors.
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Affiliation(s)
- Anna Kłopot
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Adriana Zakrzewska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Dorota Lecion
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Joanna M Majewska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Marek A Harhala
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Karolina Lahutta
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Zuzanna Kaźmierczak
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Łukasz Łaczmański
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
| | - Marlena Kłak
- Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
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