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Khosravi A, Chen Q, Echterhof A, Koff JL, Bollyky PL. Phage Therapy for Respiratory Infections: Opportunities and Challenges. Lung 2024; 202:223-232. [PMID: 38772946 DOI: 10.1007/s00408-024-00700-7] [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: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 05/23/2024]
Abstract
We are entering the post-antibiotic era. Antimicrobial resistance (AMR) is a critical problem in chronic lung infections resulting in progressive respiratory failure and increased mortality. In the absence of emerging novel antibiotics to counter AMR infections, bacteriophages (phages), viruses that infect bacteria, have become a promising option for chronic respiratory infections. However, while personalized phage therapy is associated with improved outcomes in individual cases, clinical trials demonstrating treatment efficacy are lacking, limiting the therapeutic potential of this approach for respiratory infections. In this review, we address the current state of phage therapy for managing chronic respiratory diseases. We then discuss how phage therapy may address major microbiologic obstacles which hinder disease resolution of chronic lung infections with current antibiotic-based treatment practices. Finally, we highlight the challenges that must be addressed for successful phage therapy clinical trials. Through this discussion, we hope to expand on the potential of phages as an adjuvant therapy in chronic lung infections, as well as the microbiologic challenges that need to be addressed for phage therapy to expand beyond personalized salvage therapy.
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Affiliation(s)
- Arya Khosravi
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA.
- Division of Infectious Diseases, Department of Medicine, Stanford University, 279 Campus Drive, Beckman Center, Room B237, Stanford, CA, 94305, USA.
| | - Qingquan Chen
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
| | - Arne Echterhof
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jonathan L Koff
- Section of Pulmonary, Critical Care & Sleep Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Paul L Bollyky
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA, USA
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2
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Thanki AM, Osei EK, Whenham N, Salter MG, Bedford MR, Masey O’Neill HV, Clokie MRJ. Broad host range phages target global Clostridium perfringens bacterial strains and clear infection in five-strain model systems. Microbiol Spectr 2024; 12:e0378423. [PMID: 38511948 PMCID: PMC11064546 DOI: 10.1128/spectrum.03784-23] [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: 10/26/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Clostridium perfringens is a prevalent bacterial pathogen in poultry, and due to the spread of antimicrobial resistance, alternative treatments are needed to prevent and treat infection. Bacteriophages (phages), viruses that kill bacteria, offer a viable option and can be used therapeutically to treat C. perfringens infections. The aim of this study was to isolate phages against C. perfringens strains currently circulating on farms across the world and establish their virulence and development potential using host range screening, virulence assays, and larva infection studies. We isolated 32 phages of which 19 lysed 80%-92% of our global C. perfringens poultry strain collection (n = 97). The virulence of these individual phages and 32 different phage combinations was quantified in liquid culture at multiple doses. We then developed a multi-strain C. perfringens larva infection model, to mimic an effective poultry model used by the industry. We tested the efficacy of 16/32 phage cocktails in the larva model. From this, we identified that our phage cocktail consisting of phages CPLM2, CPLM15, and CPLS41 was the most effective at reducing C. perfringens colonization in infected larvae when administered before bacterial challenge. These data suggest that phages do have significant potential to prevent and treat C. perfringens infection in poultry. IMPORTANCE Clostridium perfringens causes foodborne illness worldwide, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection causes necrotic enteritis, and associated mortality rates can be up to 50%. However, treating infections is difficult as the bacterium is becoming antibiotic-resistant. Furthermore, the poultry industry is striving toward reduced antibiotic usage. Bacteriophages (phages) offer a promising alternative, and to progress this approach, robust suitable phages and laboratory models that mimic C. perfringens infections in poultry are required. In our study, we isolated phages targeting C. perfringens and found that many lyse C. perfringens strains isolated from chickens worldwide. Consistent with other published studies, in the model systems we assayed here, when some phages were combined as cocktails, the infection was cleared most effectively compared to individual phage use.
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Affiliation(s)
- Anisha M. Thanki
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Emmanuel K. Osei
- Department of Agriculture, Food and the Marine, Teagasc Food Research Centre, Moorepark, Ireland
- APC Microbiome Ireland, University College, Cork, Ireland
| | - Natasha Whenham
- AB Agri, Innovation Way, Peterborough Business Park, Peterborough, United Kingdom
| | - Michael G. Salter
- AB Agri, Innovation Way, Peterborough Business Park, Peterborough, United Kingdom
| | - Mike R. Bedford
- AB Vista, Woodstock Court, Marlborough Business Park, Marlborough, Wiltshire, United Kingdom
| | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
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3
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Vega-Heredia S, Giffard-Mena I, Reverter M. Bacterial and viral co-infections in aquaculture under climate warming: co-evolutionary implications, diagnosis, and treatment. DISEASES OF AQUATIC ORGANISMS 2024; 158:1-20. [PMID: 38602294 DOI: 10.3354/dao03778] [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: 04/12/2024]
Abstract
Climate change and the associated environmental temperature fluctuations are contributing to increases in the frequency and severity of disease outbreaks in both wild and farmed aquatic species. This has a significant impact on biodiversity and also puts global food production systems, such as aquaculture, at risk. Most infections are the result of complex interactions between multiple pathogens, and understanding these interactions and their co-evolutionary mechanisms is crucial for developing effective diagnosis and control strategies. In this review, we discuss current knowledge on bacteria-bacteria, virus-virus, and bacterial and viral co-infections in aquaculture as well as their co-evolution in the context of global warming. We also propose a framework and different novel methods (e.g. advanced molecular tools such as digital PCR and next-generation sequencing) to (1) precisely identify overlooked co-infections, (2) gain an understanding of the co-infection dynamics and mechanisms by knowing species interactions, and (3) facilitate the development multi-pathogen preventive measures such as polyvalent vaccines. As aquaculture disease outbreaks are forecasted to increase both due to the intensification of practices to meet the protein demand of the increasing global population and as a result of global warming, understanding and treating co-infections in aquatic species has important implications for global food security and the economy.
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Affiliation(s)
- Sarahí Vega-Heredia
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México, Egresada del Programa de Ecología Molecular y Biotecnología, carretera transpeninsular Ensenada-Tijuana No. 3917, C.P. 22860, México
| | - Ivone Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México
| | - Miriam Reverter
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Devon PL4 8AA, UK
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4
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Biosca EG, Delgado Santander R, Morán F, Figàs-Segura À, Vázquez R, Català-Senent JF, Álvarez B. First European Erwinia amylovora Lytic Bacteriophage Cocktails Effective in the Host: Characterization and Prospects for Fire Blight Biocontrol. BIOLOGY 2024; 13:176. [PMID: 38534446 DOI: 10.3390/biology13030176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a highly contagious and difficult-to-control disease due to its efficient dissemination and survival and the scarcity of effective control methods. Copper and antibiotics are the most used treatments but pose environmental and human health risks. Bacteriophages (phages) constitute an ecological, safe, and sustainable fire blight control alternative. The goal of this study was to search for specific E. amylovora phages from plant material, soil, and water samples in Mediterranean environments. A collection of phages able to specifically infect and lyse E. amylovora strains was generated from former fire blight-affected orchards in Eastern Spain. Following in vitro characterization, assays in immature fruit revealed that preventively applying some of the phages or their combinations delayed the onset of fire blight symptoms and reduced the disease's severity, suggesting their biocontrol potential in Spain and other countries. The morphological and molecular characterization of the selected E. amylovora phages classified them as members of the class Caudoviricetes (former Myoviridae family) and genus Kolesnikvirus. This study reveals Mediterranean settings as plausible sources of E. amylovora-specific bacteriophages and provides the first effective European phage cocktails in plant material for the development of sustainable fire blight management measures.
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Affiliation(s)
- Elena G Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Ricardo Delgado Santander
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
- Irrigated Agriculture Research and Extension Center, Department of Plant Pathology, Washington State University, Prosser, WA 99350, USA
| | - Félix Morán
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Rosa Vázquez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | | | - Belén Álvarez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
- Departamento de Investigación Aplicada y Extensión Agraria, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), 28805 Madrid, Spain
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5
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Merabishvili M, Pirnay JP, De Vos D. Guidelines to Compose an Ideal Bacteriophage Cocktail. Methods Mol Biol 2024; 2734:49-66. [PMID: 38066362 DOI: 10.1007/978-1-0716-3523-0_4] [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
Properly designed bacteriophage therapeutics are the cornerstone for a successful outcome of bacteriophage therapy. Here we present an overview of the different strategies and steps that can be taken to develop a bacteriophage cocktail that complies with relevant quality and safety requirements. It is based on empirical bacteriophage therapy knowledge from over a century of experience, more recently performed studies, and emerging technologies. We emphasize the selection of adequate bacteriophages and describe a modified Appelmans' method to improve the overall performance of therapeutic bacteriophages individually and collectively in the cocktail. We present two versions of the method, which differ from each other by the employed techniques to evaluate phage activity and synergy: photometric assessment of bacterial growth versus measurement of bacterial respiration via the Omnilog® system.
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Affiliation(s)
- 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
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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6
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Akturk E, Melo LD, Oliveira H, Crabbé A, Coenye T, Azeredo J. Combining phages and antibiotic to enhance antibiofilm efficacy against an in vitro dual species wound biofilm. Biofilm 2023; 6:100147. [PMID: 37662851 PMCID: PMC10474582 DOI: 10.1016/j.bioflm.2023.100147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Chronic wound management is extremely challenging because of the persistence of biofilm-forming pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus, which are the prevailing bacterial species that co-infect chronic wounds. Phage therapy has gained an increased interest to treat biofilm-associated infections, namely when combined with antibiotics. Here, we tested the effect of gentamicin as a co-adjuvant of phages in a dual species-biofilm wound model formed on artificial dermis. The biofilm-killing capacity of the tested treatments was significantly increased when phages were combined with gentamicin and applied multiple times as multiple dose (three doses, every 8 h). Our results suggest that gentamycin is an effective adjuvant of phage therapy particularly when applied simultaneously with phages and in three consecutive doses. The multiple and simultaneous dose treatment seems to be essential to avoid bacterial resistance development to each of the antimicrobial agents.
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Affiliation(s)
- Ergun Akturk
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS – Associate Laboratory, Braga, Guimarães, Portugal
| | - Luís D.R. Melo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS – Associate Laboratory, Braga, Guimarães, Portugal
- ESCMID Study Group for Biofilms (ESGB), Switzerland
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS – Associate Laboratory, Braga, Guimarães, Portugal
- ESCMID Study Group for Biofilms (ESGB), Switzerland
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Ghent, Belgium
- ESCMID Study Group for Biofilms (ESGB), Switzerland
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS – Associate Laboratory, Braga, Guimarães, Portugal
- ESCMID Study Group for Biofilms (ESGB), Switzerland
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7
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Halawa EM. Challenges of bacteriophages application in controlling bacterial plant diseases and how to overcome them. J Genet Eng Biotechnol 2023; 21:98. [PMID: 37815601 PMCID: PMC10564689 DOI: 10.1186/s43141-023-00549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Due to the emergence of antibiotic-resistant bacteria in agricultural sector, controlling bacterial plant diseases using antibiotics has become challenging. Researchers have turned to alternative methods, such as using bacteriophages as a biocide for plants instead of antibiotics, to control pathogenic bacterial plant diseases. However, the application of bacteriophages as a biocide in agriculture faces several challenges that may impede its success. In this review article, we discuss the various issues that could lead to the failure of its application. We also propose solutions to address each problem to increase awareness and familiarity before implementing the method to better ensure its success.
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Affiliation(s)
- Esraa M Halawa
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.
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8
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Jo SJ, Kwon J, Kim SG, Lee SJ. The Biotechnological Application of Bacteriophages: What to Do and Where to Go in the Middle of the Post-Antibiotic Era. Microorganisms 2023; 11:2311. [PMID: 37764155 PMCID: PMC10534921 DOI: 10.3390/microorganisms11092311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Amid the escalating challenges of antibiotic resistance, bacterial infections have emerged as a global threat. Bacteriophages (phages), viral entities capable of selectively infecting bacteria, are gaining momentum as promising alternatives to traditional antibiotics. Their distinctive attributes, including host specificity, inherent self-amplification, and potential synergy with antibiotics, render them compelling candidates. Phage engineering, a burgeoning discipline, involves the strategic modification of bacteriophages to enhance their therapeutic potential and broaden their applications. The integration of CRISPR-Cas systems facilitates precise genetic modifications, enabling phages to serve as carriers of functional genes/proteins, thereby enhancing diagnostics, drug delivery, and therapy. Phage engineering holds promise in transforming precision medicine, addressing antibiotic resistance, and advancing diverse applications. Emphasizing the profound therapeutic potential of phages, this review underscores their pivotal role in combatting bacterial diseases and highlights their significance in the post-antibiotic era.
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Affiliation(s)
- Su Jin Jo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan City 54596, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Seung-Jun Lee
- Department of Pharmaceutical Science and Engineering, Seowon University, 377-3 Musimseoro, Seowon-gu, Cheong-ju City 28674, Republic of Korea
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9
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Abedon ST. Automating Predictive Phage Therapy Pharmacology. Antibiotics (Basel) 2023; 12:1423. [PMID: 37760719 PMCID: PMC10525195 DOI: 10.3390/antibiotics12091423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses that infect as well as often kill bacteria are called bacteriophages, or phages. Because of their ability to act bactericidally, phages increasingly are being employed clinically as antibacterial agents, an infection-fighting strategy that has been in practice now for over one hundred years. As with antibacterial agents generally, the development as well as practice of this phage therapy can be aided via the application of various quantitative frameworks. Therefore, reviewed here are considerations of phage multiplicity of infection, bacterial likelihood of becoming adsorbed as a function of phage titers, bacterial susceptibility to phages also as a function of phage titers, and the use of Poisson distributions to predict phage impacts on bacteria. Considered in addition is the use of simulations that can take into account both phage and bacterial replication. These various approaches can be automated, i.e., by employing a number of online-available apps provided by the author, the use of which this review emphasizes. In short, the practice of phage therapy can be aided by various mathematical approaches whose implementation can be eased via online automation.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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10
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Jo SJ, Kim SG, Lee YM, Giri SS, Kang JW, Lee SB, Jung WJ, Hwang MH, Park J, Cheng C, Roh E, Park SC. Evaluation of the Antimicrobial Potential and Characterization of Novel T7-Like Erwinia Bacteriophages. BIOLOGY 2023; 12:biology12020180. [PMID: 36829459 PMCID: PMC9953017 DOI: 10.3390/biology12020180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
The recent outbreak of blight in pome fruit plants has been a major concern as there are two indistinguishable Erwinia species, Erwinia amylovora and E. pyrifoliae, which cause blight in South Korea. Although there is a strict management protocol consisting of antibiotic-based prevention, the area and the number of cases of outbreaks have increased. In this study, we isolated four bacteriophages, pEp_SNUABM_03, 04, 11, and 12, that infect both E. amylovora and E. pyrifoliae and evaluated their potential as antimicrobial agents for administration against Erwinia-originated blight in South Korea. Morphological analysis revealed that all phages had podovirus-like capsids. The phage cocktail showed a broad spectrum of infectivity, infecting 98.91% of E. amylovora and 100% of E. pyrifoliae strains. The antibacterial effect was observed after long-term cocktail treatment against E. amylovora, whereas it was observed for both short- and long-term treatments against E. pyrifoliae. Genomic analysis verified that the phages did not encode harmful genes such as antibiotic resistance or virulence genes. All phages were stable under general orchard conditions. Collectively, we provided basic data on the potential of phages as biocontrol agents that target both E. amylovora and E. pyrifoliae.
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Affiliation(s)
- Su Jin Jo
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Mae Hyun Hwang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehong Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Chi Cheng
- Laboratory of Aquatic Nutrition and Ecology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: ; Tel.: +82-2-880-1282; Fax: +82-2-873-1213
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11
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Shymialevich D, Wójcicki M, Wardaszka A, Świder O, Sokołowska B, Błażejak S. Application of Lytic Bacteriophages and Their Enzymes to Reduce Saprophytic Bacteria Isolated from Minimally Processed Plant-Based Food Products-In Vitro Studies. Viruses 2022; 15:9. [PMID: 36680050 PMCID: PMC9865725 DOI: 10.3390/v15010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of this study was to isolate phage enzymes and apply them in vitro for eradication of the dominant saprophytic bacteria isolated from minimally processed food. Four bacteriophages-two Enterobacter-specific and two Serratia-specific, which produce lytic enzymes-were used in this research. Two methods of phage enzyme isolation were tested, namely precipitation with acetone and ultracentrifugation. It was found that the number of virions could be increased almost 100 times due to the extension of the cultivation time (72 h). The amplification of phage particles and lytic proteins was dependent on the time of cultivation. Considering the influence of isolated enzymes on the growth kinetics of bacterial hosts, proteins isolated with acetone after 72-hour phage propagation exhibited the highest inhibitory effect. The reduction of bacteria count was dependent on the concentration of enzymes in the lysates. The obtained results indicate that phages and their lytic enzymes could be used in further research aiming at the improvement of microbiological quality and safety of minimally processed food products.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Artur Wardaszka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland
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12
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Ramadhan F, Alfiko Y, Purwantomo S, Mubarok AF, Budinarta W, Suwanto A, Budiarti S. A New Approach for Controlling Agrobacterium tumefaciens Post Transformation Using Lytic Bacteriophage. PLANTS (BASEL, SWITZERLAND) 2022; 11:3124. [PMID: 36432853 PMCID: PMC9698577 DOI: 10.3390/plants11223124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Overgrowth of Agrobacterium tumefaciens has frequently been found in Agrobacterium-mediated plant transformation. This overgrowth can reduce transformation efficiency and even lead to explant death. Therefore, this research investigates an alternative way to mitigate or eliminate Agrobacterium after transformation using a bacteriophage. To develop this alternative method, we conducted effectiveness studies of two lytic bacteriophages (ΦK2 and ΦK4) and performed an application test to control Agrobacterium growth after transformation. According to plaque morphological characterization and molecular analysis, the two bacteriophages used in this experiment were distinct. Moreover, some stability physicochemical and growth kinetics, such as adsorption time and susceptibility test, also showed that both bacteriophages differed. On the other hand, the optimum temperature and pH of both phages were the same at 28-30 °C and pH 7. Further investigation showed that both ΦK2 and ΦK4 were able to reduce the overgrowth of A. tumefaciens post transformation. Moreover, applying the cocktail (mixture of ΦK2 and ΦK4) with antibiotic application eradicated A. tumefaciens (0% overgrowth percentage). This result indicates that the application of bacteriophage could be used as an alternative way to eradicate the overgrowth of A. tumefaciens subsequent to transformation.
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Affiliation(s)
- Fiqih Ramadhan
- Graduate School of Biotechnology, IPB University, Bogor 16680, Indonesia
| | - Yuzer Alfiko
- Biotech Laboratory, Wilmar Benih Indonesia, Bekasi 17530, Indonesia
| | - Sigit Purwantomo
- Biotech Laboratory, Wilmar Benih Indonesia, Bekasi 17530, Indonesia
| | | | - Widyah Budinarta
- Biotech Laboratory, Wilmar Benih Indonesia, Bekasi 17530, Indonesia
| | - Antonius Suwanto
- Graduate School of Biotechnology, IPB University, Bogor 16680, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Sri Budiarti
- Graduate School of Biotechnology, IPB University, Bogor 16680, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
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13
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Kim SG, Lee SB, Jo SJ, Cho K, Park JK, Kwon J, Giri SS, Kim SW, Kang JW, Jung WJ, Lee YM, Roh E, Park SC. Phage Cocktail in Combination with Kasugamycin as a Potential Treatment for Fire Blight Caused by Erwinia amylovora. Antibiotics (Basel) 2022; 11:1566. [PMID: 36358221 PMCID: PMC9686651 DOI: 10.3390/antibiotics11111566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
Recently, there has been an increasing number of blight disease reports associated with Erwinia amylovora and Erwinia pyrifoliae in South Korea. Current management protocols that have been conducted with antibiotics have faced resistance problems and the outbreak has not decreased. Because of this concern, the present study aimed to provide an alternative method to control the invasive fire blight outbreak in the nation using bacteriophages (phages) in combination with an antibiotic agent (kasugamycin). Among 54 phage isolates, we selected five phages, pEa_SNUABM_27, 31, 32, 47, and 48, based on their bacteriolytic efficacy. Although only phage pEa_SNUABM_27 showed host specificity for E. amylovora, all five phages presented complementary lytic potential that improved the host infectivity coverage of each phage All the phages in the cocktail solution could lyse phage-resistant strains. These strains had a decreased tolerance to the antibiotic kasugamycin, and a synergistic effect of phages and antibiotics was demonstrated both in vitro and on immature wound-infected apples. It is noteworthy that the antibacterial effect of the phage cocktail or phage cocktail-sub-minimal inhibitory concentration (MIC) of kasugamycin was significantly higher than the kasugamycin at the MIC. The selected phages were experimentally stable under environmental factors such as thermal or pH stress. Genomic analysis revealed these are novel Erwinia-infecting phages, and did not encode antibiotic-, virulence-, or lysogenic phage-related genes. In conclusion, we suggest the potential of the phage cocktail and kasugamycin combination as an effective strategy that would minimize the use of antibiotics, which are being excessively used in order to control fire blight pathogens.
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Affiliation(s)
- Sang-Guen Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sung-Bin Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Su-Jin Jo
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jung-Kum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sang-Wha Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jeong-Woo Kang
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Won-Joon Jung
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Young-Min Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Se-Chang Park
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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14
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Igler C. Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack. Virus Evol 2022; 8:veac086. [PMID: 36225237 PMCID: PMC9547521 DOI: 10.1093/ve/veac086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/11/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, the viruses of bacteria, have been studied for over a century. They were not only instrumental in laying the foundations of molecular biology, but they are also likely to play crucial roles in shaping our biosphere and may offer a solution to the control of drug-resistant bacterial infections. However, it remains challenging to predict the conditions for bacterial eradication by phage predation, sometimes even under well-defined laboratory conditions, and, most curiously, if the majority of surviving cells are genetically phage-susceptible. Here, I propose that even clonal phage and bacterial populations are generally in a state of continuous 'phenotypic flux', which is caused by transient and nongenetic variation in phage and bacterial physiology. Phenotypic flux can shape phage infection dynamics by reducing the force of infection to an extent that allows for coexistence between phages and susceptible bacteria. Understanding the mechanisms and impact of phenotypic flux may be key to providing a complete picture of phage-bacteria coexistence. I review the empirical evidence for phenotypic variation in phage and bacterial physiology together with the ways they have been modeled and discuss the potential implications of phenotypic flux for ecological and evolutionary dynamics between phages and bacteria, as well as for phage therapy.
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Affiliation(s)
- Claudia Igler
- Department of Environmental Systems Science, ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zurich 8092, Switzerland
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15
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Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 2022; 377:eabm4096. [PMID: 35951700 PMCID: PMC10028730 DOI: 10.1126/science.abm4096] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
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Affiliation(s)
- Linyi Alex Gao
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
- Correspondence: (F.Z.) or (L.A.G.)
| | - Max E. Wilkinson
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (F.Z.) or (L.A.G.)
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16
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Segredo-Otero E, Sanjuán R. Cooperative Virus-Virus Interactions: An Evolutionary Perspective. BIODESIGN RESEARCH 2022; 2022:9819272. [PMID: 37850129 PMCID: PMC10521650 DOI: 10.34133/2022/9819272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/21/2022] [Indexed: 10/19/2023] Open
Abstract
Despite extensive evidence of virus-virus interactions, not much is known about their biological significance. Importantly, virus-virus interactions could have evolved as a form of cooperation or simply be a by-product of other processes. Here, we review and discuss different types of virus-virus interactions from the point of view of social evolution, which provides a well-established framework for interpreting the fitness costs and benefits of such traits. We also classify interactions according to their mechanisms of action and speculate on their evolutionary implications. As in any other biological system, the evolutionary stability of viral cooperation critically requires cheaters to be excluded from cooperative interactions. We discuss how cheater viruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.
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Affiliation(s)
- Ernesto Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
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17
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In Vitro Techniques and Measurements of Phage Characteristics That Are Important for Phage Therapy Success. Viruses 2022; 14:v14071490. [PMID: 35891470 PMCID: PMC9323186 DOI: 10.3390/v14071490] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023] Open
Abstract
Validated methods for phage selection, host range expansion, and lytic activity determination are indispensable for maximizing phage therapy outcomes. In this review, we describe some relevant methods, highlighting their advantages and disadvantages, and categorize them as preliminary or confirmatory methods where appropriate. Experimental conditions, such as the composition and consistency of culture media, have an impact on bacterial growth and, consequently, phage propagation and the selection of phage-resistant mutants. The phages require different experimental conditions to be tested to fully reveal their characteristics and phage therapy potential in view of their future use in therapy. Phage lytic activity or virulence should be considered as a result of the phage, its host, and intracellular/environmental factors, including the ability of a phage to recognize receptors on the bacterial cell surface. In vitro quantitative and qualitative measurements of phage characteristics, further validated by in vivo experiments, could be incorporated into one system or mathematical model/formula, which could predict a potential successful outcome of clinical applications.
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18
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Wu S, Wu B, Liu Y, Deng S, Lei L, Zhang H. Mini Review Therapeutic Strategies Targeting for Biofilm and Bone Infections. Front Microbiol 2022; 13:936285. [PMID: 35774451 PMCID: PMC9238355 DOI: 10.3389/fmicb.2022.936285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 12/21/2022] Open
Abstract
Bone infection results in a complex inflammatory response and bone destruction. A broad spectrum of bacterial species has been involved for jaw osteomyelitis, hematogenous osteomyelitis, vertebral osteomyelitis or diabetes mellitus, such as Staphylococcus aureus (S. aureus), coagulase-negative Staphylococcus species, and aerobic gram-negative bacilli. S. aureus is the major pathogenic bacterium for osteomyelitis, which results in a complex inflammatory response and bone destruction. Although various antibiotics have been applied for bone infection, the emergence of drug resistance and biofilm formation significantly decrease the effectiveness of those agents. In combination with gram-positive aerobes, gram-negative aerobes and anaerobes functionally equivalent pathogroups interact synergistically, developing as pathogenic biofilms and causing recurrent infections. The adhesion of biofilms to bone promotes bone destruction and protects bacteria from antimicrobial agent stress and host immune system infiltration. Moreover, bone is characterized by low permeability and reduced blood flow, further hindering the therapeutic effect for bone infections. To minimize systemic toxicity and enhance antibacterial effectiveness, therapeutic strategies targeting on biofilm and bone infection can serve as a promising modality. Herein, we focus on biofilm and bone infection eradication with targeting therapeutic strategies. We summarize recent targeting moieties on biofilm and bone infection with peptide-, nucleic acid-, bacteriophage-, CaP- and turnover homeostasis-based strategies. The antibacterial and antibiofilm mechanisms of those therapeutic strategies include increasing antibacterial agents’ accumulation by bone specific affinity, specific recognition of phage-bacteria, inhibition biofilm formation in transcription level. As chronic inflammation induced by infection can trigger osteoclast activation and inhibit osteoblast functioning, we additionally expand the potential applications of turnover homeostasis-based therapeutic strategies on biofilm or infection related immunity homeostasis for host-bacteria. Based on this review, we expect to provide useful insights of targeting therapeutic efficacy for biofilm and bone infection eradication.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Binjie Wu
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Shu Deng
- Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, United States
| | - Lei Lei
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Lei Lei,
| | - Hui Zhang
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
- Hui Zhang,
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19
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
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20
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Sanchez BC, Heckmann ER, Green SI, Clark JR, Kaplan HB, Ramig RF, Muldrew KL, Hines-Munson C, Skelton F, Trautner BW, Maresso AW. Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. Front Microbiol 2022; 13:796132. [PMID: 35620093 PMCID: PMC9127763 DOI: 10.3389/fmicb.2022.796132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
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Affiliation(s)
- Belkys C. Sanchez
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Emmaline R. Heckmann
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth Houston, Houston, TX, United States
| | - Robert F. Ramig
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Kenneth L. Muldrew
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Pathology and Laboratory Medicine, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Casey Hines-Munson
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States,Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Anthony W. Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Anthony W. Maresso,
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21
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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22
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A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)—viruses targeting bacteria—offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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23
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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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24
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Koonjan S, Cardoso Palacios C, Nilsson AS. Population Dynamics of a Two Phages–One Host Infection System Using Escherichia coli Strain ECOR57 and Phages vB_EcoP_SU10 and vB_EcoD_SU57. Pharmaceuticals (Basel) 2022; 15:ph15030268. [PMID: 35337066 PMCID: PMC8953519 DOI: 10.3390/ph15030268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we looked at the population dynamics of a two phages-one host system using phages vB_EcoP_SU10 (SU10) and vB_EcoD_SU57 (SU57) and the bacteria Escherichia coli, strain ECOR57. Phage-specific growth curves were observed where infections by SU10 resulted in a moderate production of phages and infections by SU57 resulted in a fast and extensive production of phage progeny. Sequentially adding SU10 followed by SU57 did not produce a significant change in growth rates, whereas adding SU57 followed by SU10 resulted in a decrease in SU10 titer The efficiency of the plating assays showed that ECOR57 exhibited a resistance spectrum after infection by both the single and combined phages. Phage-resistant bacteria exhibited four different morphotypes (i.e., normal, slimy, edgy, and pointy). The normal and edgy morphotypes had a high frequency of developing resistance. Bacterial growth and biofilm assays indicated that the edgy and pointy morphotypes reached a stationary phase faster and produced more biofilm compared to the wild type. These findings suggest that the dynamic structure of phage–bacteria communities dictate resistance evolution and development. Understanding when and how resistances arise and phage(s)–hosts interactions could aid in the design of phage therapy treatments.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Correspondence: (S.K.); (A.S.N.)
| | - Carlos Cardoso Palacios
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-739 93 Riddarhyttan, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Correspondence: (S.K.); (A.S.N.)
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25
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Singh A, Padmesh S, Dwivedi M, Kostova I. How Good are Bacteriophages as an Alternative Therapy to Mitigate Biofilms of Nosocomial Infections. Infect Drug Resist 2022; 15:503-532. [PMID: 35210792 PMCID: PMC8860455 DOI: 10.2147/idr.s348700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteria survive on any surface through the generation of biofilms that provide a protective environment to grow as well as making them drug resistant. Extracellular polymeric matrix is a crucial component in biofilm formation. The presence of biofilms consisting of common opportunistic and nosocomial, drug-resistant pathogens has been reported on medical devices like catheters and prosthetics, leading to many complications. Several approaches are under investigation to combat drug-resistant bacteria. Deployment of bacteriophages is one of the promising approaches to invade biofilm that may expose bacteria to the conditions adverse for their growth. Penetration into these biofilms and their destruction by bacteriophages is brought about due to their small size and ability of their progeny to diffuse through the bacterial cell wall. The other mechanisms employed by phages to infect biofilms may include their relocation through water channels to embedded host cells, replication at local sites followed by infection to the neighboring cells and production of depolymerizing enzymes to decompose viscous biofilm matrix, etc. Various research groups are investigating intricacies involved in phage therapy to mitigate the bacterial infection and biofilm formation. Thus, bacteriophages represent a good control over different biofilms and further understanding of phage-biofilm interaction at molecular level may overcome the clinical challenges in phage therapy. The present review summarizes the comprehensive details on dynamic interaction of phages with bacterial biofilms and the role of phage-derived enzymes - endolysin and depolymerases in extenuating biofilms of clinical and medical concern. The methodology employed was an extensive literature search, using several keywords in important scientific databases, such as Scopus, Web of Science, PubMed, ScienceDirect, etc. The keywords were also used with Boolean operator "And". More than 250 relevant and recent articles were selected and reviewed to discuss the evidence-based data on the application of phage therapy with recent updates, and related potential challenges.
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Affiliation(s)
- Aditi Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Sudhakar Padmesh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Irena Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University, Sofia, 1000, Bulgaria
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26
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Molina F, Menor-Flores M, Fernández L, Vega-Rodríguez MA, García P. Systematic analysis of putative phage-phage interactions on minimum-sized phage cocktails. Sci Rep 2022; 12:2458. [PMID: 35165352 PMCID: PMC8844382 DOI: 10.1038/s41598-022-06422-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
The application of bacteriophages as antibacterial agents has many benefits in the “post-antibiotic age”. To increase the number of successfully targeted bacterial strains, phage cocktails, instead of a single phage, are commonly formulated. Nevertheless, there is currently no consensus pipeline for phage cocktail development. Thus, although large cocktails increase the spectrum of activity, they could produce side effects such as the mobilization of virulence or antibiotic resistance genes. On the other hand, coinfection (simultaneous infection of one host cell by several phages) might reduce the potential for bacteria to evolve phage resistance, but some antagonistic interactions amongst phages might be detrimental for the outcome of phage cocktail application. With this in mind, we introduce here a new method, which considers the host range and each individual phage-host interaction, to design the phage mixtures that best suppress the target bacteria while minimizing the number of phages to restrict manufacturing costs. Additionally, putative phage-phage interactions in cocktails and phage-bacteria networks are compared as the understanding of the complex interactions amongst bacteriophages could be critical in the development of realistic phage therapy models in the future.
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Campylobacter Bacteriophage Cocktail Design Based on an Advanced Selection Scheme. Antibiotics (Basel) 2022; 11:antibiotics11020228. [PMID: 35203830 PMCID: PMC8868561 DOI: 10.3390/antibiotics11020228] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Campylobacteriosis is a worldwide-occurring disease and has been the most commonly reported zoonotic gastrointestinal infection in the European Union in recent years. The development of successful phage-based intervention strategies will require a better understanding of phage–bacteria interactions to facilitate advances in phage cocktail design. Therefore, this study aimed to investigate the effects of newly isolated group II and group III phages and their combinations on current Campylobacter field strains. A continuous workflow for host range and efficiency of plating (EOP) value determination was combined with a qPCR-based phage group identification and a liquid-based planktonic killing assay (PKA). An advanced analysis scheme allowed us to evaluate phage cocktails by their efficacy in inhibiting bacterial population growth and the resulting phage concentrations. The results of this study indicate that data obtained from PKAs are more accurate than host range data based on plaque formation (EOP). Planktonic killing assays with Campylobacter appear to be a useful tool for a straightforward cocktail design. Results show that a group II phage vB_CcM-LmqsCP218-2c2 and group III phage vB_CjM-LmqsCP1-1 mixture would be most promising for practical applications against Campylobacter coli and Campylobacter jejuni.
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28
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Zuppi M, Hendrickson HL, O’Sullivan JM, Vatanen T. Phages in the Gut Ecosystem. Front Cell Infect Microbiol 2022; 11:822562. [PMID: 35059329 PMCID: PMC8764184 DOI: 10.3389/fcimb.2021.822562] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 12/23/2022] Open
Abstract
Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.
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Affiliation(s)
- Michele Zuppi
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Heather L. Hendrickson
- The School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Justin M. O’Sullivan
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Tommi Vatanen
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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29
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Rahimi-Midani A, Lee SW, Choi TJ. Potential Solutions Using Bacteriophages against Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121496. [PMID: 34943708 PMCID: PMC8698741 DOI: 10.3390/antibiotics10121496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are viruses that specifically infect a bacterial host. They play a great role in the modern biotechnology and antibiotic-resistant microbe era. Since the discovery of phages, their application as a control agent has faced challenges that made antibiotics a better fit for combating pathogenic bacteria. Recently, with the novel sequencing technologies providing new insight into the nature of bacteriophages, their application has a second chance to be used. However, novel challenges need to be addressed to provide proper strategies for their practical application. This review focuses on addressing these challenges by initially introducing the nature of bacteriophages and describing the phage-host-dependent strategies for phage application. We also describe the effect of the long-term application of phages in natural environments and other bacterial communities. Overall, this review gathered crucial information for the future application of phages. We predict the use of phages will not be the only control strategy against pathogenic bacteria. Therefore, more studies must be done for low-risk control methods against antimicrobial-resistant bacteria.
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Affiliation(s)
- Aryan Rahimi-Midani
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
- Correspondence:
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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31
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Martino G, Holtappels D, Vallino M, Chiapello M, Turina M, Lavigne R, Wagemans J, Ciuffo M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses 2021; 13:2083. [PMID: 34696512 PMCID: PMC8537276 DOI: 10.3390/v13102083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial kiwifruit vine disease (Pseudomonas syringae pv. actinidiae, Psa) and halo blight of bean (P. syringae pv. phaseolicola, Pph) are routinely treated with copper, leading to environmental pollution and bacterial copper resistance. An alternative sustainable control method could be based on bacteriophages, as phage biocontrol offers high specificity and does not result in the spread of toxic residues into the environment or the food chain. In this research, specific phages suitable for phage-based biocontrol strategies effective against Psa and Pph were isolated and characterized. In total, sixteen lytic Pph phage isolates and seven lytic Psa phage isolates were isolated from soil in Piedmont and Veneto in northern Italy. Genome characterization of fifteen selected phages revealed that the isolated Pph phages were highly similar and could be considered as isolates of a novel species, whereas the isolated Psa phages grouped into four distinct clades, two of which represent putative novel species. No lysogeny-, virulence- or toxin-related genes were found in four phages, making them suitable for potential biocontrol purposes. A partial biological characterization including a host range analysis was performed on a representative subset of these isolates. This analysis was a prerequisite to assess their efficacy in greenhouse and in field trials, using different delivery strategies.
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Affiliation(s)
- Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
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32
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Abedon ST, Danis-Wlodarczyk KM, Wozniak DJ. Phage Cocktail Development for Bacteriophage Therapy: Toward Improving Spectrum of Activity Breadth and Depth. Pharmaceuticals (Basel) 2021; 14:1019. [PMID: 34681243 PMCID: PMC8541335 DOI: 10.3390/ph14101019] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Phage therapy is the use of bacterial viruses as antibacterial agents. A primary consideration for commercial development of phages for phage therapy is the number of different bacterial strains that are successfully targeted, as this defines the breadth of a phage cocktail's spectrum of activity. Alternatively, phage cocktails may be used to reduce the potential for bacteria to evolve phage resistance. This, as we consider here, is in part a function of a cocktail's 'depth' of activity. Improved cocktail depth is achieved through inclusion of at least two phages able to infect a single bacterial strain, especially two phages against which bacterial mutation to cross resistance is relatively rare. Here, we consider the breadth of activity of phage cocktails while taking both depth of activity and bacterial mutation to cross resistance into account. This is done by building on familiar algorithms normally used for determination solely of phage cocktail breadth of activity. We show in particular how phage cocktails for phage therapy may be rationally designed toward enhancing the number of bacteria impacted while also reducing the potential for a subset of those bacteria to evolve phage resistance, all as based on previously determined phage properties.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Daniel J. Wozniak
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
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33
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Ngiam L, Schembri MA, Weynberg K, Guo J. Bacteriophage isolated from non-target bacteria demonstrates broad host range infectivity against multidrug-resistant bacteria. Environ Microbiol 2021; 23:5569-5586. [PMID: 34390602 DOI: 10.1111/1462-2920.15714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance represents a global health challenge. The emergence of multidrug-resistant (MDR) bacteria such as uropathogenic Escherichia coli (UPEC) has attracted significant attention due to increased MDR properties, even against the last line of antibiotics. Bacteriophage, or simply phage, represents an alternative treatment to antibiotics. However, phage applications still face some challenges, such as host range specificity and development of phage resistant mutants. In this study, using both UPEC and non-UPEC hosts, five different phages were isolated from wastewater. We found that the inclusion of commensal Escherichia coli as target hosts during screening improved the capacity to select phage with desirable characteristics for phage therapy. Whole-genome sequencing revealed that four out of five phages adopt strictly lytic lifestyles and are taxonomically related to different phage families belonging to the Myoviridae and Podoviridae. In comparison to single phage treatment, the application of phage cocktails targeting different cell surface receptors significantly enhanced the suppression of UPEC hosts. The emergence of phage-resistant mutants after single phage treatment was attributed to mutational changes in outer membrane protein components, suggesting the potential receptors recognized by these phages. The findings highlight the use of commensal E. coli as target hosts to isolate broad host range phage with infectivity against MDR bacteria.
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Affiliation(s)
- Lyman Ngiam
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld, Australia
| | - Karen Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
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34
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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35
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Onsea J, Uyttebroek S, Chen B, Wagemans J, Lood C, Van Gerven L, Spriet I, Devolder D, Debaveye Y, Depypere M, Dupont L, De Munter P, Peetermans WE, van Noort V, Merabishvili M, Pirnay JP, Lavigne R, Metsemakers WJ. Bacteriophage Therapy for Difficult-to-Treat Infections: The Implementation of a Multidisciplinary Phage Task Force ( The PHAGEFORCE Study Protocol). Viruses 2021; 13:1543. [PMID: 34452408 PMCID: PMC8402896 DOI: 10.3390/v13081543] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/22/2022] Open
Abstract
In times where only a few novel antibiotics are to be expected, antimicrobial resistance remains an expanding global health threat. In case of chronic infections caused by therapy-resistant pathogens, physicians have limited therapeutic options, which are often associated with detrimental consequences for the patient. This has resulted in a renewed interest in alternative strategies, such as bacteriophage (phage) therapy. However, there are still important hurdles that currently impede the more widespread implementation of phage therapy in clinical practice. First, the limited number of good-quality case series and clinical trials have failed to show the optimal application protocol in terms of route of administration, frequency of administration, treatment duration and phage titer. Second, there is limited information on the systemic effects of phage therapy. Finally, in the past, phage therapy has been applied intuitively in terms of the selection of phages and their combination as parts of phage cocktails. This has led to an enormous heterogeneity in previously published studies, resulting in a lack of reliable safety and efficacy data for phage therapy. We hereby present a study protocol that addresses these scientific hurdles using a multidisciplinary approach, bringing together the experience of clinical, pharmaceutical and molecular microbiology experts.
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Affiliation(s)
- Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium; (B.C.); (W.-J.M.)
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Saartje Uyttebroek
- Department of Otorhinolaryngology, University Hospitals Leuven, 3000 Leuven, Belgium; (S.U.); (L.V.G.)
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, 3000 Leuven, Belgium
| | - Baixing Chen
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium; (B.C.); (W.-J.M.)
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, 3000 Leuven, Belgium; (J.W.); (C.L.); (R.L.)
| | - Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, 3000 Leuven, Belgium; (J.W.); (C.L.); (R.L.)
- Center of Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
| | - Laura Van Gerven
- Department of Otorhinolaryngology, University Hospitals Leuven, 3000 Leuven, Belgium; (S.U.); (L.V.G.)
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, 3000 Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, 3000 Leuven, Belgium
| | - Isabel Spriet
- Pharmacy Department, University Hospitals Leuven, 3000 Leuven, Belgium; (I.S.); (D.D.)
- Department of Pharmaceutical and Pharmacological Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, 3000 Leuven, Belgium
| | - David Devolder
- Pharmacy Department, University Hospitals Leuven, 3000 Leuven, Belgium; (I.S.); (D.D.)
- Department of Pharmaceutical and Pharmacological Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Yves Debaveye
- Department of Intensive Care Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Melissa Depypere
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Lieven Dupont
- Department of Pneumology, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Paul De Munter
- Department of Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (P.D.M.); (W.E.P.)
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Willy E. Peetermans
- Department of Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (P.D.M.); (W.E.P.)
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Vera van Noort
- Center of Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (M.M.); (J.-P.P.)
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (M.M.); (J.-P.P.)
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, 3000 Leuven, Belgium; (J.W.); (C.L.); (R.L.)
| | - Willem-Jan Metsemakers
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium; (B.C.); (W.-J.M.)
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
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36
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Improving Phage-Biofilm In Vitro Experimentation. Viruses 2021; 13:v13061175. [PMID: 34205417 PMCID: PMC8234374 DOI: 10.3390/v13061175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting.
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37
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Fong K, Wong CW, Wang S, Delaquis P. How Broad Is Enough: The Host Range of Bacteriophages and Its Impact on the Agri-Food Sector. PHAGE 2021; 2:83-91. [PMID: 36148040 PMCID: PMC9041489 DOI: 10.1089/phage.2020.0036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Novel bacteriophages (phages) possessing a broad host range are consistently and routinely reported, yet there is presently no consensus on the definition of “broad host range.” As phages are increasingly being used in the development of methods for the detection and biocontrol of human pathogens, it is important to address the limitations associated with the host range. For instance, unanticipated host range breadth may result in the detection of nonpathogenic targets, thereby increasing the false-positive rate. Moreover, a broad host range is generally favored in biocontrol applications despite the risk of undesirable ancillary effects against nontarget species. Here, we discuss the research progress, applications, and implications of broad host range phages with a focus on tailed broad host range phages infecting human pathogens of concern in the Agri-Food sector.
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Affiliation(s)
- Karen Fong
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, Canada
- Address correspondence to: Karen Fong, PhD, Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Postal Box 5000, Summerland BC V0H1Z0, Canada
| | - Catherine W.Y. Wong
- Food, Nutrition and Health, University of British Columbia, Vancouver, Canada
| | - Siyun Wang
- Food, Nutrition and Health, University of British Columbia, Vancouver, Canada
| | - Pascal Delaquis
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, Canada
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Kauppinen A, Siponen S, Pitkänen T, Holmfeldt K, Pursiainen A, Torvinen E, Miettinen IT. Phage Biocontrol of Pseudomonas aeruginosa in Water. Viruses 2021; 13:928. [PMID: 34067885 PMCID: PMC8156286 DOI: 10.3390/v13050928] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50-55 min) and burst size (124-134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log10 reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log10) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments.
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Affiliation(s)
- Ari Kauppinen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, FI-70701 Kuopio, Finland; (S.S.); (T.P.); (A.P.); (I.T.M.)
| | - Sallamaari Siponen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, FI-70701 Kuopio, Finland; (S.S.); (T.P.); (A.P.); (I.T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland;
| | - Tarja Pitkänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, FI-70701 Kuopio, Finland; (S.S.); (T.P.); (A.P.); (I.T.M.)
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Sciences, Linnaeus University, SE-39231 Kalmar, Sweden;
| | - Anna Pursiainen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, FI-70701 Kuopio, Finland; (S.S.); (T.P.); (A.P.); (I.T.M.)
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland;
| | - Ilkka T. Miettinen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, FI-70701 Kuopio, Finland; (S.S.); (T.P.); (A.P.); (I.T.M.)
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Abraha HB, Kim K, Sbhatu DB. Bacteriophages for detection and control of foodborne bacterial pathogens—The case of
Bacillus cereus
and their phages. J Food Saf 2021. [DOI: 10.1111/jfs.12906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haftom Baraki Abraha
- Department of Food Science and Technology Jeonbuk National University Jeonju Republic of Korea
| | - Kwang‐Pyo Kim
- Department of Food Science and Technology Jeonbuk National University Jeonju Republic of Korea
- Department of Agricultural Convergence Technology Collage of Agriculture and Life Sciences, Jeonbuk National University Jeonju Republic of Korea
| | - Desta Berhe Sbhatu
- Department of Biological and Chemical Engineering Mekelle Institute of Technology, Mekelle University Mekelle Ethiopia
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40
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Haines MEK, Hodges FE, Nale JY, Mahony J, van Sinderen D, Kaczorowska J, Alrashid B, Akter M, Brown N, Sauvageau D, Sicheritz-Pontén T, Thanki AM, Millard AD, Galyov EE, Clokie MRJ. Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria. Front Microbiol 2021; 12:613529. [PMID: 33868187 PMCID: PMC8044893 DOI: 10.3389/fmicb.2021.613529] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/23/2021] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as "critical" for research. Bacteriophages (phages), as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no "gold standard" for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in United Kingdom hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay (PKA) and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%), for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the PKA data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that PKAs are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows "phage synergy" to inform cocktail design.
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Affiliation(s)
- Melissa E. K. Haines
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Francesca E. Hodges
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Janet Y. Nale
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Joanna Kaczorowska
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mahmuda Akter
- International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh
| | - Nathan Brown
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Anisha M. Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Edouard E. Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Bagińska N, Cieślik M, Górski A, Jończyk-Matysiak E. The Role of Antibiotic Resistant A. baumannii in the Pathogenesis of Urinary Tract Infection and the Potential of Its Treatment with the Use of Bacteriophage Therapy. Antibiotics (Basel) 2021; 10:281. [PMID: 33803438 PMCID: PMC8001842 DOI: 10.3390/antibiotics10030281] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/20/2022] Open
Abstract
Acinetobacter baumannii are bacteria that belong to the critical priority group due to their carbapenems and third generation cephalosporins resistance, which are last-chance antibiotics. The growing multi-drug resistance and the ability of these bacteria to form biofilms makes it difficult to treat infections caused by this species, which often affects people with immunodeficiency or intensive care unit patients. In addition, most of the infections are associated with catheterization of patients. These bacteria are causative agents, inter alia, of urinary tract infections (UTI) which can cause serious medical and social problems, because of treatment difficulties as well as the possibility of recurrence and thus severely decrease patients' quality of life. Therefore, a promising alternative to standard antibiotic therapy can be bacteriophage therapy, which will generate lower costs and will be safer for the treated patients and has real potential to be much more effective. The aim of the review is to outline the important role of drug-resistant A. baumannii in the pathogenesis of UTI and highlight the potential for fighting these infections with bacteriophage therapy. Further studies on the use of bacteriophages in the treatment of UTIs in animal models may lead to the use of bacteriophage therapy in human urinary tract infections caused by A. baumannii in the future.
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Affiliation(s)
- Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (N.B.); (M.C.); (A.G.)
| | - Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (N.B.); (M.C.); (A.G.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (N.B.); (M.C.); (A.G.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (N.B.); (M.C.); (A.G.)
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42
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Pires DP, Costa AR, Pinto G, Meneses L, Azeredo J. Current challenges and future opportunities of phage therapy. FEMS Microbiol Rev 2021; 44:684-700. [PMID: 32472938 DOI: 10.1093/femsre/fuaa017] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance is a major public health challenge worldwide, whose implications for global health might be devastating if novel antibacterial strategies are not quickly developed. As natural predators of bacteria, (bacterio)phages may play an essential role in escaping such a dreadful future. The rising problem of antibiotic resistance has revived the interest in phage therapy and important developments have been achieved over the last years. But where do we stand today and what can we expect from phage therapy in the future? This is the question we set to answer in this review. Here, we scour the outcomes of human phage therapy clinical trials and case reports, and address the major barriers that stand in the way of using phages in clinical settings. We particularly address the potential of phage resistance to hinder phage therapy and discuss future avenues to explore the full capacity of phage therapy.
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Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luciana Meneses
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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43
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Niu YD, Liu H, Du H, Meng R, Sayed Mahmoud E, Wang G, McAllister TA, Stanford K. Efficacy of Individual Bacteriophages Does Not Predict Efficacy of Bacteriophage Cocktails for Control of Escherichia coli O157. Front Microbiol 2021; 12:616712. [PMID: 33717006 PMCID: PMC7943454 DOI: 10.3389/fmicb.2021.616712] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/18/2021] [Indexed: 01/21/2023] Open
Abstract
Effectiveness of bacteriophages AKFV33 (Tequintavirus, T5) and AHP24 (Rogunavirus, T1), wV7 (Tequatrovirus, T4), and AHP24S (Vequintavirus, rV5), as well as 11 cocktails of combinations of the four phages, were evaluated in vitro for biocontrol of six common phage types of Escherichia coli O157 (human and bovine origins) at different multiplicities of infection (MOIs; 0.01–1,000), temperatures (37 or 22°C), and exposure times (10–22 h). Phage efficacy against O157 was highest at MOI 1,000 (P < 0.001) and after 14-18 h of exposure at 22°C (P < 0.001). The activity of individual phages against O157 did not predict the activity of a cocktail of these phages even at the same temperature and MOI. Combinations of phages were neutral (no better or worse than the most effective constituent phages acting alone), displayed facilitation (greater efficacy than the most effective constituent phages acting alone), or antagonistic (lower efficacy than the most effective constituent phages acting alone). Across MOIs, temperatures, exposure time, and O157 strains, a cocktail of T1, T4, and rV5 was most effective (P < 0.05) against O157, although T1 and rV5 were less effective (P < 0.001) than other individual phages. T5 was the most effective individual phages (P < 0.05), but was antagonistic to other phages, particularly rV5 and T4 + rV5. Interactions among phages were influenced by phage genera and phage combination, O157 strains, MOIs, incubation temperatures, and times. Based on this study, future development of phage cocktails should, as a minimum, include confirmation of a lack of antagonism among constituent phages and preferably confirmation of facilitation or synergistic effects.
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Affiliation(s)
- Yan D Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hui Liu
- Hohhot Bureau of Ecology and Environment, Hohhot, China.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Hechao Du
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.,College of Animal Science and Technology, Jinling Institute of Technology, Nanjing, China
| | - Ruiqiang Meng
- Inner Mongolia C. P. Livestock Husbandry Co., Ltd., Hohhot, China
| | - El Sayed Mahmoud
- School of Applied Computing, Faculty of Applied Science and Technology, Sheridan College, Oakville, ON, Canada
| | - Guihua Wang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kim Stanford
- Department of Biological Science, University of Lethbridge, Lethbridge, AB, Canada
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Abstract
Antibiotic resistance represents a threat to human health. It has been suggested that by 2050, antibiotic-resistant infections could cause ten million deaths each year. In orthopaedics, many patients undergoing surgery suffer from complications resulting from implant-associated infection. In these circumstances secondary surgery is usually required and chronic and/or relapsing disease may ensue. The development of effective treatments for antibiotic-resistant infections is needed. Recent evidence shows that bacteriophage (phages; viruses that infect bacteria) therapy may represent a viable and successful solution. In this review, a brief description of bone and joint infection and the nature of bacteriophages is presented, as well as a summary of our current knowledge on the use of bacteriophages in the treatment of bacterial infections. We present contemporary published in vitro and in vivo data as well as data from clinical trials, as they relate to bone and joint infections. We discuss the potential use of bacteriophage therapy in orthopaedic infections. This area of research is beginning to reveal successful results, but mostly in nonorthopaedic fields. We believe that bacteriophage therapy has potential therapeutic value for implant-associated infections in orthopaedics. Cite this article: Bone Joint J 2021;103-B(2):234-244.
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Affiliation(s)
- Bryan P Gibb
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Michael Hadjiargyrou
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
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45
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Makalatia K, Kakabadze E, Wagemans J, Grdzelishvili N, Bakuradze N, Natroshvili G, Macharashvili N, Sedrakyan A, Arakelova K, Ktsoyan Z, Zakharyan M, Gevorgyan Z, Mnatsakanyan A, Tishkova F, Lood C, Vandenheuvel D, Lavigne R, Pirnay JP, De Vos D, Chanishvili N, Merabishvili M. Characterization of Salmonella Isolates from Various Geographical Regions of the Caucasus and Their Susceptibility to Bacteriophages. Viruses 2020; 12:v12121418. [PMID: 33321823 PMCID: PMC7764154 DOI: 10.3390/v12121418] [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: 10/10/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 02/05/2023] Open
Abstract
Non-typhoidal Salmonella present a major threat to animal and human health as food-borne infectious agents. We characterized 91 bacterial isolates from Armenia and Georgia in detail, using a suite of assays including conventional microbiological methods, determining antimicrobial susceptibility profiles, matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, serotyping (using the White-Kauffmann-Le Minor scheme) and genotyping (repetitive element sequence-based PCR (rep-PCR)). No less than 61.5% of the isolates were shown to be multidrug-resistant. A new antimicrobial treatment strategy is urgently needed. Phage therapy, the therapeutic use of (bacterio-) phages, the bacterial viruses, to treat bacterial infections, is increasingly put forward as an additional tool for combatting antibiotic resistant infections. Therefore, we used this representative set of well-characterized Salmonella isolates to analyze the therapeutic potential of eleven single phages and selected phage cocktails from the bacteriophage collection of the Eliava Institute (Georgia). All isolates were shown to be susceptible to at least one of the tested phage clones or their combinations. In addition, genome sequencing of these phages revealed them as members of existing phage genera (Felixounavirus, Seunavirus, Viunavirus and Tequintavirus) and did not show genome-based counter indications towards their applicability against non-typhoidal Salmonella in a phage therapy or in an agro-food setting.
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Affiliation(s)
- Khatuna Makalatia
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
- Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
- Correspondence:
| | - Elene Kakabadze
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
- Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium; (J.W.); (C.L.); (R.L.)
| | - Nino Grdzelishvili
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
- Department of Natural Sciences and Medicine, Ilia State University, Tbilisi 0162, Georgia
| | - Nata Bakuradze
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
- Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Gulnara Natroshvili
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
| | - Nino Macharashvili
- Bacteriology Laboratory, Infectious Diseases and AIDS Center, Tbilisi 0160, Georgia;
| | - Anahit Sedrakyan
- Laboratory of Molecular Genetics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia; (A.S.); (K.A.); (Z.K.); (M.Z.)
| | - Karine Arakelova
- Laboratory of Molecular Genetics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia; (A.S.); (K.A.); (Z.K.); (M.Z.)
| | - Zhanna Ktsoyan
- Laboratory of Molecular Genetics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia; (A.S.); (K.A.); (Z.K.); (M.Z.)
| | - Magdalina Zakharyan
- Laboratory of Molecular Genetics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia; (A.S.); (K.A.); (Z.K.); (M.Z.)
| | - Zaruhi Gevorgyan
- Department of Clinical Laboratory Diagnostics, Yerevan State Medical University after Mkhitar Heratsi, Yerevan 0025, Armenia;
| | - Armine Mnatsakanyan
- Microbiological Laboratory, Nork Infectious Clinical Hospital, Ministry of Health of the Republic of Armenia, Yerevan 0047, Armenia;
| | - Farida Tishkova
- Virology Laboratory, Tajik Research Institute of Preventive Medicine, 734025 Dushanbe, Tajikistan;
| | - Cédric Lood
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium; (J.W.); (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, 3000 Leuven, Belgium
| | - Dieter Vandenheuvel
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerp, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium; (J.W.); (C.L.); (R.L.)
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (J.-P.P.); (D.D.V.)
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (J.-P.P.); (D.D.V.)
| | - Nina Chanishvili
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
| | - Maia Merabishvili
- Research & Development Department, George Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0160, Georgia; (E.K.); (N.G.); (N.B.); (G.N.); (N.C.); (M.M.)
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (J.-P.P.); (D.D.V.)
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46
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Pereira C, Costa P, Duarte J, Balcão VM, Almeida A. Phage therapy as a potential approach in the biocontrol of pathogenic bacteria associated with shellfish consumption. Int J Food Microbiol 2020; 338:108995. [PMID: 33316593 DOI: 10.1016/j.ijfoodmicro.2020.108995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Infectious human diseases acquired from bivalve shellfish consumption constitute a public health threat. These health threats are largely related to the filter-feeding phenomenon, by which bivalve organisms retain and concentrate pathogenic bacteria from their surrounding waters. Even after depuration, bivalve shellfish are still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new and efficient strategies to control transmission of shellfish infection. Bacteriophage (or phage) therapy represents a promising, tailor-made approach to control human pathogens in bivalves, but its success depends on a deep understanding of several factors that include the bacterial communities present in the harvesting waters, the appropriate selection of phage particles, the multiplicity of infection that produces the best bacterial inactivation, chemical and physical factors, the emergence of phage-resistant bacterial mutants and the life cycle of bivalves. This review discusses the need to advance phage therapy research for bivalve decontamination, highlighting their efficiency as an antimicrobial strategy and identifying critical aspects to successfully apply this therapy to control human pathogens associated with bivalve consumption.
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Affiliation(s)
- Carla Pereira
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - Pedro Costa
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, São Paulo, Brazil
| | - Adelaide Almeida
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
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Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient. Viruses 2020; 12:v12101138. [PMID: 33049935 PMCID: PMC7600146 DOI: 10.3390/v12101138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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Ameh EM, Tyrrel S, Harris JA, Pawlett M, Orlova EV, Ignatiou A, Nocker A. Lysis Performance of Bacteriophages with Different Plaque Sizes and Comparison of Lysis Kinetics After Simultaneous and Sequential Phage Addition. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:149-157. [PMID: 36147827 PMCID: PMC9041478 DOI: 10.1089/phage.2020.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Although bacteriophages see a revival for specifically removing undesired bacteria, there is still much uncertainty about how to achieve the most rapid and long-lasting clearance. Materials and Methods: This study investigated the lysis kinetics of three distinct environmental coliphages, reproducibly forming different plaque sizes (big, medium, and small). Lysis performance by individual phages was compared with the one obtained after simultaneous or sequential addition of all three phages. Kinetics was monitored by density absorbance or by flow cytometry, with the latter having the advantage of providing higher sensitivity. Results: Plaque size happened to correlate with lysis kinetics in liquid suspensions, with phages producing big (phage B), medium (phage M), and small (phage S) plaques showing maximal bacterial clearance under the chosen conditions within ∼6, 12, and 18 h, respectively. Use of a phage cocktail (all three phages added simultaneously) resulted in slower initial lysis compared with the fastest lysing phage with the greatest plaque size alone, but it showed longer efficacy in suppression. When adding phages sequentially, overall lysis kinetics could be influenced by administering phages at different time points. The lowest bacterial concentration after 36 h was obtained when administering phages in the sequence S, M, and B although this combination initially took the longest to achieve bacterial clearance. Conclusions: Results support that timing and order of phage addition can modulate strength and duration of bacterial suppression and, thus, influence the overall success of phage treatment.
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Affiliation(s)
- Ekwu M. Ameh
- Cranfield Water Science Institute, School of Environment, Energy and Agrifood, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Sean Tyrrel
- Cranfield Water Science Institute, School of Environment, Energy and Agrifood, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Jim A. Harris
- Cranfield Institute for Resilient Futures, School of Environment, Energy and Agrifood, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Mark Pawlett
- Cranfield Soil and Agrifood Institute, School of Environment, Energy and Agrifood, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Elena V. Orlova
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Athanasios Ignatiou
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Andreas Nocker
- Cranfield Water Science Institute, School of Environment, Energy and Agrifood, Cranfield University, Cranfield, Bedfordshire, United Kingdom
- Applied Microbiology, IWW Water Centre, Mülheim an der Ruhr, Germany
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Luong T, Salabarria AC, Roach DR. Phage Therapy in the Resistance Era: Where Do We Stand and Where Are We Going? Clin Ther 2020; 42:1659-1680. [DOI: 10.1016/j.clinthera.2020.07.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
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50
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Loessner H, Schlattmeier I, Anders-Maurer M, Bekeredjian-Ding I, Rohde C, Wittmann J, Pokalyuk C, Krut O, Kamp C. Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy. Antibiotics (Basel) 2020; 9:E408. [PMID: 32674401 PMCID: PMC7400656 DOI: 10.3390/antibiotics9070408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022] Open
Abstract
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage-host pair during the course of infection. We have elaborated such a kinetic fingerprint for a human urinary tract Klebsiella pneumoniae isolate and its phage vB_KpnP_Lessing by a modeling approach based on data from in vitro co-culture. We found a faster depletion of the initially sensitive bacterial population than expected from simple mass action kinetics. A possible explanation for the rapid decline of the bacterial population is a synergistic interaction of phages which can be a favorable feature for phage therapies. In addition to this interaction characteristic, analysis of the kinetic fingerprint of this bacteria and phage combination revealed several relevant aspects of their population dynamics: A reduction of the bacterial concentration can be achieved only at high multiplicity of infection whereas bacterial extinction is hardly accomplished. Furthermore the binding affinity of the phage to bacteria is identified as one of the most crucial parameters for the reduction of the bacterial population size. Thus, kinetic fingerprinting can be used to infer phage-host interactions and to explore emergent dynamics which facilitates a rational design of phage therapies.
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Affiliation(s)
- Holger Loessner
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Insea Schlattmeier
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Marie Anders-Maurer
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | | | - Christine Rohde
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Cornelia Pokalyuk
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Oleg Krut
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Christel Kamp
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
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