1
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Chaudhary V, Kajla P, Lather D, Chaudhary N, Dangi P, Singh P, Pandiselvam R. Bacteriophages: a potential game changer in food processing industry. Crit Rev Biotechnol 2024; 44:1325-1349. [PMID: 38228500 DOI: 10.1080/07388551.2023.2299768] [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] [Received: 02/25/2023] [Revised: 08/16/2023] [Accepted: 10/03/2023] [Indexed: 01/18/2024]
Abstract
In the food industry, despite the widespread use of interventions such as preservatives and thermal and non-thermal processing technologies to improve food safety, incidences of foodborne disease continue to happen worldwide, prompting the search for alternative strategies. Bacteriophages, commonly known as phages, have emerged as a promising alternative for controlling pathogenic bacteria in food. This review emphasizes the potential applications of phages in biological sciences, food processing, and preservation, with a particular focus on their role as biocontrol agents for improving food quality and preservation. By shedding light on recent developments and future possibilities, this review highlights the significance of phages in the food industry. Additionally, it addresses crucial aspects such as regulatory status and safety concerns surrounding the use of bacteriophages. The inclusion of up-to-date literature further underscores the relevance of phage-based strategies in reducing foodborne pathogenic bacteria's presence in both food and the production environment. As we look ahead, new phage products are likely to be targeted against emerging foodborne pathogens. This will further advance the efficacy of approaches that are based on phages in maintaining the safety and security of food.
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Affiliation(s)
- Vandana Chaudhary
- Department of Dairy Technology, College of Dairy Science and Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Priyanka Kajla
- Department of Food Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Deepika Lather
- Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nisha Chaudhary
- Department of Food Science and Technology, College of Agriculture, Agriculture University, Jodhpur, Rajasthan, India
| | - Priya Dangi
- Department of Food and Nutrition and Food Technology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Punit Singh
- Department of Mechanical Engineering, Institute of Engineering and Technology, GLA University Mathura, Mathura, Uttar Pradesh, India
| | - Ravi Pandiselvam
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR -Central Plantation Crops Research Institute, Kasaragod, Kerala, India
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2
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Lapras B, Marchand C, Merienne C, Medina M, Kolenda C, Laurent F, Pirot F. Rationalisation of the purification process for a phage active pharmaceutical ingredient. Eur J Pharm Biopharm 2024; 203:114438. [PMID: 39111580 DOI: 10.1016/j.ejpb.2024.114438] [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] [Received: 05/14/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 09/14/2024]
Abstract
The resurgence of phage therapy, once abandoned in the early 20th century in part due to issues related to the purification process and stability, is spurred by the global threat of antibiotic resistance. Engineering advances have enabled more precise separation unit operations, improving overall purification efficiency. The present review discusses the physicochemical properties of impurities commonly found in a phage lysate, e.g., contaminants, phage-related impurities, and propagation-related impurities. Differences in phages and bacterial impurities properties are leveraged to elaborate a four-step phage purification process: clarification, capture and concentration, subsequent purification and polishing. Ultimately, a framework for rationalising the development of a purification process is proposed, considering three operational characteristics, i.e., scalability, transferability to various phages and duration. This guide facilitates the preselection of a sequence of unit operations, which can then be confronted with the expected impurities to validate the theoretical capacity of the process to purify the phage lysate.
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Affiliation(s)
- B Lapras
- Hospices Civils de Lyon, Edouard Herriot Hospital, Pharmacy Department, FRIPHARM®, F-69437 Lyon, France; Claude Bernard Lyon 1 University, French National Centre for Scientific Research (CNRS), Institut de Biologie et de Chimie des Protéines (IBCP), Tissue Biology and Therapeutic Engineering Laboratory (LBTI), UMR 5305, F-69007 Lyon, France.
| | - C Marchand
- Hospices Civils de Lyon, Edouard Herriot Hospital, Pharmacy Department, FRIPHARM®, F-69437 Lyon, France
| | - C Merienne
- Hospices Civils de Lyon, Edouard Herriot Hospital, Pharmacy Department, FRIPHARM®, F-69437 Lyon, France
| | - M Medina
- Hospices Civils de Lyon, Croix Rousse Hospital, Bacteriology Department, French National Reference Centre for Staphylococci, F-69317 Lyon, France; Claude Bernard Lyon 1 University, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR 5308, F- 69365 Lyon, France
| | - C Kolenda
- Hospices Civils de Lyon, Croix Rousse Hospital, Bacteriology Department, French National Reference Centre for Staphylococci, F-69317 Lyon, France; Claude Bernard Lyon 1 University, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR 5308, F- 69365 Lyon, France
| | - F Laurent
- Hospices Civils de Lyon, Croix Rousse Hospital, Bacteriology Department, French National Reference Centre for Staphylococci, F-69317 Lyon, France; Claude Bernard Lyon 1 University, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR 5308, F- 69365 Lyon, France
| | - F Pirot
- Hospices Civils de Lyon, Edouard Herriot Hospital, Pharmacy Department, FRIPHARM®, F-69437 Lyon, France; Claude Bernard Lyon 1 University, French National Centre for Scientific Research (CNRS), Institut de Biologie et de Chimie des Protéines (IBCP), Tissue Biology and Therapeutic Engineering Laboratory (LBTI), UMR 5305, F-69007 Lyon, France
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3
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Woudstra C, Sørensen AN, Sørensen MCH, Brøndsted L. Strategies for developing phages into novel antimicrobial tailocins. Trends Microbiol 2024; 32:996-1006. [PMID: 38580606 DOI: 10.1016/j.tim.2024.03.003] [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] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Tailocins are high-molecular-weight bacteriocins produced by bacteria to kill related environmental competitors by binding and puncturing their target. Tailocins are promising alternative antimicrobials, yet the diversity of naturally occurring tailocins is limited. The structural similarities between phage tails and tailocins advocate using phages as scaffolds for developing new tailocins. This article reviews three strategies for producing tailocins: disrupting the capsid-tail junction of phage particles, blocking capsid assembly during phage propagation, and creating headless phage particles synthetically. Particularly appealing is the production of tailocins through synthetic biology using phages with contractile tails as scaffolds to unlock the antimicrobial potential of tailocins.
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Affiliation(s)
- Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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4
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Wang WX, Wu JZ, Zhang BL, Yu JY, Han LM, Lu XL, Li H, Fu SY, Ren YY, Dong H, Xu Y, Wang GT, Gao JH, Wang C, Chen XZ, Liu DX, Huang Y, Yu JH, Wang SW, Yang YF, Chen W. Phage therapy combats pan drug-resistant Acinetobacter baumannii infection safely and efficiently. Int J Antimicrob Agents 2024; 64:107220. [PMID: 38810939 DOI: 10.1016/j.ijantimicag.2024.107220] [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] [Received: 07/12/2023] [Revised: 04/20/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Phage therapy offers a promising approach to combat the growing threat of antimicrobial resistance. Yet, key questions remain regarding dosage, administration routes, combination therapy, and the causes of therapeutic failure. In this study, we focused on a novel lytic phage, ФAb4B, which specifically targeted the Acinetobacter baumannii strains with KL160 capsular polysaccharide, including the pan-drug resistant A. baumannii YQ4. ФAb4B exhibited the ability to effectively inhibit biofilm formation and eradicate mature biofilms independently of dosage. Additionally, it demonstrated a wide spectrum of antibiotic-phage synergy and did not show any cytotoxic or haemolytic effects. Continuous phage injections, both intraperitoneally and intravenously over 7 d, showed no acute toxicity in vivo. Importantly, phage therapy significantly improved neutrophil counts, outperforming ciprofloxacin. However, excessive phage injections suppressed neutrophil levels. The combinatorial treatment of phage-ciprofloxacin rescued 91% of the mice, a superior outcome compared to phage alone (67%). The efficacy of the combinatorial treatment was independent of phage dosage. Notably, prophylactic administration of the combinatorial regimen provided no protection, but even when combined with a delayed therapeutic regimen, it saved all the mice. Bacterial resistance to the phage was not a contributing factor to treatment failure. Our preclinical study systematically describes the lytic phage's effectiveness in both in vitro and in vivo settings, filling in crucial details about phage treatment against bacteriemia caused by A. baumannii, which will provide a robust foundation for the future of phage therapy.
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Affiliation(s)
- Wei-Xiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Zhen Wu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiao-Yang Yu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China; Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Li-Mei Han
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao-Liang Lu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hui Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shi-Yong Fu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun-Yao Ren
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Dong
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Xu
- Department of Geriatric Medicine, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Gong-Ting Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jing-Han Gao
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Chun Wang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiu-Zhen Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Du-Xian Liu
- Department of pathology, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Huang
- Department of Infection Control and Management, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Hong Yu
- Department of Clinical Laboratory, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Shi-Wei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yong-Feng Yang
- The Clinical Infectious Disease Center of Nanjing, Nanjing, China.
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
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5
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Guo Z, Yuan M, Chai J. Mini review advantages and limitations of lytic phages compared with chemical antibiotics to combat bacterial infections. Heliyon 2024; 10:e34849. [PMID: 39148970 PMCID: PMC11324966 DOI: 10.1016/j.heliyon.2024.e34849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024] Open
Abstract
The overuse of antibiotics has caused the emergence of antibiotic-resistant strains, such as multidrug-resistant, extensively drug-resistant, and pandrug-resistant bacteria. The treatment of infections caused by such strains has become a formidable challenge. In the post-antibiotic era, phage therapy is an attractive solution for this problem and some successful phase 1 and 2 studies have demonstrated the efficacy and safety of phage therapy over the last decade. It is a form of evolutionary medicine, phages exhibit immunomodulatory and anti-inflammatory properties. However, phage therapy is limited by factors, such as the narrow spectrum of host strains, the special pharmacokinetics and pharmacodynamics in vivo, immune responses, and the development of phage resistance. The aim of this minireview was to compare the potencies of lytic phages and chemical antibiotics to treat bacterial infections. The advantages of phage therapy has fewer side effects, self-replication, evolution, bacterial biofilms eradication, immunomodulatory and anti-inflammatory properties compared with chemical antibiotics. Meanwhile, the disadvantages of phage therapy include the narrow spectrum of available host strains, the special pharmacokinetics and pharmacodynamics in vivo, immune responses, and phage resistance hurdles. Recently, some researchers continue to make efforts to overcome these limitations of phage therapy. Phage therapy will be a welcome addition to the gamut of options available for treating antibiotic-resistant bacterial infections. We focus on the advantages and limitations of phage therapy with the intention of exploiting the advantages and overcoming the limitations.
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Affiliation(s)
- Zhimin Guo
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, 130021, China
| | - Mengyao Yuan
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, 130021, China
| | - Jiannan Chai
- Department of Laboratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China
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6
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Villa N, Tartari E, Glicenstein S, de Villiers de la Noue H, Picard E, Marcoux PR, Zelsmann M, Resch G, Hadji E, Houdré R. Optical Trapping and Fast Discrimination of Label-Free Bacteriophages at the Single Virion Level. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308814. [PMID: 38282203 DOI: 10.1002/smll.202308814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/13/2023] [Indexed: 01/30/2024]
Abstract
There is a recent resurgence of interest in phage therapy (the therapeutic use of bacterial viruses) as an approach to eliminating difficult-to-treat infections. However, existing approaches for therapeutic phage selection and virulence testing are time-consuming, host-dependent, and facing reproducibility issues. Here, this study presents an innovative approach wherein integrated resonant photonic crystal (PhC) cavities in silicon are used as optical nanotweezers for probing and manipulating single bacteria and single virions with low optical power. This study demonstrates that these nanocavities differentiate between a bacterium and a phage without labeling or specific surface bioreceptors. Furthermore, by tailoring the spatial extent of the resonant optical mode in the low-index medium, phage distinction across phenotypically distinct phage families is demonstrated. The work paves the road to the implementation of optical nanotweezers in phage therapy protocols.
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Affiliation(s)
- Nicolas Villa
- Institut de Physique, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Enrico Tartari
- Institut de Physique, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Simon Glicenstein
- Univ. Grenoble Alpes, CEA, Grenoble INP, IRIG, PHELIQS, Grenoble, 38000, France
| | - Hugues de Villiers de la Noue
- Laboratory of Bacteriophages and Phage Therapy, Center for Research and Innovation in Clinical Pharmaceutical Sciences (CRISP), Lausanne University Hospital (CHUV), Lausanne, 1011, Switzerland
| | - Emmanuel Picard
- Univ. Grenoble Alpes, CEA, Grenoble INP, IRIG, PHELIQS, Grenoble, 38000, France
| | - Pierre R Marcoux
- Univ. Grenoble Alpes, CEA, LETI, DTIS, L4IV, Grenoble, 38000, France
| | - Marc Zelsmann
- Université Grenoble Alpes, CNRS, CEA/LETI Minatec, LTM, Grenoble, 38000, France
| | - Grégory Resch
- Laboratory of Bacteriophages and Phage Therapy, Center for Research and Innovation in Clinical Pharmaceutical Sciences (CRISP), Lausanne University Hospital (CHUV), Lausanne, 1011, Switzerland
| | - Emmanuel Hadji
- Univ. Grenoble Alpes, CEA, Grenoble INP, IRIG, PHELIQS, Grenoble, 38000, France
| | - Romuald Houdré
- Institut de Physique, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
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7
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Saqr E, Sadik MW, El-Didamony G, Askora A. Analysis of a new phage, KZag1, infecting biofilm of Klebsiella pneumoniae: genome sequence and characterization. BMC Microbiol 2024; 24:211. [PMID: 38877452 PMCID: PMC11179266 DOI: 10.1186/s12866-024-03355-9] [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: 12/01/2023] [Accepted: 05/29/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND This study investigates the effectiveness of the bacteriophage KZag1 against drug-resistant Klebsiella pneumoniae, aiming to assess its potential as a therapeutic agent. The novelty lies in the characterization of KZag1, a Myovirus with specific efficacy against multidrug-resistant K. pneumoniae strains. This highlights the significance of exploring alternative strategies, particularly phage therapy, in addressing biofilm-associated infections. METHODS KZag1, characterized by a typical Myovirus structure with a 75 ± 5 nm diameter icosahedral head and a 15 ± 5 nm short tail, was evaluated in experimental trials against 15 strains of K. pneumoniae. The infection cycle duration was determined to be 50 min, resulting in an estimated burst size of approximately 83 plaque-forming units per colony-forming unit (PFU/CFU). Stability assessments were conducted within a pH range of 4 to 12 and temperatures ranging from 45°C to 60°C. Biofilm biomass reduction was observed, particularly at a multiplicity of infection (MOI) of 10. RESULTS KZag1 demonstrated infection efficacy against 12 out of 15 tested K. pneumoniae strains. The phage exhibited stability across a broad pH range and at elevated temperatures. Notably, treatment with KZag1 significantly reduced K. pneumoniae biofilm biomass, emphasizing its potential in combating biofilm formation. Genomic analysis revealed a complete genome of 157,089 base pairs with a GC content of 46.38%, encompassing 203 open reading frames (ORFs) and a cysteine-specific tRNA sequence. Comparison with phage GP4 highlighted similarities, with KZag1 having a longer genome by approximately 4829 base pairs and a higher GC content by approximately 0.93%. Phylogenetic analysis classified KZag1 within the Myoviridae family. CONCLUSION The efficacy of KZag1 against K. pneumoniae biofilm suggests its potential as a therapeutic candidate, especially for drug-resistant infections. Further clinical research is warranted to explore its synergy with other treatments, elucidate genomic traits, compare with Myoviridae phages, and understand its host interactions. These findings underscore the promising role of KZag1 in addressing drug-resistant bacterial infections.
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Affiliation(s)
- Ebtsam Saqr
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Mahmoud W Sadik
- Department of Environmental Biotechnology, College of Biotechnology, Misr University for Science and Technology, Giza, Egypt
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Gamal El-Didamony
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Ahmed Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
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8
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Wang X, Wang S, Huang M, He Y, Guo S, Yang K, Wang N, Sun T, Yang H, Yang T, Xu Y, Shen Q, Friman VP, Wei Z. Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness. mBio 2024; 15:e0301623. [PMID: 38780276 PMCID: PMC11237578 DOI: 10.1128/mbio.03016-23] [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: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 05/25/2024] Open
Abstract
Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities. IMPORTANCE Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Mingcong Huang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yilin He
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Saisai Guo
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ningqi Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tianyu Sun
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Hongwu Yang
- China National Tobacco Corporation Hunan Company, Changsha, Hunan, China
| | - Tianjie Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
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9
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Xepapadaki P, Megremis S, Rovina N, Wardzyńska A, Pasioti M, Kritikou M, Papadopoulos NG. Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the "Constructing a 'Eubiosis Reinstatement Therapy' for Asthma-CURE" Project. Pulm Ther 2024; 10:171-182. [PMID: 38814533 PMCID: PMC11282048 DOI: 10.1007/s41030-024-00261-3] [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: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
The asthma pandemic imposes a huge burden on patients and health systems in both developed and developing countries. Despite available treatments, symptom control is generally suboptimal, and hospitalizations and deaths remain at unacceptably high levels. A pivotal aspect of asthma that warrants further exploration is the influence of the respiratory microbiome and virome in modulating disease activity. A plethora of studies report that the respiratory microbiome is characteristically dysbiotic in asthma. In addition, our data suggest that dysbiosis is also observed on the respiratory virome, partly characterized by the reduced abundance of bacteriophages (phages). Even though phages can naturally infect and control their bacterial prey, phage therapy has been grossly neglected in the Western world, although more recently it is more widely used as a novel tool against bacterial infections. However, it has never been used for tackling microbiome dysbiosis in human non-communicable diseases. This review provides an up-to-date understanding of the microbiome and virome's role within the airways in relation to asthma morbidity. It also advances the rationale and hypothesis for the CURE project. Specifically, the CURE project suggests that managing the respiratory microbiome through phage therapy is viable and may result in restoring eubiosis within the asthmatic airway. This entails controlling immune dysregulation and the clinical manifestation of the disease. To accomplish this goal, it is crucial to predict the effects of introducing specific phage mixtures into the intricate ecology of the airways and devise suitable interventions.
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Affiliation(s)
- Paraskevi Xepapadaki
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece.
| | - Spyridon Megremis
- Department of Genetics and Genome Biology, Centre for Phage Research, University of Leicester, Leicester, UK
| | - Nikoletta Rovina
- 1st Department of Respiratory Medicine, Sotiria Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | | | - Maria Pasioti
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Maria Kritikou
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
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10
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Kim SM, Heo HR, Kim CS, Shin HH. Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents. Front Bioeng Biotechnol 2024; 12:1319830. [PMID: 38725991 PMCID: PMC11079243 DOI: 10.3389/fbioe.2024.1319830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.
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Affiliation(s)
- Seong-Min Kim
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hye Ryoung Heo
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Chang Sup Kim
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Hwa Hui Shin
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
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11
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Liu Y, Liang Z, Yu S, Ye Y, Lin Z. CRISPR RNA-Guided Transposases Facilitate Dispensable Gene Study in Phage. Viruses 2024; 16:422. [PMID: 38543787 PMCID: PMC10974960 DOI: 10.3390/v16030422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 05/23/2024] Open
Abstract
Phages provide a potential therapy for multi-drug-resistant (MDR) bacteria. However, a significant portion of viral genes often remains unknown, posing potential dangers. The identification of non-essential genes helps dissect and simplify phage genomes, but current methods have various limitations. In this study, we present an in vivo two-plasmid transposon insertion system to assess the importance of phage genes, which is based on the V. cholerae transposon Tn6677, encoding a nuclease-deficient type I-F CRISPR-Cas system. We first validated the system in Pseudomonas aeruginosa PAO1 and its phage S1. We then used the selection marker AcrVA1 to protect transposon-inserted phages from CRISPR-Cas12a and enriched the transposon-inserted phages. For a pool of selected 10 open-reading frames (2 known functional protein genes and 8 hypothetical protein genes) of phage S1, we identified 5 (2 known functional protein genes and 3 hypothetical protein genes) as indispensable genes and the remaining 5 (all hypothetical protein genes) as dispensable genes. This approach offers a convenient, site-specific method that does not depend on homologous arms and double-strand breaks (DSBs), holding promise for future applications across a broader range of phages and facilitating the identification of the importance of phage genes and the insertion of genetic cargos.
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Affiliation(s)
- Yanmei Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Zizhen Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Shuting Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.L.); (Z.L.); (S.Y.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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12
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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [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: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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13
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Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, Whitehead N, Soothill J, Michell S, Temperton B. The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK. Microorganisms 2024; 12:253. [PMID: 38399657 PMCID: PMC10893117 DOI: 10.3390/microorganisms12020253] [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: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
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Affiliation(s)
- Julie Fletcher
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Robyn Manley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christian Fitch
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christina Bugert
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Michelle Michelsen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Shayma Alathari
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Nicola Senior
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Alice Mills
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - Natalie Whitehead
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - James Soothill
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - Stephen Michell
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Ben Temperton
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
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14
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Romeyer Dherbey J, Bertels F. The untapped potential of phage model systems as therapeutic agents. Virus Evol 2024; 10:veae007. [PMID: 38361821 PMCID: PMC10868562 DOI: 10.1093/ve/veae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant for well-established phage model systems. The knowledge acquired from decades of research on their structure, life cycle, and evolution ensures safe application and efficient handling. However, one major downside of the established phage model systems is their inability to infect pathogenic bacteria. This problem is not insurmountable; phage host range can be extended through genetic engineering or evolution experiments. In the future, breeding model phages to infect pathogens could provide a new avenue to develop phage therapeutic agents.
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Affiliation(s)
- Jordan Romeyer Dherbey
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
| | - Frederic Bertels
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
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15
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Pirnay JP, Merabishvili M, De Vos D, Verbeken G. Bacteriophage Production in Compliance with Regulatory Requirements. Methods Mol Biol 2024; 2734:89-115. [PMID: 38066364 DOI: 10.1007/978-1-0716-3523-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
In this chapter, we discuss production requirements for therapeutic bacteriophage preparations. We review the current regulatory expectancies and focus on pragmatic production processes, implementing relevant controls to ensure the quality, safety, and efficacy of the final products. The information disclosed in this chapter can also serve as a basis for discussions with competent authorities regarding the implementation of expedited bacteriophage product development and licensing pathways, taking into account some peculiarities of bacteriophages (as compared to conventional medicines), such as their specificity for, and co-evolution with, their bacterial hosts. To maximize the potential of bacteriophages as natural controllers of bacterial populations, the implemented regulatory frameworks and manufacturing processes should not only cater to defined bacteriophage products. But, they should also facilitate personalized approaches in which bacteriophages are selected ad hoc and even trained to target the patient's infecting bacterial strain(s), whether or not in combination with other antimicrobials such as antibiotics.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium.
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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16
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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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17
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Zalewska-Piątek B. Phage Therapy-Challenges, Opportunities and Future Prospects. Pharmaceuticals (Basel) 2023; 16:1638. [PMID: 38139765 PMCID: PMC10747886 DOI: 10.3390/ph16121638] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
The increasing drug resistance of bacteria to commonly used antibiotics creates the need to search for and develop alternative forms of treatment. Phage therapy fits this trend perfectly. Phages that selectively infect and kill bacteria are often the only life-saving therapeutic option. Full legalization of this treatment method could help solve the problem of multidrug-resistant infectious diseases on a global scale. The aim of this review is to present the prospects for the development of phage therapy, the ethical and legal aspects of this form of treatment given the current situation of such therapy, and the benefits of using phage products in persons for whom available therapeutic options have been exhausted or do not exist at all. In addition, the challenges faced by this form of therapy in the fight against bacterial infections are also described. More clinical studies are needed to expand knowledge about phages, their dosage, and a standardized delivery system. These activities are necessary to ensure that phage-based therapy does not take the form of an experiment but is a standard medical treatment. Bacterial viruses will probably not become a miracle cure-a panacea for infections-but they have a chance to find an important place in medicine.
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Affiliation(s)
- Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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18
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Malik DJ, Goncalves-Ribeiro H, GoldSchmitt D, Collin J, Belkhiri A, Fernandes D, Weichert H, Kirpichnikova A. Advanced Manufacturing, Formulation and Microencapsulation of Therapeutic Phages. Clin Infect Dis 2023; 77:S370-S383. [PMID: 37932112 DOI: 10.1093/cid/ciad555] [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: 11/08/2023] Open
Abstract
Manufacturing and formulation of stable, high purity, and high dose bacteriophage drug products (DPs) suitable for clinical usage would benefit from improved process monitoring and control of critical process parameters that affect product quality attributes. Chemistry, Manufacturing, and Controls (CMC) for both upstream (USP) and downstream processes (DSP) need mapping of critical process parameters (CPP) and linking these to critical quality attributes (CQA) to ensure quality and consistency of phage drug substance (DS) and DPs development. Single-use technologies are increasingly becoming the go-to manufacturing option with benefits both for phage bioprocess development at the engineering run research stage and for final manufacture of the phage DS. Future phage DPs under clinical development will benefit from implementation of process analytical technologies (PAT) for better process monitoring and control. These are increasingly being used to improve process robustness (to reduce batch-to-batch variability) and productivity (yielding high phage titers). Precise delivery of stable phage DPs that are suitably formulated as liquids, gels, solid-oral dosage forms, and so forth, could significantly enhance efficacy of phage therapy outcomes. Pre-clinical development of phage DPs must include at an early stage of development, considerations for their formulation including their characterization of physiochemical properties (size, charge, etc.), buffer pH and osmolality, compatibility with regulatory approved excipients, storage stability (packaging, temperature, humidity, etc.), ease of application, patient compliance, ease of manufacturability using scalable manufacturing unit operations, cost, and regulatory requirements.
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Affiliation(s)
- Danish J Malik
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | | | - Dirk GoldSchmitt
- Division of Computing Science and Mathematics, University of Stirling, Stirling, United Kingdom
- Department of Psychology, University of Sheffield, Sheffield, United Kingdom
| | - Joe Collin
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | - Aouatif Belkhiri
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | - Diogo Fernandes
- Nanomaterials Characterisation, Malvern Panalytical, Malvern, United Kingdom
| | - Henry Weichert
- Process Analytical Technology, Sartorius Stedim Biotech GmbH, Germany
| | - Anya Kirpichnikova
- Division of Computing Science and Mathematics, University of Stirling, Stirling, United Kingdom
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19
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Kumar A, Yadav A. Synthetic phage and its application in phage therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:61-89. [PMID: 37739560 DOI: 10.1016/bs.pmbts.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Synthetic phage analysis has been implemented in progressive various areas of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been altered for developing gene circuits to program biological systems. Due to their extremely potent potency, phages also provide greater medical availability against bacterial agents and bacterial diagnostic agents. Its host specificity and our growing ability to manipulate, them further expand its possibility. New Phages also genetically redesign programmable biomaterials with highly tunable properties. Moreover, new phages are central to powerful directed evolution platforms. It is used to enhance existing biological, functions to create new phages. In other sites, the mining of antibiotics, and the emergence and dissemination of more than one type of drug-resistant microbe, a human health concerns. The major point in controlling and treating microbial infections. At present, genetic modifications and biochemical treatments are used to modify phages. Among these, genetic engineering involves the identification of defective proteins, modification of host bodies, recognized receptors, and disruption of bacterial phage resistance signaling gateways.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
| | - Anuj Yadav
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
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20
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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21
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Diallo K, Dublanchet A. A Century of Clinical Use of Phages: A Literature Review. Antibiotics (Basel) 2023; 12:751. [PMID: 37107113 PMCID: PMC10135294 DOI: 10.3390/antibiotics12040751] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Growing antibiotic resistance and the broken antibiotic market have renewed interest in the use of phages, a century-old therapy that fell into oblivion in the West after two decades of promising results. This literature review with a particular focus on French literature aims to complement current scientific databases with medical and non-medical publications on the clinical use of phages. While several cases of successful treatment with phages have been reported, prospective randomized clinical trials are needed to confirm the efficacy of this therapy.
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Affiliation(s)
- Kevin Diallo
- Department of Infective and Tropical Diseases and Internal Medicine, University Hospital of la Reunion, 97448 Saint-Pierre, France
| | - Alain Dublanchet
- Independent Researcher, 2465 Rue Céline Robert, 94300 Vincennes, France
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22
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Torres Di Bello D, Narváez DM, Groot de Restrepo H, Vives MJ. Cytotoxic Evaluation in HaCaT Cells of the Pa.7 Bacteriophage from Cutibacterium ( Propionibacterium) acnes, Free and Encapsulated Within Liposomes. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:26-34. [PMID: 37214651 PMCID: PMC10196082 DOI: 10.1089/phage.2022.0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Introduction Acne is a multifactorial disease involving the colonization of skin follicles by Cutibacterium (formerly Propionibacterium) acnes. A combination of different retinoid-derived products, antibiotics, and hormonal antiandrogens are used to treat the disease, but these treatments require extended periods, may have secondary effects, are expensive, and not always effective. Owing to antibiotic resistance, the use of bacteriophages has been proposed as an alternative treatment. However, if they are intended for a cosmetic or pharmaceutical use, it is necessary to evaluate the safety of the phages and the preparations containing them. Materials and Methods In this study, the cytotoxicity of Pa.7 bacteriophage was evaluated in HaCaT cells, along with a liposome suitable for their encapsulation, using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and trypan blue assays. Results We found that Pa.7 was not cytotoxic for HaCaT cells. Also, 30 mM of liposomes, or below are considered noncytotoxic concentrations. Conclusion Phages encapsulated in the liposomes presented in this study can be used safely for skin treatments.
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Affiliation(s)
- Daniela Torres Di Bello
- Microbiology Research Center–CIMIC, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Diana M. Narváez
- Human Genetics Laboratory, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Helena Groot de Restrepo
- Human Genetics Laboratory, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Martha J. Vives
- Microbiology Research Center–CIMIC, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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23
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Karczewska M, Strzelecki P, Szalewska-Pałasz A, Nowicki D. How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight. Int J Mol Sci 2023; 24:ijms24054447. [PMID: 36901878 PMCID: PMC10003480 DOI: 10.3390/ijms24054447] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Bacteriophage-based applications have a renaissance today, increasingly marking their use in industry, medicine, food processing, biotechnology, and more. However, phages are considered resistant to various harsh environmental conditions; besides, they are characterized by high intra-group variability. Phage-related contaminations may therefore pose new challenges in the future due to the wider use of phages in industry and health care. Therefore, in this review, we summarize the current knowledge of bacteriophage disinfection methods, as well as highlight new technologies and approaches. We discuss the need for systematic solutions to improve bacteriophage control, taking into account their structural and environmental diversity.
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Affiliation(s)
- Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Patryk Strzelecki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR7504, 23 rue du Loess, CEDEX 2, F-67034 Strasbourg, France
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Nowicki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-523-6065
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24
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Nazir A, Song J, Chen Y, Liu Y. Phage-Derived Depolymerase: Its Possible Role for Secondary Bacterial Infections in COVID-19 Patients. Microorganisms 2023; 11:microorganisms11020424. [PMID: 36838389 PMCID: PMC9961776 DOI: 10.3390/microorganisms11020424] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
As of 29 July 2022, there had been a cumulative 572,239,451 confirmed cases of COVID-19 worldwide, including 6,390,401 fatalities. COVID-19 patients with severe symptoms are usually treated with a combination of virus- and drug-induced immuno-suppression medicines. Critical clinical complications of the respiratory system due to secondary bacterial infections (SBIs) could be the reason for the high mortality rate in COVID-19 patients. Unfortunately, antimicrobial resistance is increasing daily, and only a few options are available in our antimicrobial armory. Hence, alternative therapeutic options such as enzymes derived from bacteriophages can be considered for treating SBIs in COVID-19 patients. In particular, phage-derived depolymerases have high antivirulent potency that can efficiently degrade bacterial capsular polysaccharides, lipopolysaccharides, and exopolysaccharides. They have emerged as a promising class of new antibiotics and their therapeutic role for bacterial infections is already confirmed in animal models. This review provides an overview of the rising incidence of SBIs among COVID-19 patients. We present a practicable novel workflow for phage-derived depolymerases that can easily be adapted for treating SBIs in COVID-19 patients.
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Affiliation(s)
| | | | - Yibao Chen
- Correspondence: (Y.C.); (Y.L.); Tel./Fax: +86-531-6665-5093 (Y.C. & Y.L.)
| | - Yuqing Liu
- Correspondence: (Y.C.); (Y.L.); Tel./Fax: +86-531-6665-5093 (Y.C. & Y.L.)
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25
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Isolation, characterization, and genomic analysis of vB_PaeS_TUMS_P81, a lytic bacteriophage against Pseudomonas aeruginosa. Virus Genes 2023; 59:132-141. [PMID: 36357763 DOI: 10.1007/s11262-022-01954-0] [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: 08/13/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that can lead to nosocomial infections which are in turn life threatening. The increase in antibiotic resistance, at an alarming rate, has resulted in a pressing need for alternative therapeutic approaches such as phage therapy, which hold promise according to several studies. This study featured the isolation and characterization of vB_PaeS_TUMS_P81, a new lytic Pseudomonas phage. The whole-genome sequencing indicated that it has a genome of 73,167 bp containing 93 predicted coding sequences. Genes involved in virulence or lysogeny pathway were nowhere to be found in the genome, so it is potentially safe when it comes to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P81 is a member of the genus Litunavirus, belonging to Schitoviridae family. The present study lays the groundwork for further research on treatment of P. aeruginosa infections.
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26
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Xu Z, Ding Z, Zhang Y, Liu X, Wang Q, Shao S, Liu Q. Shelf-life prediction and storage stability of Aeromonas bacteriophage vB_AsM_ZHF. Virus Res 2023; 323:198997. [PMID: 36334617 PMCID: PMC10194148 DOI: 10.1016/j.virusres.2022.198997] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/25/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022]
Abstract
Phage therapy is a potential alternative to antibiotics for the treatment of bacterial infections. Due to the good antibacterial and therapeutic effects of phages, phage therapy has received attention and the demand for clinical applications has gradually increased. Phage storage stability and shelf life are key aspects of biopharmaceutical development and registration. In this study, Aeromonas salmonicida phage was stored at different temperatures for 12 months. We found that 4 °C was the optimal storage temperature. In the case of cryopreservation, 10% dimethyl sulfoxide (DMSO) was more effective at protecting the phage at -20 °C and -80 °C than 30% glycerin. Indeed, the phage titer decreased by only one order of magnitude within one year when DMSO was added. Hydroxyapatite (HAP) reduced the inactivation of phages by six orders of magnitude during storage at 28ºC for 1 year, significantly lower than that of in SM buffer. In addition, for excipients in lyophilization, tryptic soy broth (TSB) and tryptone or skim milk powder (SMP) in combination with trehalose alleviated phage inactivation during lyophilization and subsequent storage at 28 °C. Furthermore, a model for predicting the phage shelf-life was established with the Accelerated Stability Assessment Program (ASAP) based on the Arrhenius equation. The error of the model was less than 15% by comparing the predicted value with the actual value at 28 °C, indicating high accuracy. The study demonstrated the storage stability and shelf-life model of phage for the first time, which provided a theoretical basis for the development and application of phage products.
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Affiliation(s)
- Zhenhe Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zihan Ding
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Xiaohong Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China.
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27
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Composition of Bacteriophages for Therapeutic and Prophylactic Use in Monkeys. Bull Exp Biol Med 2023; 174:376-379. [PMID: 36723746 DOI: 10.1007/s10517-023-05711-7] [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: 06/21/2022] [Indexed: 02/02/2023]
Abstract
Keeping rhesus monkeys as laboratory animals requires timely prevention and treatment of infections, including diseases of bacterial etiology. Based on our own studies of the microflora of healthy and sick monkeys, as well as analysis of published reports, we identified clinically significant representatives of pathogenic and opportunistic bacteria: E. coli, Staphylococcus aureus, Klebsiella spp., Proteus spp. The isolates of these bacterial species and genera circulating in monkeys kept in the enclosure were isolated, four virulent bacteriophage strains with a wide spectrum of lytic activity against these isolates were selected and newly isolated. The composition based on virulent bacteriophage strains was tested on monkeys with assessment of its safety and its dynamics of detection of phage-specific DNA.
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28
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Kamyab H, Torkashvand N, Shahverdi AR, Khoshayand MR, Sharifzadeh M, Sepehrizadeh Z. Isolation, characterization, and genomic analysis of vB_PaeP_TUMS_P121, a new lytic bacteriophage infecting Pseudomonas aeruginosa. Arch Virol 2022; 168:8. [PMID: 36565337 DOI: 10.1007/s00705-022-05692-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/28/2022] [Indexed: 12/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that can cause life-threatening nosocomial infections. The alarming increase in antibiotic resistance has led to an urgent need for alternative therapeutic approaches, such as phage therapy, which has shown promising results in many studies. In this study, P121, a new lytic Pseudomonas phage, was isolated and characterized. Whole-genome sequencing showed that it has a genome of 73,001 bp that contains 91 predicted coding sequences. No genes involved in virulence or lysogeny were found in the genome, thus making it potentially safe for therapeutic applications. Genomic and phylogenetic analysis indicated that P121 is a member of the genus Litunavirus, family Schitoviridae. The present study provides some basic information for further research on treatment of P. aeruginosa infections.
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Affiliation(s)
- Haniyeh Kamyab
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Narges Torkashvand
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khoshayand
- Department of Food and Drug Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sharifzadeh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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29
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Abbas RZ, Alsayeqh AF, Aqib AI. Role of Bacteriophages for Optimized Health and Production of Poultry. Animals (Basel) 2022; 12:ani12233378. [PMID: 36496899 PMCID: PMC9736383 DOI: 10.3390/ani12233378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
The poultry sector is facing infections from Salmonella, Campylobacter, Listeria and Staphylococcus spp., and Escherichia coli, that have developed multidrug resistance aptitude. Antibiotics cause disturbances in the balance of normal microbiota leading to dysbiosis, immunosuppression, and the development of secondary infections. Bacteriophages have been reported to lower the colonization of Salmonella and Campylobacter in poultry. The specificity of bacteriophages is greater than that of antibiotics and can be used as a cocktail for enhanced antibacterial activity. Specie-specific phages have been prepared, e.g., Staphylophage (used against Staphylococcus bacteria) that specifically eliminate bacterial pathogens. Bacteriophage products, e.g., BacWashTM and Ecolicide PX have been developed as antiseptics and disinfectants for effective biosecurity and biosafety measures. The success of phage therapy is influenced by time to use, the amount used, the delivery mechanism, and combination therapy with other therapeutics. It is a need of time to build a comprehensive understanding of the use of bacteriophages in poultry production. The current review thus focuses on mechanisms of bacteriophages against poultry pathogens, their applications in various therapeutics, impacts on the economy, and current challenges.
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Affiliation(s)
- Rao Zahid Abbas
- Department of Parasitology, University of Agriculture, Faisalabad 38000, Pakistan
- Correspondence:
| | - Abdullah F Alsayeqh
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah 51452, Saudi Arabia
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
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30
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Ling H, Lou X, Luo Q, He Z, Sun M, Sun J. Recent advances in bacteriophage-based therapeutics: Insight into the post-antibiotic era. Acta Pharm Sin B 2022; 12:4348-4364. [PMID: 36561998 PMCID: PMC9764073 DOI: 10.1016/j.apsb.2022.05.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is one of the biggest threats to global health, as it can make the treatment of bacterial infections in humans difficult owing to their high incidence rate, mortality, and treatment costs. Bacteriophage, which constitutes a type of virus that can kill bacteria, is a promising alternative strategy against antibiotic-resistant bacterial infections. Although bacteriophage therapy was first used nearly a century ago, its development came to a standstill after introducing the antibiotics. Nowadays, with the rise in antibiotic resistance, bacteriophage therapy is in the spotlight again. As bacteriophage therapy is safe and has significant anti-bacterial activity, some specific types of bacteriophages (such as bacteriophage phiX174 and Pyo bacteriophage complex liquid) entered into phase III clinical trials. Herein, we review the key points of the antibiotic resistance crisis and illustrate the factors that support the renewal of bacteriophage applications. By summarizing recent state-of-the-art studies and clinical data on bacteriophage treatment, we introduced (i) the pharmacological mechanisms and advantages of antibacterial bacteriophages, (ii) bacteriophage preparations with clinical potential and bacteriophage-derived anti-bacterial treatment strategies, and (iii) bacteriophage therapeutics aimed at multiple infection types and infection-induced cancer treatments. Finally, we highlighted the challenges and critical perspectives of bacteriophage therapy for future clinical development.
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Affiliation(s)
- Hao Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xinyu Lou
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Qiuhua Luo
- Department of Pharmacy, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengchi Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China,Corresponding authors.
| | - Jin Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China,Corresponding authors.
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31
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Cui JQ, Liu WH, Zang YX, Zhang C, Zou L, Sun HZ, Pan Q, Ren HY. Characterization and complete genome analysis of a bacteriophage vB_EcoM_DE7 infecting donkey-derived Escherichia coli. Virus Res 2022; 321:198913. [PMID: 36064043 DOI: 10.1016/j.virusres.2022.198913] [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: 05/19/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A lytic bacteriophage vB_EcoM_DE7 (hereafter designated DE7) that could infect donkey-derived Escherichia coli was isolated. The bacteriophage was examined by transmission electron microscopy, and the result showed that DE7 belonged to the family Myoviridae. The microbiological characterization revealed that DE7 was stable over a broad range of pHs (3 ∼10) at 40-50 °C. The latent period was 10 min, and the burst size was 43 PFUs/infected cell. The whole-genome sequencing showed that DE7 was a dsDNA virus and had a genome of 86,130 bp. The genome contained 124 predicted open reading frames (ORFs), 35 of which had known functions, including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. Twenty tRNA genes were identified, but no genes associated with bacterial pathogenicity, lysogeny and drug resistance were identified. BLASTN analysis revealed that phage DE7 had a high sequence identity (96%) with Salmonella phage vB_SPuM_SP116, but it could not lyse any Salmonella strain tested in this study. DE7 was classified as a Felix O1-like virus based on its general characterization and genomic information. Since phage DE7 exhibited high efficacy in lysing E. coli and lacked genes associated with bacterial virulence, antimicrobial resistance and lysogeny, it could be potentially used to control foal diarrhoea caused by E. coli.
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Affiliation(s)
- Jia-Qi Cui
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wen-Hua Liu
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ya-Xin Zang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Zou
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hu-Zhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Hui-Ying Ren
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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32
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Hibstu Z, Belew H, Akelew Y, Mengist HM. Phage Therapy: A Different Approach to Fight Bacterial Infections. Biologics 2022; 16:173-186. [PMID: 36225325 PMCID: PMC9550173 DOI: 10.2147/btt.s381237] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
Phage therapy is one of the alternatives to treat infections caused by both antibiotic-sensitive and antibiotic-resistant bacteria, with no or low toxicity to patients. It was started a century ago, although rapidly growing bacterial antimicrobial resistance, resulting in high levels of morbidity, mortality, and financial cost, has initiated the revival of phage therapy. It involves the use of live lytic, bioengineered, phage-encoded biological products, in combination with chemical antibiotics to treat bacterial infections. Importantly, phages will be removed from the body within seven days of clearing an infection. They target specific bacterial strains and cause minimal disruption to the microbial balance in humans. Phages for medication must be screened for the absence of resistant genes, virulent genes, cytotoxicity, and their interaction with the host tissue and organs. Since they are immunogenic, applying a high phage titer for therapy exposes them and activates the host immune system. To date, no serious side effects have been reported with human phage therapy. In this review, we describe phage–phagocyte interaction, bacterial resistance to phages, how phages conquer bacterial resistance, the role of genetic engineering and other technologies in phage therapy, and the therapeutic application of modified phages and phage-encoded products. We also highlight the comparison of antibiotics and lytic phage therapy, the pros and cons of phage therapy, determinants of human phage therapy trials, phage quality and safety requirements, phage storage and handling, and current challenges in phage therapy.
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Affiliation(s)
- Zigale Hibstu
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia,Correspondence: Zigale Hibstu, Email
| | - Habtamu Belew
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Akelew
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Hylemariam Mihiretie Mengist
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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33
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Kolenda C, Medina M, Bonhomme M, Laumay F, Roussel-Gaillard T, Martins-Simoes P, Tristan A, Pirot F, Ferry T, Laurent F. Phage Therapy against Staphylococcus aureus: Selection and Optimization of Production Protocols of Novel Broad-Spectrum Silviavirus Phages. Pharmaceutics 2022; 14:pharmaceutics14091885. [PMID: 36145633 PMCID: PMC9503876 DOI: 10.3390/pharmaceutics14091885] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Phage therapy a promising antimicrobial strategy to address antimicrobial resistance for infections caused by the major human pathogen Staphylococcus aureus. Development of therapeutic phages for human use should follow pharmaceutical standards, including selection of strictly lytic bacteriophages with high therapeutic potential and optimization of their production process. Results: Here, we describe three novel Silviavirus phages active against 82% of a large collection of strains (n = 150) representative of various methicillin-susceptible and -resistant S. aureus clones circulating worldwide. We also investigated the optimization of the efficiency and safety of phage amplification protocols. To do so, we selected a well-characterized bacterial strain in order to (i) maximize phage production yields, reaching phage titres of 1011 PFU/mL in only 4 h; and (ii) facilitate phage purity while minimizing the risk of the presence of contaminants originating from the bacterial host; i.e., secreted virulence factors or induced temperate phages. Conclusions: In sum, we propose a quality-by-design approach for the amplification of broad-spectrum anti-S. aureus phages, facilitating the subsequent steps of the manufacturing process; namely, purification and quality control.
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Affiliation(s)
- Camille Kolenda
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Correspondence: ; Tel.: +33-4-72-00-37-80
| | - Mathieu Medina
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Mélanie Bonhomme
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Floriane Laumay
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Tiphaine Roussel-Gaillard
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
| | - Patricia Martins-Simoes
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Anne Tristan
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Fabrice Pirot
- Plateforme FRIPHARM, Service pharmaceutique, Groupement Hospitalier Edouard Herriot, Hospices Civils de Lyon, 69003 Lyon, France
- Laboratoire de Recherche et Développement de Pharmacie Galénique Industrielle, Plateforme FRIPHARM, Faculté de Pharmacie, Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, MR 5305, Université Claude Bernard Lyon 1, 69008 Lyon, France
| | - Tristan Ferry
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
- Department of Infectious Diseases, Hospices Civils de Lyon, 69004 Lyon, France
| | - Frédéric Laurent
- Bacteriology Department, French National Reference Centre for Staphylococci, Institute for Infectious Agents, Hospices Civils de Lyon, 69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
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Glonti T, Pirnay JP. In Vitro Techniques and Measurements of Phage Characteristics That Are Important for Phage Therapy Success. Viruses 2022; 14:1490. [PMID: 35891470 PMCID: PMC9323186 DOI: 10.3390/v14071490] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Affiliation(s)
- Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, B-1120 Brussels, Belgium;
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Racenis K, Rezevska D, Madelane M, Lavrinovics E, Djebara S, Petersons A, Kroica J. Use of Phage Cocktail BFC 1.10 in Combination With Ceftazidime-Avibactam in the Treatment of Multidrug-Resistant Pseudomonas aeruginosa Femur Osteomyelitis-A Case Report. Front Med (Lausanne) 2022; 9:851310. [PMID: 35547216 PMCID: PMC9081798 DOI: 10.3389/fmed.2022.851310] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/25/2022] [Indexed: 01/03/2023] Open
Abstract
High-energy trauma with severe bone fractures can be complicated by infection, leading to the development of osteomyelitis. Pseudomonas aeruginosa is an important causative agent of such infections because of its high virulence profile and ability to develop resistance against a wide range of antimicrobials quickly. P. aeruginosa biofilms cause treatment failure and relapsing infections. Bacteriophages are viruses that can be used to treat biofilm-associated infections. Moreover, the combination of phages with certain antimicrobials have demonstrated synergistic and additive effects. We present a case of a 21-year-old patient with relapsing multidrug-resistant (MDR) P. aeruginosa femur osteomyelitis that developed after a road accident, with a proximal right femoral Grade III B open fracture and severe soft tissue damage. Despite extensive antimicrobial treatment and multiple surgical interventions with wound debridement, the infection persisted, with subsequent development of femoral osteomyelitis with a fistula. Patient care management included femoral head excision with wound debridement, intravenous (IV) ceftazidime-avibactam, and the local application of the lytic Pseudomonas bacteriophage cocktail BFC 1.10. Nine months after the intervention, the patient did not show any clinical, radiological, or laboratory signs of inflammation; therefore, hip replacement was performed. Nevertheless, recurrent P. aeruginosa infection evolved at the distal side of the femur and was successfully treated with conventional antimicrobials. In this case, wound debridement combined with antibiotics and bacteriophages resulted in bacterial eradication of proximal femoral segment, avoiding leg amputation, but failed to treat osteomyelitis in distal bone segment. An in vitro assessment of the isolated MDR P. aeruginosa strain for biofilm formation and phage susceptibility was performed. Additionally, the antimicrobial effects of ceftazidime-avibactam and BFC 1.10 were determined on planktonic cell growth and bacterial biofilm prevention was evaluated. The isolated bacterial strains were susceptible to the bacteriophage cocktail. Strong biofilm formation was detected 6 h after inoculation. Ceftazidime-avibactam combined with BFC 1.10 was most effective in preventing planktonic cell growth and biofilm formation. In both cases, the required concentration of ceftazidime-avibactam decreased two-fold. This study demonstrates the possible use of bacteriophages and antibiotics in difficult-to-treat bone and soft tissue infections, where the additive effects of phages and antibiotics were observed.
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Affiliation(s)
- Karlis Racenis
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Center of Nephrology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Dace Rezevska
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Joint Laboratory, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Monta Madelane
- Department of Infectology, Riga Stradins University, Riga, Latvia.,Department of Infection Control, Riga East University Hospital, Riga, Latvia
| | - Ervins Lavrinovics
- Latvian Center for Plastic, Reconstructive and Microsurgery, Riga, Latvia
| | - Sarah Djebara
- Centre for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Aivars Petersons
- Center of Nephrology, Pauls Stradins Clinical University Hospital, Riga, Latvia.,Department of Internal Diseases, Riga Stradins University, Riga, Latvia
| | - Juta Kroica
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia
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ILOMUANYA MO, ENWURU NV, ADENOKUN E, FATUNMBI ABIGAIL, ADELUOLA A, IGWILO CI. Chitosan-Based Microparticle Encapsulated <i>cinetobacter baumannii</i> Phage Cocktail in Hydrogel Matrix for the Management of Multidrug Resistant Chronic Wound Infection. Turk J Pharm Sci 2022; 19:187-195. [DOI: 10.4274/tjps.galenos.2021.72547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Tkachev PV, Pchelin IM, Azarov DV, Gorshkov AN, Shamova OV, Dmitriev AV, Goncharov AE. Two Novel Lytic Bacteriophages Infecting Enterococcus spp. Are Promising Candidates for Targeted Antibacterial Therapy. Viruses 2022; 14:831. [PMID: 35458561 PMCID: PMC9030284 DOI: 10.3390/v14040831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
The rapid emergence of antibiotic resistance is of major concern globally. Among the most worrying pathogenic bacteria are vancomycin-resistant enterococci. Phage therapy is a highly promising method for controlling enterococcal infections. In this study, we described two virulent tailed bacteriophages possessing lytic activity against Enterococcus faecalis and E. faecium isolates. The SSsP-1 bacteriophage belonged to the Saphexavirus genus of the Siphoviridae family, and the GVEsP-1 bacteriophage belonged to the Schiekvirus genus of Herelleviridae. The genomes of both viruses carried putative components of anti-CRISPR systems and did not contain known genes coding for antibiotic-resistance determinants and virulence factors. The conservative arrangement of protein-coding sequences in Saphexavirus and Schiekvirus genomes taken together with positive results of treating enterococcal peritonitis in an animal infection model imply the potential suitability of GVEsP-1 and SSsP-1 bacteriophages for clinical applications.
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Affiliation(s)
- Pavel V. Tkachev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
| | - Ivan M. Pchelin
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
| | - Daniil V. Azarov
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
| | - Andrey N. Gorshkov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia;
- Laboratory of Pathomorphology, Almazov National Research Centre, 197341 Saint Petersburg, Russia
| | - Olga V. Shamova
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
| | - Alexander V. Dmitriev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
| | - Artemiy E. Goncharov
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia; (I.M.P.); (D.V.A.); (O.V.S.); (A.V.D.)
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38
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Vázquez R, Díez-Martínez R, Domingo-Calap P, García P, Gutiérrez D, Muniesa M, Ruiz-Ruigómez M, Sanjuán R, Tomás M, Tormo-Mas MÁ, García P. Essential Topics for the Regulatory Consideration of Phages as Clinically Valuable Therapeutic Agents: A Perspective from Spain. Microorganisms 2022; 10:microorganisms10040717. [PMID: 35456768 PMCID: PMC9025261 DOI: 10.3390/microorganisms10040717] [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: 03/03/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistance is one of the major challenges that humankind shall face in the short term. (Bacterio)phage therapy is a valuable therapeutic alternative to antibiotics and, although the concept is almost as old as the discovery of phages, its wide application was hindered in the West by the discovery and development of antibiotics in the mid-twentieth century. However, research on phage therapy is currently experiencing a renaissance due to the antimicrobial resistance problem. Some countries are already adopting new ad hoc regulations to favor the short-term implantation of phage therapy in clinical practice. In this regard, the Phage Therapy Work Group from FAGOMA (Spanish Network of Bacteriophages and Transducing Elements) recently contacted the Spanish Drugs and Medical Devices Agency (AEMPS) to promote the regulation of phage therapy in Spain. As a result, FAGOMA was asked to provide a general view on key issues regarding phage therapy legislation. This review comes as the culmination of the FAGOMA initiative and aims at appropriately informing the regulatory debate on phage therapy.
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Affiliation(s)
- Roberto Vázquez
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium;
| | | | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - Pedro García
- Center for Biological Research Margarita Salas (CIB-CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 28040 Madrid, Spain;
| | - Diana Gutiérrez
- Telum Therapeutics SL, 31110 Noáin, Spain; (R.D.-M.); (D.G.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain;
| | - María Ruiz-Ruigómez
- Internal Medicine, Infectious Diseases Unit, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - María Tomás
- Department of Microbiology, Hospital Universitario de A Coruña (INIBIC-CHUAC, SERGAS), 15006 A Coruña, Spain;
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María Ángeles Tormo-Mas
- Severe Infection Group, Hospital Universitari i Politècnic La Fe, Health Research Institute Hospital La Fe, IISLaFe, 46026 Valencia, Spain;
| | - Pilar García
- Dairy Research Institute of Asturias, IPLA-CSIC, 33300 Villaviciosa, Spain
- DairySafe Group, Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence:
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Abstract
Antimicrobial resistance has become increasingly common across the globe, claiming over 33,000 lives annually in Europe and 23,000 lives in the United States alone. The problem lies in trying to find potential solutions capable of tackling resistance and being able to fight infections that may resist various antimicrobials. Since Alexander Fleming's discovery in 1928, every antimicrobial synthesized in the past 70 years has developed at least one or more strands of resistant bacteria. One particular alternative to antimicrobials has brought hope to many in the scientific community; its name is the bacteriophage. Bacteriophages are viruses that can replicate within bacteria triggering genetic alterations and changes in pathways of protein expression by encoding a few to hundreds of genes within their genomes. The bacteriophage can hijack the cell, using the cell's genetic apparatus to replicate within the bacterium until bacterial lysis. This therapy has been used in the genodermatosis Netherton syndrome which has been associated with the increased risk of Staphylococcus aureus infections. Emerging data support the potential role of bacteriophage therapy for Cutibacterium acnes in acne vulgaris, with a potential role in genetic disorders with severe acne vulgaris including Apert's syndrome. Bacteriophages hold benefits for genodermatoses associated with recurrent cutaneous infections, i.e. the immunodeficiencies with distinctive cutaneous features as well as conditions such as atopic dermatitis in which bacterial colonization plays a strong role.
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40
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Würstle S, Stender J, Hammerl JA, Vogele K, Rothe K, Willy C, Bugert JJ. Practical Assessment of an Interdisciplinary Bacteriophage Delivery Pipeline for Personalized Therapy of Gram-Negative Bacterial Infections. Pharmaceuticals (Basel) 2022; 15:186. [PMID: 35215298 PMCID: PMC8879309 DOI: 10.3390/ph15020186] [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: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/24/2022] Open
Abstract
Despite numerous advances in personalized phage therapy, smooth logistics are challenging, particularly for multidrug-resistant Gram-negative bacterial infections requiring high numbers of specific lytic phages. We conducted this study to pave the way for efficient logistics for critically ill patients by (1) closely examining and improving a current pipeline under realistic conditions, (2) offering guidelines for each step, leading to safe and high-quality phage supplies, and (3) providing a tool to evaluate the pipeline's efficiency. Due to varying stipulations for quality and safety in different countries, we focused the pipeline on all steps up to a required phage product by a cell-free extract system. The first of three study runs included patients with respiratory bacterial infections from four intensive care units, and it revealed a cumulative time of up to 23 days. Ultimately, adjustment of specific set points of the vulnerable components of the pipeline, phage isolation, and titration increased the pipeline's efficiency by 15% and decreased the maximum required time to 13 days. We present a site-independent practical approach to establish and optimize pipelines for personalized phage delivery, the co-organization of pipeline components between different institutions, non-binding guidelines for every step, and an efficiency check for phage laboratories.
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Affiliation(s)
- Silvia Würstle
- Department of Internal Medicine II, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Jana Stender
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany;
| | - Jens André Hammerl
- Unit Epidemiology, Zoonoses and Antimicrobial Resistances, Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | - Kilian Vogele
- Physics of Synthetic Biological Systems-E14, Physics-Department and ZNN, Technical University Munich, 85748 Munich, Germany;
| | - Kathrin Rothe
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
| | - Christian Willy
- Trauma & Orthopaedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Bundeswehr (Military) Academic Hospital Berlin, 10115 Berlin, Germany;
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Abstract
Intestinal microbiota, dominated by bacteria, plays an important role in the occurrence and the development of alcohol-associated liver disease (ALD), which is one of the most common liver diseases around the world. With sufficient studies focusing on the gut bacterial community, chronic alcohol consumption is now known as a key factor that alters the composition of gut bacterial community, increases intestinal permeability, causes intestinal dysfunction, induces bacterial translocation, and exacerbates the process of ALD via gut-liver axis. However, gut non-bacterial communities including fungi, viruses, and archaea, which may also participate in the disease, has received little attention relative to the gut bacterial community. This paper will systematically collect the latest literatures reporting non-bacterial communities in mammalian health and disease, and review their mechanisms in promoting the development of ALD including CLEC7A pathway, Candidalysin (a peptide toxin secreted by Candida albicans), metabolites, and other chemical substances secreted or regulated by gut commensal mycobiome, virome, and archaeome, hoping to bring novel insights on our current knowledge of ALD.
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Affiliation(s)
- Wenkang Gao
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jin Ye
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,CONTACT Huikuan Chu Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
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42
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Carascal MB, dela Cruz-Papa DM, Remenyi R, Cruz MCB, Destura RV. Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia. Front Microbiol 2022; 13:820572. [PMID: 35154059 PMCID: PMC8830912 DOI: 10.3389/fmicb.2022.820572] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.
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Affiliation(s)
- Mark B. Carascal
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Donna May dela Cruz-Papa
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
- Research Center for Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Roland Remenyi
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
| | - Mely Cherrylynne B. Cruz
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Raul V. Destura
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines
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Lood C, Haas PJ, van Noort V, Lavigne R. Shopping for phages? Unpacking design rules for therapeutic phage cocktails. Curr Opin Virol 2021; 52:236-243. [PMID: 34971929 DOI: 10.1016/j.coviro.2021.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022]
Abstract
In bacteriophage therapy, the combination of different phages into a single cocktail is of critical importance to overcome the narrow host range of single phage isolates. Today, the design of therapeutic cocktails is often akin to a black box and relies largely on intuition and (pre-)availability of isolates in local collections. Here we show that straightforward host range analysis can disclose design rules and we propose to apply/translate a data mining approach, historically applied in the field of marketing ('shopping cart analysis') to explore patterns in phage combinations. The technique is broadly applicable to host range datasets and can serve in combination with other molecular-based approaches to propose rationales for phage cocktail design.
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Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium.
| | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13. Viruses 2021; 14:v14010006. [PMID: 35062209 PMCID: PMC8778798 DOI: 10.3390/v14010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.
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45
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Ferry T, Kolenda C, Briot T, Souche A, Lustig S, Josse J, Batailler C, Pirot F, Medina M, Leboucher G, Laurent F. Past and Future of Phage Therapy and Phage-Derived Proteins in Patients with Bone and Joint Infection. Viruses 2021; 13:v13122414. [PMID: 34960683 PMCID: PMC8708067 DOI: 10.3390/v13122414] [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: 09/15/2021] [Revised: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
Phage-derived therapies comprise phage therapy and the use of phage-derived proteins as anti-bacterial therapy. Bacteriophages are natural viruses that target specific bacteria. They were proposed to be used to treat bacterial infections in the 1920s, before the discovery and widespread over-commercialized use of antibiotics. Phage therapy was totally abandoned in Western countries, whereas it is still used in Poland, Georgia and Russia. We review here the history of phage therapy by focusing on bone and joint infection, and on the development of phage therapy in France in this indication. We discuss the rationale of its use in bacterial infection and show the feasibility of phage therapy in the 2020s, based on several patients with complex bone and joint infection who recently received phages as compassionate therapy. Although the status of phage therapy remains to be clarified by health care authorities, obtaining pharmaceutical-grade therapeutic phages (i.e., following good manufacturing practice guidelines or being “GMP-like”) targeting bacterial species of concern is essential. Moreover, multidisciplinary clinical expertise has to determine what could be the relevant indications to perform clinical trials. Finally “phage therapy 2.0” has to integrate the following steps: (i) follow the status of phage therapy, that is not settled and defined; (ii) develop in each country a close relationship with the national health care authority; (iii) develop industrial–academic partnerships; (iv) create academic reference centers; (v) identify relevant clinical indications; (vi) use GMP/GMP-like phages with guaranteed quality bioproduction; (vii) start as salvage therapy; (vii) combine with antibiotics and adequate surgery; and (viii) perform clinical trials, to finally (ix) demonstrate in which clinical settings phage therapy provides benefit. Phage-derived proteins such as peptidoglycan hydrolases, polysaccharide depolymerases or lysins are enzymes that also have anti-biofilm activity. In contrast to phages, their development has to follow the classical process of medicinal products. Phage therapy and phage-derived products also have a huge potential to treat biofilm-associated bacterial diseases, and this is of crucial importance in the worldwide spread of antimicrobial resistance.
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Affiliation(s)
- Tristan Ferry
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
- StaPath Team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69008 Lyon, France
- Correspondence:
| | - Camille Kolenda
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
- StaPath Team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69008 Lyon, France
| | - Thomas Briot
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
| | - Aubin Souche
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
- StaPath Team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69008 Lyon, France
| | - Sébastien Lustig
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
| | - Jérôme Josse
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
- StaPath Team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69008 Lyon, France
| | - Cécile Batailler
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
| | - Fabrice Pirot
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Laboratoire de Recherche et Développement de Pharmacie Galénique Industrielle, Faculté de Pharmacie, EA 4169 “Fonctions Physiologiques et Pathologiques de la Barrière Cutanée”, Université Claude-Bernard Lyon 1, 8, Avenue Rockefeller, CEDEX 08, 69373 Lyon, France
| | - Mathieu Medina
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
| | - Gilles Leboucher
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
| | - Frédéric Laurent
- Hospices Civils de Lyon, 69004 Lyon, France; (C.K.); (T.B.); (A.S.); (S.L.); (J.J.); (C.B.); (F.P.); (M.M.); (G.L.); (F.L.)
- Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Centre de Références des IOA Complexes de Lyon, CRIOAc Lyon, 69004 Lyon, France
- StaPath Team, Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69008 Lyon, France
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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Functional diversity increases the efficacy of phage combinations. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001110. [PMID: 34850676 PMCID: PMC8743627 DOI: 10.1099/mic.0.001110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023]
Abstract
Phage therapy is a promising alternative to traditional antibiotics for treating bacterial infections. Such phage-based therapeutics typically contain multiple phages, but how the efficacy of phage combinations scales with phage richness, identity and functional traits is unclear. Here, we experimentally tested the efficacy of 827 unique phage combinations ranging in phage richness from one to 12 phages. The efficacy of phage combinations increased with phage richness. However, complementarity between functionally diverse phages allowed efficacy to be maximized at lower levels of phage richness in functionally diverse combinations. These findings suggest that phage functional diversity is the key property of effective phage combinations, enabling the design of simple but effective phage therapies that overcome the practical and regulatory hurdles that limit development of more diverse phage therapy cocktails.
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Affiliation(s)
- Rosanna C. T. Wright
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Biology, University of York, York, UK
- Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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Alomari MMM, Dec M, Urban-Chmiel R. Bacteriophages as an Alternative Method for Control of Zoonotic and Foodborne Pathogens. Viruses 2021; 13:2348. [PMID: 34960617 PMCID: PMC8709489 DOI: 10.3390/v13122348] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
The global increase in multidrug-resistant infections caused by various pathogens has raised concerns in human and veterinary medicine. This has renewed interest in the development of alternative methods to antibiotics, including the use of bacteriophages for controlling bacterial infections. The aim of this review is to present potential uses of bacteriophages as an alternative to antibiotics in the control of bacterial infections caused by multidrug-resistant bacteria posing a risk to humans, with particular emphasis on foodborne and zoonotic pathogens. A varied therapeutic and immunomodulatory (activation or suppression) effect of bacteriophages on humoral and cellular immune response mechanisms has been demonstrated. The antibiotic resistance crisis caused by global antimicrobial resistance among bacteria creates a compelling need for alternative safe and selectively effective antibacterial agents. Bacteriophages have many properties indicating their potential suitability as therapeutic and/or prophylactic agents. In many cases, bacteriophages can also be used in food quality control against microorganisms such as Salmonella, Escherichia coli, Listeria, Campylobacter and others. Future research will provide potential alternative solutions using bacteriophages to treat infections caused by multidrug-resistant bacteria.
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Affiliation(s)
| | - Marta Dec
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine University of Life Sciences in Lublin, 20-033 Lublin, Poland;
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine University of Life Sciences in Lublin, 20-033 Lublin, Poland;
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Terwilliger A, Clark J, Karris M, Hernandez-Santos H, Green S, Aslam S, Maresso A. Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection. Viruses 2021; 13:v13102049. [PMID: 34696479 PMCID: PMC8541385 DOI: 10.3390/v13102049] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 01/29/2023] Open
Abstract
We rationally designed a bacteriophage cocktail to treat a 56-year-old male liver transplant patient with complex, recurrent prostate and urinary tract infections caused by an extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) (UCS1). We screened our library for phages that killed UCS1, with four promising candidates chosen for their virulence, mucolytic properties, and ability to reduce bacterial resistance. The patient received 2 weeks of intravenous phage cocktail with concomitant ertapenem for 6 weeks. Weekly serum and urine samples were collected to track the patient’s response. The patient tolerated the phage therapy without any adverse events with symptom resolution. The neutralization of the phage activity occurred with sera collected 1 to 4 weeks after the first phage treatment. This was consistent with immunoassays that detected the upregulation of immune stimulatory analytes. The patient developed asymptomatic recurrent bacteriuria 6 and 11 weeks following the end of phage therapy—a condition that did not require antibiotic treatment. The bacteriuria was caused by a sister strain of E. coli (UCS1.1) that remained susceptible to the original phage cocktail and possessed putative mutations in the proteins involved in adhesion and invasion compared to UCS1. This study highlights the utility of rationally designed phage cocktails with antibiotics at controlling E. coli infection and suggests that microbial succession, without complete eradication, may produce desirable clinical outcomes.
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Affiliation(s)
- Austen Terwilliger
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Justin Clark
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Maile Karris
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA;
| | - Haroldo Hernandez-Santos
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Sabrina Green
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Saima Aslam
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA;
- Correspondence: (S.A.); (A.M.); Tel.: +1-858-657-7643 (S.A.); +1-713-798-7369 (A.M.)
| | - Anthony Maresso
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
- Correspondence: (S.A.); (A.M.); Tel.: +1-858-657-7643 (S.A.); +1-713-798-7369 (A.M.)
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Gelman D, Yerushalmy O, Alkalay-Oren S, Rakov C, Ben-Porat S, Khalifa L, Adler K, Abdalrhman M, Coppenhagen-Glazer S, Aslam S, Schooley RT, Nir-Paz R, Hazan R. Clinical Phage Microbiology: a suggested framework and recommendations for the in-vitro matching steps of phage therapy. THE LANCET MICROBE 2021; 2:e555-e563. [DOI: 10.1016/s2666-5247(21)00127-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
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Preclinical Development of a Bacteriophage Cocktail for Treating Multidrug Resistant Pseudomonas aeruginosa Infections. Microorganisms 2021; 9:microorganisms9092001. [PMID: 34576896 PMCID: PMC8464757 DOI: 10.3390/microorganisms9092001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 01/21/2023] Open
Abstract
A Pseudomonas aeruginosa (P. aeruginosa) airway infection is one of the predominant causes contributing to the high morbidity and mortality rates in cystic fibrosis (CF) patients. The emergence of antibiotic resistant P. aeruginosa strains has led to an urgent need for new therapeutic approaches. Bacteriophages (phages) are viruses that can infect and lyse specific bacteria, providing a potential alternative approach in targeting antibiotic-resistant strains. We aim to isolate and characterise novel P. aeruginosa phages for combination in a cocktail to kill P. aeruginosa. One particular phage, PA4, could lyse 14/20 clinical isolates as observed through spot assays. This phage could significantly reduce the growth of bacteria in vitro, as determined through planktonic adsorption and inhibition assays as well as crystal violet- and LIVE/DEAD-stained biofilm assays. A morphological and genomic analysis revealed that PA4 belongs to the Myoviridae family and contained 66,450 bp. The broad infectivity profile, good stability in various pH and temperature conditions, lytic ability and the absence of the absences of antibiotic resistance, toxic and lysogenic genes suggest that PA4 is a good candidate for clinical grade use. Overall, phage therapy represents a promising alternative treatment option to antibiotics when treating a P. aeruginosa infection.
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