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Vu NT, Kim H, Lee S, Hwang IS, Kwon CT, Oh CS. Bacteriophage cocktail for biocontrol of soft rot disease caused by Pectobacterium species in Chinese cabbage. Appl Microbiol Biotechnol 2024; 108:11. [PMID: 38159122 DOI: 10.1007/s00253-023-12881-x] [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: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Pectobacterium spp. are necrotrophic plant pathogens that cause the soft rot disease in Chinese cabbage, resulting in severe yield loss. The use of conventional antimicrobial agents, copper-based bactericides, and antibiotics has encountered several limitations, such as bioaccumulation on plants and microbial resistance. Bacteriophages (phages) are considered promising alternative antimicrobial agents against diverse phytopathogens. In this study, we isolated and characterized two virulent phages (phiPccP-2 and phiPccP-3) to develop a phage cocktail. Morphological and genomic analyses revealed that two phages belonged to the Tevenvirinae and Mccorquodalevirinae subfamilies, respectively. The phiPccP-2 and phiPccP-3 phages, which have a broad host range, were stable at various environmental conditions, such as various pHs and temperatures and exposure to ultraviolet light. The phage cocktail developed using these two lytic phages inhibited the emergence of phage-resistant bacteria compared to single-phage treatments in in vitro challenge assays. The phage cocktail treatment effectively prevented the development of soft rot symptom in matured Chinese cabbage leaves. Additionally, the phage cocktail comprising three phages (phiPccP-1, phiPccP-2, and phiPccP-3) showed superior biocontrol efficacy against the mixture of Pectobacterium strains in Chinese cabbage seedlings. These results suggest that developing phage cocktails is an effective approach for biocontrol of soft rot disease caused by Pectobacterium strains in crops compared to single-phage treatments. KEY POINTS: •Two newly isolated Pectobacterium phages, phiPccP-2 and phiPccP-3, infected diverse Pectobacterium species and effectively inhibited the emergence of phage-resistant bacteria. •Genomic and physiological analyses suggested that both phiPccP-2 and phiPccP-3 are lytic phages and that their lytic activities are stable in the environmental conditions under which Chinese cabbage grows. •Treatment using a phage cocktail comprising phiPccP-2 and phiPccP-3 efficiently suppressed soft rot disease in detached mature leaves and seedlings of Chinese cabbage, indicating the applicability of the phage cocktail as an alternative antimicrobial agent.
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Affiliation(s)
- Nguyen Trung Vu
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyeongsoon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soohong Lee
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choon-Tak Kwon
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Chang-Sik Oh
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Braunstein R, Hubanic G, Yerushalmy O, Oren-Alkalay S, Rimon A, Coppenhagen-Glazer S, Niv O, Marom H, Barsheshet A, Hazan R. Successful phage-antibiotic therapy of P. aeruginosa implant-associated infection in a Siamese cat. Vet Q 2024; 44:1-9. [PMID: 38726795 PMCID: PMC11089911 DOI: 10.1080/01652176.2024.2350661] [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: 09/09/2023] [Accepted: 04/27/2024] [Indexed: 05/15/2024] Open
Abstract
Antibiotic-resistant pathogens are a growing global issue, leading to untreatable infectious diseases in both humans and animals. Personalized bacteriophage (phage) therapy, the use of specific anti-bacterial viruses, is currently a leading approach to combat antibiotic-resistant infections. The implementation of phage therapy has primarily been focused on humans, almost neglecting the impact of such infections on the health and welfare of companion animals. Pets also have the potential to spread resistant infections to their owners or the veterinary staff through zoonotic transmission. Here, we showcase personalized phage-antibiotic treatment of a cat with a multidrug-resistant Pseudomonas aeruginosa implant-associated infection post-arthrodesis surgery. The treatment encompassed a tailored combination of an anti-P. aeruginosa phage and ceftazidime, precisely matched to the pathogen. The phage was topically applied to the surgical wound while the antibiotic was administered intramuscularly. After two treatment courses spanning 7 and 3 weeks, the surgical wound, which had previously remained open for five months, fully closed. To the best of our knowledge, this is the first case of personalized phage therapy application in felines, which provides further evidence of the effectiveness of this approach. The successful outcome paves the way for personalized phage-antibiotic treatments against persistent infections therapy in veterinary practice.
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Affiliation(s)
- Ron Braunstein
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Goran Hubanic
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Sivan Oren-Alkalay
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
- Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Ofir Niv
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | - Hilik Marom
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | | | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
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Li X, Zhang C, Li S, Liang S, Xu X, Zhao Z. Quorum sensing positively regulates CPS-dependent Autographiviridae phage infection in Vibrio alginolyticus. Appl Environ Microbiol 2024; 90:e0221023. [PMID: 39072624 DOI: 10.1128/aem.02210-23] [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: 12/11/2023] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Quorum sensing (QS) orchestrates many bacterial behaviors, including virulence and biofilm formation, across bacterial populations. Nevertheless, the underlying mechanism by which QS regulates capsular polysaccharide (CPS)-dependent phage-bacterium interactions remains unclear. In this study, we report that QS upregulates the expression of CPS-dependent phage receptors, thus increasing phage adsorption and infection rates in Vibrio alginolyticus. We found that QS upregulated the expression of the ugd gene, leading to increased synthesis of Autographiviridae phage receptor CPS synthesis in V. alginolyticus. The signal molecule autoinducer-2 released by Vibrio from different sources can potentially enhance CPS-dependent phage infections. Therefore, our data suggest that inhibiting QS may reduce, rather than improve, the therapeutic efficacy of CPS-specific phages. IMPORTANCE Phage resistance is a direct threat to phage therapy, and understanding phage-host interactions, especially how bacteria block phage infection, is essential for developing successful phage therapy. In the present study, we demonstrate for the first time that Vibrio alginolyticus uses quorum sensing (QS) to promote capsular polysaccharide (CPS)-specific phage infection by upregulating ugd expression, which is necessary for the synthesis of Autographiviridae phage receptor CPS. Although increased CPS-specific phage susceptibility is a novel trade-off mediated by QS, it results in the upregulation of virulence factors, promoting biofilm development and enhanced capsular polysaccharide production in V. alginolyticus. This suggests that inhibiting QS may improve the effectiveness of antibiotic treatment, but it may also reduce the efficacy of phage therapy.
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Affiliation(s)
- Xixi Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Chen Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Shenao Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Sixuan Liang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Xuefei Xu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
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Ranta K, Skurnik M, Kiljunen S. fENko-Kae01 is a flagellum-specific jumbo phage infecting Klebsiella aerogenes. BMC Microbiol 2024; 24:234. [PMID: 38951769 PMCID: PMC11218385 DOI: 10.1186/s12866-024-03387-1] [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: 02/13/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Klebsiella aerogenes is an opportunistic pathogen that causes a wide variety of infections. Due to the rising problem of antibiotic resistance, novel antibiotics and strategies to combat bacterial infections are needed. Host-specific bacteriophages are natural enemies of bacteria and can be used in phage therapy as an alternative form of treatment against bacterial infections. Jumbo phages are defined as phages with genomes larger than 200 kb. Relatively few studies have been done on jumbo phages compared to smaller phages. RESULTS A novel phage, fENko-Kae01, was isolated from a commercial phage cocktail. Genomic analysis revealed that fENko-Kae01 is a lytic jumbo phage with a 360 kb genome encoding 578 predicted genes. No highly similar phage genomes were identified and fENko-Kae01 may be a completely new genus representative. No known genes associated with lysogenic life cycle, bacterial virulence, or antibiotic resistance were identified. The phage had myovirus morphology and a narrow host range. Phage resistant bacterial mutants emerged under phage selection. Whole genome sequencing revealed that the biogenesis of the flagellum was affected in four mutants and the lack of functional flagellum was confirmed in motility assays. Furthermore, phage fENKo-Kae01 failed to adsorb on the non-motile mutants indicating that the bacterial flagellum is the phage-binding receptor. CONCLUSIONS fENko-Kae01 is a novel jumbo bacteriophage that is considered safe for phage therapy. fENko-Kae01 uses the flagellum as the phage-binding receptor and may represent a completely novel genus.
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Affiliation(s)
- Kira Ranta
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Saija Kiljunen
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [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: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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6
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Alipour-Khezri E, Skurnik M, Zarrini G. Pseudomonas aeruginosa Bacteriophages and Their Clinical Applications. Viruses 2024; 16:1051. [PMID: 39066214 PMCID: PMC11281547 DOI: 10.3390/v16071051] [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: 04/19/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance poses a serious risk to contemporary healthcare since it reduces the number of bacterial illnesses that may be treated with antibiotics, particularly for patients with long-term conditions like cystic fibrosis (CF). People with a genetic predisposition to CF often have recurrent bacterial infections in their lungs due to a buildup of sticky mucus, necessitating long-term antibiotic treatment. Pseudomonas aeruginosa infections are a major cause of CF lung illness, and P. aeruginosa airway isolates are frequently resistant to many antibiotics. Bacteriophages (also known as phages), viruses that infect bacteria, are a viable substitute for antimicrobials to treat P. aeruginosa infections in individuals with CF. Here, we reviewed the utilization of P. aeruginosa bacteriophages both in vivo and in vitro, as well as in the treatment of illnesses and diseases, and the outcomes of the latter.
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Affiliation(s)
- Elaheh Alipour-Khezri
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 51368, Iran;
| | - Mikael Skurnik
- Human Microbiome Research Program, and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Gholamreza Zarrini
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 51368, Iran;
- Microbial Biotechnology Research Group, University of Tabriz, Tabriz 51368, Iran
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7
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Peters TL, Schow J, Spencer E, Van Leuven JT, Wichman H, Miller C. Directed evolution of bacteriophages: impacts of prolific prophage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601269. [PMID: 38979301 PMCID: PMC11230397 DOI: 10.1101/2024.06.28.601269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Various directed evolution methods exist that seek to procure bacteriophages with expanded host ranges, typically targeting phage-resistant or non-permissive bacterial hosts. The general premise of these methods is to propagate phage on multiple bacterial hosts, pool the lysate, and repeat the propagation process until phage(s) can form plaques on the target host(s). In theory, this propagation process produces a phage lysate that contains input phages and their evolved phage progeny. However, in practice, this phage lysate can also include prophages originating from bacterial hosts. Here we describe our experience implementing one directed evolution method, the Appelmans protocol, to study phage evolution in the Pseudomonas aeruginosa phage-host system, in which we observed rapid host-range expansion of the phage cocktail. Further experimentation and sequencing analysis revealed that this observed host-range expansion was due to a Casadabanvirus prophage that originated from one of the Appelmans hosts. Host-range analysis of the prophage showed that it could infect five of eight bacterial hosts initially used, allowing it to proliferate and persist through the end of the experiment. This prophage was represented in half of the sequenced phage samples isolated from the Appelmans experiment. This work highlights the impact of prophages in directed evolution experiments and the importance of incorporating sequencing data in analyses to verify output phages, particularly for those attempting to procure phages intended for phage therapy applications. This study also notes the usefulness of intraspecies antagonism assays between bacterial host strains to establish a baseline for inhibitory activity and determine presence of prophage. IMPORTANCE Directed evolution is a common strategy for evolving phages to expand host range, often targeting pathogenic strains of bacteria. In this study we investigated phage host-range expansion using directed evolution in the Pseudomonas aeruginosa system. We show that prophage are active players in directed evolution and can contribute to observation of host-range expansion. Since prophage are prevalent in bacterial hosts, particularly pathogenic strains of bacteria, and all directed evolution approaches involve iteratively propagating phage on one or more bacterial hosts, the presence of prophage in phage preparations is a factor that needs to be considered in experimental design and interpretation of results. These results highlight the importance of screening for prophages either genetically or through intraspecies antagonism assays during selection of bacterial strains and will contribute to improving experimental design of future directed evolution studies.
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Onallah H, Yerushalmy O, Braunstein R, Alkalay-Oren S, Rimon A, Gelman D, Coppenhagen-Glazer S, Hazan R, Nir-Paz R. Protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections. STAR Protoc 2024; 5:102949. [PMID: 38691464 PMCID: PMC11070627 DOI: 10.1016/j.xpro.2024.102949] [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: 11/22/2023] [Revised: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 05/03/2024] Open
Abstract
Phage therapy has re-emerged as a promising treatment for non-resolving infections. Given the lack of approved phage treatments, there is a need to establish a compassionate use pipeline. Here, we present a protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections. We describe steps for consultation and request implementation, evaluating and comparing different aspects of phage activity, and phage production. We then detail procedures for multidisciplinary meetings, ethics approvals, phage therapy, and follow-up. For complete details on the use and execution of this protocol, please refer to Onallah et al.1,2.
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Affiliation(s)
- Hadil Onallah
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel
| | - Ortal Yerushalmy
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ron Braunstein
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sivan Alkalay-Oren
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amit Rimon
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Gelman
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ronen Hazan
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Ran Nir-Paz
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel.
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Bozidis P, Markou E, Gouni A, Gartzonika K. Does Phage Therapy Need a Pan-Phage? Pathogens 2024; 13:522. [PMID: 38921819 PMCID: PMC11206709 DOI: 10.3390/pathogens13060522] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
The emergence of multidrug-resistant bacteria is undoubtedly one of the most serious global health threats. One response to this threat that has been gaining momentum over the past decade is 'phage therapy'. According to this, lytic bacteriophages are used for the treatment of bacterial infections, either alone or in combination with antimicrobial agents. However, to ensure the efficacy and broad applicability of phage therapy, several challenges must be overcome. These challenges encompass the development of methods and strategies for the host range manipulation and bypass of the resistance mechanisms developed by pathogenic bacteria, as has been the case since the advent of antibiotics. As our knowledge and understanding of the interactions between phages and their hosts evolves, the key issue is to define the host range for each application. In this article, we discuss the factors that affect host range and how this determines the classification of phages into different categories of action. For each host range group, recent representative examples are provided, together with suggestions on how the different groups can be used to combat certain types of bacterial infections. The available methodologies for host range expansion, either through sequential adaptation to a new pathogen or through genetic engineering techniques, are also reviewed.
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Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Athanasia Gouni
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Konstantina Gartzonika
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
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10
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Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [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: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
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Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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11
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Romero J, Blas-Chumacero S, Urzúa V, Villasante A, Opazo R, Gajardo F, Miranda CD, Rojas R. Lysin and Lytic Phages Reduce Vibrio Counts in Live Feed and Fish Larvae. Microorganisms 2024; 12:904. [PMID: 38792735 PMCID: PMC11123823 DOI: 10.3390/microorganisms12050904] [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: 03/01/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 05/26/2024] Open
Abstract
Vibrio species are naturally found in estuarine and marine ecosystems, but are also recognized as significant human enteropathogens, often linked to seafood-related illnesses. In aquaculture settings, Vibrio poses a substantial risk of infectious diseases, resulting in considerable stock losses and prompting the use of antimicrobials. However, this practice contributes to the proliferation of antimicrobial-resistant (AMR) bacteria and resistance genes. Our investigation aimed to explore the potential of biological agents such as bacteriophage CH20 and endolysin LysVPp1 in reducing Vibrio bacterial loads in both rotifer and fish larvae. LysVPp1's lytic activity was assessed by measuring absorbance reduction against various pathogenic Vibrio strains. Phage CH20 exhibited a limited host range, affecting only Vibrio alginolyticus GV09, a highly pathogenic strain. Both CH20 and LysVPp1 were evaluated for their effectiveness in reducing Vibrio load in rotifers or fish larvae through short-setting bioassays. Our results demonstrated the significant lytic effect of endolysin LysVPp1 on strains of Vibrio alginolyticus, Vibrio parahaemolyticus, and Vibrio splendidus. Furthermore, we have showcased the feasibility of reducing the load of pathogenic Vibrio in live feed and fish larvae by using a non-antibiotic-based approach, such as lytic phage and endolysin LysVPp1, thus contributing to the progress of a sustainable aquaculture from a One Health perspective.
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Affiliation(s)
- Jaime Romero
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Sergueia Blas-Chumacero
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Victoria Urzúa
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Alejandro Villasante
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Rafael Opazo
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Felipe Gajardo
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (S.B.-C.); (V.U.); (A.V.); (R.O.); (F.G.)
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
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12
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Bhandare S, Lawal OU, Colavecchio A, Cadieux B, Zahirovich-Jovich Y, Zhong Z, Tompkins E, Amitrano M, Kukavica-Ibrulj I, Boyle B, Wang S, Levesque RC, Delaquis P, Danyluk M, Goodridge L. Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species. Microorganisms 2024; 12:695. [PMID: 38674639 PMCID: PMC11052255 DOI: 10.3390/microorganisms12040695] [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: 03/08/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.
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Affiliation(s)
- Sudhakar Bhandare
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham LE12 5RD, UK
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Brigitte Cadieux
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Yella Zahirovich-Jovich
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Zeyan Zhong
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Elizabeth Tompkins
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Margot Amitrano
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Irena Kukavica-Ibrulj
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Brian Boyle
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Siyun Wang
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Roger C. Levesque
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada
| | - Michelle Danyluk
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
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13
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Bull JJ, Wichman HA, Krone SM, Molineux IJ. Controlling Recombination to Evolve Bacteriophages. Cells 2024; 13:585. [PMID: 38607024 PMCID: PMC11011186 DOI: 10.3390/cells13070585] [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: 12/22/2023] [Revised: 03/07/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Recombination among different phages sometimes facilitates their ability to grow on new hosts. Protocols to direct the evolution of phage host range, as might be used in the application of phage therapy, would then benefit from including steps to enable recombination. Applying mathematical and computational models, in addition to experiments using phages T3 and T7, we consider ways that a protocol may influence recombination levels. We first address coinfection, which is the first step to enabling recombination. The multiplicity of infection (MOI, the ratio of phage to cell concentration) is insufficient for predicting (co)infection levels. The force of infection (the rate at which cells are infected) is also critical but is more challenging to measure. Using both a high force of infection and high MOI (>1) for the different phages ensures high levels of coinfection. We also apply a four-genetic-locus model to study protocol effects on recombinant levels. Recombinants accumulate over multiple generations of phage growth, less so if one phage outgrows the other. Supplementing the phage pool with the low-fitness phage recovers some of this 'lost' recombination. Overall, fine tuning of phage recombination rates will not be practical with wild phages, but qualitative enhancement can be attained with some basic procedures.
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Affiliation(s)
- James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
| | - Stephen M. Krone
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA;
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, USA
| | - Ian J. Molineux
- Institute for Cell and Molecular Biology, Department of Molecular Biosciences, LaMontagne Center for Infectious Diseases, The University of Texas, Austin, TX 78712, USA;
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Faltus T. The Medicinal Phage-Regulatory Roadmap for Phage Therapy under EU Pharmaceutical Legislation. Viruses 2024; 16:443. [PMID: 38543808 PMCID: PMC10974108 DOI: 10.3390/v16030443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 05/23/2024] Open
Abstract
Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target and kill pathogenic bacteria. The legal handling of this type of therapy raises several questions. These include whether phage therapeutics belong to a specially regulated class of medicinal products, and which legal framework should be followed with regard to the various technical ways in which phage therapeutics can be manufactured and administered. The article shows to which class of medicinal products phage therapeutics from wild type phages and from genetically modified (designer) phages do or do not belong. Furthermore, the article explains which legal framework is relevant for the manufacture and administration of phage therapeutics, which are manufactured in advance in a uniform, patient-independent manner, and for tailor-made patient-specific phage therapeutics. For the systematically coherent, successful translation of phage therapy, the article considers pharmaceutical law and related legal areas, such as genetic engineering law. Finally, the article shows how the planned legislative revisions of Directive 2001/83/EC and Regulation (EC) No 726/2004 may affect the legal future of phage therapy.
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Affiliation(s)
- Timo Faltus
- Chair of Public Law, Law School, Faculty of Law, Economics and Business, Martin-Luther-University Halle-Wittenberg, 06099 Halle an der Saale, Germany
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15
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Pelyuntha W, Ngasaman R, Yingkajorn M, Chukiatsiri K, Guyonnet V, Vongkamjan K. Phage cocktail administration to reduce Salmonella load in broilers. Res Vet Sci 2024; 169:105163. [PMID: 38295630 DOI: 10.1016/j.rvsc.2024.105163] [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: 06/25/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Salmonella is a serious foodborne pathogen that can cause gastrointestinal disease through the consumption of contaminated foods; including poultry meat. Salmonella is commonly present in the intestinal tract of poultry and farm environments, posing a potential risk of contamination during the processing of poultry meat. This study was a continuation in evaluating the effects of our previously developed phage cocktail targeting Salmonella at large-scale trials in commercial broiler farms, in which this cocktail considerably lowered Salmonella colonization in the gut of broilers. The phage cocktail given to broilers showed resistance to temperatures of up to 65 °C (> 60% survivability), pH ranging from 2 to 12 (> 96% survivability), 0.5 to 15% (w/v) NaCl (> 98% survivability), chlorine up to 0.5% (v/v) (53% survivability), and chlorine neutralizer (100% survivability). In the animal challenge study, phage treatments, designed as "prevention" and "exclusion" programs, could control Salmonella on day 20 and 32 of the experiment, respectively; as indicated by the absence of Salmonella detection in cloacal swabs from broilers (0% prevalence). In the commercial-scale trial I, Salmonella was not detected in the phage-treated group from cloacal swabs, boot cover swabs, and bedding material samples after 16 days (0% prevalence) of phage administration. In the commercial-scale trial II, phage treatment extended the Salmonella control period in broilers during a 40-day growout period. In summary, a phage cocktail demonstrated high efficiency in controlling various serovars of Salmonella historically linked to contamination on these broiler farms. Phage cocktail application offers an effective, alternative to enhance food safety within the poultry value chain, protecting consumers and as well as the economic sustainability of the poultry sector.
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Affiliation(s)
- Wattana Pelyuntha
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ruttayaporn Ngasaman
- Faculty of Veterinary Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Mingkwan Yingkajorn
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Kridda Chukiatsiri
- Faculty of Animal Science and Technology, Maejo University, Nongharn, Sansai, Chiang Mai 50290, Thailand
| | | | - Kitiya Vongkamjan
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
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16
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Hassannia M, Naderifar M, Salamy S, Akbarizadeh MR, Mohebi S, Moghadam MT. Engineered phage enzymes against drug-resistant pathogens: a review on advances and applications. Bioprocess Biosyst Eng 2024; 47:301-312. [PMID: 37962644 DOI: 10.1007/s00449-023-02938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
In recent decades, the expansion of multi and extensively drug-resistant (MDR and XDR) bacteria has reached an alarming rate, causing serious health concerns. Infections caused by drug-resistant bacteria have been associated with morbidity and mortality, making tackling bacterial resistance an urgent and unmet challenge that needs to be addressed properly. Endolysins are phage-encoded enzymes that can specifically degrade the bacterial cell wall and lead to bacterial death. There is remarkable evidence that corroborates the unique ability of endolysins to rapidly digest the peptidoglycan particular bonds externally without the assistance of phage. Thus, their modulation in therapeutic approaches has opened new options for therapeutic applications in the fight against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology areas. The use of genetically engineered phage enzymes (EPE) promises to generate endolysin variants with unique properties for prophylactic and therapeutic applications. These approaches have gained momentum to accelerate basic as well as translational phage research and the potential development of therapeutics in the near future. This review will focus on the novel knowledge into EPE and demonstrate that EPE has far better performance than natural endolysins and phages in dealing with antibiotic-resistant infections. Therefore, it provides essential information for clinical trials involving EPE.
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Affiliation(s)
- Mohadeseh Hassannia
- Department of Genetic, Faculty of Science, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Shakiba Salamy
- Department of Microbiology, Faculty of Pharmacy, Islamic Azad University, Tehran, Iran
| | | | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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17
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Wang M, Zhang J, Wei J, Jiang L, Jiang L, Sun Y, Zeng Z, Wang Z. Phage-inspired strategies to combat antibacterial resistance. Crit Rev Microbiol 2024; 50:196-211. [PMID: 38400715 DOI: 10.1080/1040841x.2023.2181056] [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: 12/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023]
Abstract
Antimicrobial resistance (AMR) in clinically priority pathogensis now a major threat to public health worldwide. Phages are bacterial parasites that efficiently infect or kill specific strains and represent the most abundant biological entities on earth, showing great attraction as potential antibacterial therapeutics in combating AMR. This review provides a summary of phage-inspired strategies to combat AMR. We firstly cover the phage diversity, and then explain the biological principles of phage therapy that support the use of phages in the post-antimicrobial era. Furthermore, we state the versatility methods of phage therapy both from direct access as well as collateral access. Among the direct access approaches, we discuss the use of phage cocktail therapy, phage-encoded endolysins and the bioengineering for function improvement of used phages or endolysins. On the other hand, we introduce the collateral access, including the phages antimicrobial immunity combined therapy and phage-based novel antibacterial mimic molecules. Nowadays, more and more talented and enthusiastic scientist, doctors, pharmacists, media, authorities, and industry are promoting the progress of phage therapy, and proposed more phages-inspired strategy to make them more tractable to combat AMR and benefit more people, more animal and diverse environment in "one health" framework.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Junxuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongxue Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, China
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18
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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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19
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Piña-González AM, Castelán-Sánchez HG, Hurtado-Ramírez JM, López-Leal G. Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species. Microbiol Spectr 2024; 12:e0279523. [PMID: 38088548 PMCID: PMC10782988 DOI: 10.1128/spectrum.02795-23] [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: 07/07/2023] [Accepted: 11/12/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.
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Affiliation(s)
- Adán Manuel Piña-González
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hugo G. Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciudad de México, México
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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20
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Vu TN, Clark JR, Jang E, D'Souza R, Nguyen LP, Pinto NA, Yoo S, Abadie R, Maresso AW, Yong D. Appelmans protocol - A directed in vitro evolution enables induction and recombination of prophages with expanded host range. Virus Res 2024; 339:199272. [PMID: 37981215 PMCID: PMC10730860 DOI: 10.1016/j.virusres.2023.199272] [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: 07/31/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) present significant healthcare challenges due to limited treatment options. Bacteriophage (phage) therapy offers potential as an alternative treatment. However, the high host specificity of phages poses challenges for their therapeutic application. To broaden the phage spectrum, laboratory-based phage training using the Appelmans protocol was employed in this study. As a result, the protocol successfully expanded the host range of a phage cocktail targeting CRAB. Further analysis revealed that the expanded host range phages isolated from the output cocktail were identified as recombinant derivatives originating from prophages induced from encountered bacterial strains. These findings provide valuable genetic insights into the protocol's mechanism when applied to phages infecting A. baumannii strains that have never been investigated before. However, it is noteworthy that the expanded host range phages obtained from this protocol exhibited limited stability, raising concerns about their suitability for therapeutic purposes.
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Affiliation(s)
- Thao Nguyen Vu
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Justin Ryan Clark
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Eris Jang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; University of Georgia Terry College of Business, Athens, GA, US
| | - Roshan D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Le Phuong Nguyen
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, US
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seongjun Yoo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Ricardo Abadie
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Anthony William Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, US
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.
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21
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Boroujeni MB, Mohebi S, Malekian A, Shahraeini SS, Gharagheizi Z, Shahkolahi S, Sadeghi RV, Naderifar M, Akbarizadeh MR, Soltaninejad S, Moghadam ZT, Moghadam MT, Mirzadeh F. The therapeutic effect of engineered phage, derived protein and enzymes against superbug bacteria. Biotechnol Bioeng 2024; 121:82-99. [PMID: 37881139 DOI: 10.1002/bit.28581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/18/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Defending against antibiotic-resistant infections is similar to fighting a war with limited ammunition. As the new century unfolded, antibiotic resistance became a significant concern. In spite of the fact that phage treatment has been used as an effective means of fighting infections for more than a century, researchers have had to overcome many challenges of superbug bacteria by manipulating phages and producing engineered enzymes. New enzymes and phages with enhanced properties have a significant impact on the ability to fight antibiotic-resistant infections, which is considered a window of hope for the future. This review, therefore, illustrates not only the challenges caused by antibiotic resistance and superbug bacteria but also the engineered enzymes and phages that are being developed to solve these issues. Our study found that engineered phages, phage proteins, and enzymes can be effective in treating superbug bacteria and destroying the biofilm caused by them. Combining these engineered compounds with other antimicrobial substances can increase their effectiveness against antibiotic-resistant bacteria. Therefore, engineered phages, proteins, and enzymes can be used as a substitute for antibiotics or in combination with antibiotics to treat patients with superbug infections in the future.
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Affiliation(s)
| | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azam Malekian
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Sadegh Shahraeini
- Department of Medical Biotechnology, Drug Design and Bioinformatics Unit, Biotechnology Research Centre, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Gharagheizi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shaghayegh Shahkolahi
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Rezvaneh Vahedian Sadeghi
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Nursing & Midwifery, Zabol University of Medical Sciences, Zabol, Iran
| | | | | | - Zahra Taati Moghadam
- School of Nursing and Midwifery, Guilan University of Medical Sciences, Rasht, Iran
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22
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Laanto E. Overcoming Bacteriophage Resistance in Phage Therapy. Methods Mol Biol 2024; 2738:401-410. [PMID: 37966611 DOI: 10.1007/978-1-0716-3549-0_23] [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: 11/16/2023]
Abstract
Antibiotic resistance among pathogenic bacteria is one of the most severe global challenges. It is predicted that over ten million lives will be lost annually by 2050. Phage therapy is a promising alternative to antibiotics. However, the ease of development of phage resistance during therapy is a concern. This review focuses on the possible ways to overcome phage resistance in phage therapy.
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Affiliation(s)
- Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland.
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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23
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Chen B, Benavente LP, Chittò M, Wychowaniec JK, Post V, D'Este M, Constant C, Zeiter S, Feng W, Moreno MG, Trampuz A, Wagemans J, Onsea J, Richards RG, Lavigne R, Moriarty TF, Metsemakers WJ. Alginate microbeads and hydrogels delivering meropenem and bacteriophages to treat Pseudomonas aeruginosa fracture-related infections. J Control Release 2023; 364:159-173. [PMID: 37866403 DOI: 10.1016/j.jconrel.2023.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Bacteriophage (phage) therapy has shown promise in treating fracture-related infection (FRI); however, questions remain regarding phage efficacy against biofilms, phage-antibiotic interaction, administration routes and dosing, and the development of phage resistance. The goal of this study was to develop a dual antibiotic-phage delivery system containing hydrogel and alginate microbeads loaded with a phage cocktail plus meropenem and evaluate efficacy against muti-drug resistant Pseudomonas aeruginosa. Two phages (FJK.R9-30 and MK.R3-15) displayed enhanced antibiotic activity against P. aeruginosa biofilms when tested in combination with meropenem. The antimicrobial activity of both antibiotic and phage was retained for eight days at 37 °C in dual phage and antibiotic loaded hydrogel with microbeads (PA-HM). In a mouse FRI model, phages were recovered from all tissues within all treatment groups receiving dual PA-HM. Moreover, animals that received the dual PA-HM either with or without systemic antibiotics had less incidence of phage resistance and less serum neutralization compared to phages in saline. The dual PA-HM could reduce bacterial load in soft tissue when combined with systemic antibiotics, although the infection was not eradicated. The use of alginate microbeads and injectable hydrogel for controlled release of phages and antibiotics, leads to the reduced development of phage resistance and lower exposure to the adaptive immune system, which highlights the translational potential of the dual PA-HM. However, further optimization of phage therapy and its delivery system is necessary to achieve higher bacterial killing activity in vivo in the future.
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Affiliation(s)
- Baixing Chen
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium; AO Research Institute Davos, Davos, Switzerland
| | - Luis Ponce Benavente
- Center for Musculoskeletal Surgery Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | | | | | | | | | | | | | - Wenli Feng
- AO Research Institute Davos, Davos, Switzerland
| | - Mercedes González Moreno
- Center for Musculoskeletal Surgery Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andrej Trampuz
- Center for Musculoskeletal Surgery Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | | | - Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | - Willem-Jan Metsemakers
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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24
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Chen T, Du H, Zhou H, He Y, Yang J, Li C, Wei C, Yu D, Wan H. Yinhuapinggan granule ameliorates lung injury caused by multidrug-resistant Acinetobacter baumannii via inhibiting NF-κB/NLRP3 pathway. Heliyon 2023; 9:e21871. [PMID: 38027639 PMCID: PMC10661428 DOI: 10.1016/j.heliyon.2023.e21871] [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: 05/11/2023] [Revised: 09/13/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Yinhuapinggan granule (YHPG) is a traditional Chinese medicine prescription with rich clinical experience for the treatment of colds and coughs. The aim of this study is to investigate the protective effect of YHPG on multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) infection in vivo and its potential anti-inflammatory mechanism. BALB/c mice were intranasally inoculated with MDR A. baumannii strain to establish the pneumonia infection model, and received intraperitoneally cyclophosphamide to form immunosuppression before attack. YHPG (6, 12 and 18 g/kg) was administered by gavage once a day for 3 consecutive days after infection. The protective effect of YHPG was evaluated by lung index, spleen index, thymus index, pathological changes of lung tissue and inflammatory factors (IL-1β, IL-6 and TNF-α) in serum. The expression of key targets of NF-κB/NLRP3 signaling pathway in vivo was analyzed by immunohistochemistry, immunofluorescence, reverse transcription quantitative PCR (RT-qPCR) and Western blot. The results showed that YHPG improved the lung index and its inhibition rate, immune organ indexes and lung pathological changes in infected mice, and significantly reduced IL-1β, IL-6 and TNF-α levels in serum. In addition, YHPG significantly down-regulated the mRNA and protein expression of NF-κB p65, NLRP3, ASC, Caspase-1, TNF-α, IL-6 and IL-1β in mice lung tissue. The results of the current study demonstrated that YHPG has significant protective effects on mice infected with MDR A.baumannii, which may be related to the regulation of inflammatory factors and NF-κB/NLRP3 signaling pathway, indicating that YHPG has a wide range of clinical application value and provides a theoretical basis for its treatment of MDR A.baumannii infection.
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Affiliation(s)
- Tianhang Chen
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haixia Du
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chenxing Wei
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Daojun Yu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Haitong Wan
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
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25
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Oluwarinde BO, Ajose DJ, Abolarinwa TO, Montso PK, Du Preez I, Njom HA, Ateba CN. Safety Properties of Escherichia coli O157:H7 Specific Bacteriophages: Recent Advances for Food Safety. Foods 2023; 12:3989. [PMID: 37959107 PMCID: PMC10650914 DOI: 10.3390/foods12213989] [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: 09/06/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) is typically detected on food products mainly due to cross-contamination with faecal matter. The serotype O157:H7 has been of major public health concern due to the severity of illness caused, prevalence, and management. In the food chain, the main methods of controlling contamination by foodborne pathogens often involve the application of antimicrobial agents, which are now becoming less efficient. There is a growing need for the development of new approaches to combat these pathogens, especially those that harbour antimicrobial resistant and virulent determinants. Strategies to also limit their presence on food contact surfaces and food matrices are needed to prevent their transmission. Recent studies have revealed that bacteriophages are useful non-antibiotic options for biocontrol of E. coli O157:H7 in both animals and humans. Phage biocontrol can significantly reduce E. coli O157:H7, thereby improving food safety. However, before being certified as potential biocontrol agents, the safety of the phage candidates must be resolved to satisfy regulatory standards, particularly regarding phage resistance, antigenic properties, and toxigenic properties. In this review, we provide a general description of the main virulence elements of E. coli O157:H7 and present detailed reports that support the proposals that phages infecting E. coli O157:H7 are potential biocontrol agents. This paper also outlines the mechanism of E. coli O157:H7 resistance to phages and the safety concerns associated with the use of phages as a biocontrol.
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Affiliation(s)
- Bukola Opeyemi Oluwarinde
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mahikeng 2375, South Africa; (B.O.O.); (D.J.A.); (T.O.A.); (P.K.M.)
- Antimicrobial Resistance and Phage Bio-Control Research Group (AREPHABREG), Department of Microbiology, North-West University, Mahikeng 2735, South Africa
| | - Daniel Jesuwenu Ajose
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mahikeng 2375, South Africa; (B.O.O.); (D.J.A.); (T.O.A.); (P.K.M.)
- Antimicrobial Resistance and Phage Bio-Control Research Group (AREPHABREG), Department of Microbiology, North-West University, Mahikeng 2735, South Africa
| | - Tesleem Olatunde Abolarinwa
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mahikeng 2375, South Africa; (B.O.O.); (D.J.A.); (T.O.A.); (P.K.M.)
- Antimicrobial Resistance and Phage Bio-Control Research Group (AREPHABREG), Department of Microbiology, North-West University, Mahikeng 2735, South Africa
| | - Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mahikeng 2375, South Africa; (B.O.O.); (D.J.A.); (T.O.A.); (P.K.M.)
- Antimicrobial Resistance and Phage Bio-Control Research Group (AREPHABREG), Department of Microbiology, North-West University, Mahikeng 2735, South Africa
| | - Ilse Du Preez
- Centre for Human Metabolomics, North-West University, Potchefstroom 2531, South Africa;
| | - Henry Akum Njom
- Agricultural Research Council, Private Bag X1251, Potchefstroom 2531, South Africa;
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mahikeng 2375, South Africa; (B.O.O.); (D.J.A.); (T.O.A.); (P.K.M.)
- Antimicrobial Resistance and Phage Bio-Control Research Group (AREPHABREG), Department of Microbiology, North-West University, Mahikeng 2735, South Africa
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26
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Han P, Pu M, Li Y, Fan H, Tong Y. Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae. Virol Sin 2023; 38:801-812. [PMID: 37419417 PMCID: PMC10590696 DOI: 10.1016/j.virs.2023.07.002] [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: 07/09/2023] Open
Abstract
Severe infections caused by multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) highlight the need for new therapeutics with activity against this pathogen. Phage therapy is an alternative treatment approach for multidrug-resistant K. pneumoniae infections. Here, we report a novel bacteriophage (phage) BUCT631 that can specifically lyse capsule-type K1 K. pneumoniae. Physiological characterization revealed that phage BUCT631 could rapidly adsorb to the surface of K. pneumoniae and form an obvious halo ring, and it had relatively favorable thermal stability (4-50 °C) and pH tolerance (pH = 4-12). In addition, the optimal multiplicity of infection (MOI) of phage BUCT631 was 0.01, and the burst size was approximately 303 PFU/cell. Genomic analysis showed that phage BUCT631 has double-stranded DNA (total length of 44,812 bp) with a G + C content of 54.1%, and the genome contains 57 open reading frames (ORFs) and no virulence or antibiotic resistance related genes. Based on phylogenetic analysis, phage BUCT631 could be assigned to a new species in the genus Drulisvirus of the subfamily Slopekvirinae. In addition, phage BUCT631 could quickly inhibit the growth of K. pneumoniae within 2 h in vitro and significantly elevated the survival rate of K. pneumoniae infected Galleria mellonella larvae from 10% to 90% in vivo. These studies suggest that phage BUCT631 has promising potential for development as a safe alternative for control and treatment of multidrug-resistant K. pneumoniae infection.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mingfang Pu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yahao Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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27
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Jo SJ, Kwon J, Kim SG, Lee SJ. The Biotechnological Application of Bacteriophages: What to Do and Where to Go in the Middle of the Post-Antibiotic Era. Microorganisms 2023; 11:2311. [PMID: 37764155 PMCID: PMC10534921 DOI: 10.3390/microorganisms11092311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Amid the escalating challenges of antibiotic resistance, bacterial infections have emerged as a global threat. Bacteriophages (phages), viral entities capable of selectively infecting bacteria, are gaining momentum as promising alternatives to traditional antibiotics. Their distinctive attributes, including host specificity, inherent self-amplification, and potential synergy with antibiotics, render them compelling candidates. Phage engineering, a burgeoning discipline, involves the strategic modification of bacteriophages to enhance their therapeutic potential and broaden their applications. The integration of CRISPR-Cas systems facilitates precise genetic modifications, enabling phages to serve as carriers of functional genes/proteins, thereby enhancing diagnostics, drug delivery, and therapy. Phage engineering holds promise in transforming precision medicine, addressing antibiotic resistance, and advancing diverse applications. Emphasizing the profound therapeutic potential of phages, this review underscores their pivotal role in combatting bacterial diseases and highlights their significance in the post-antibiotic era.
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Affiliation(s)
- Su Jin Jo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan City 54596, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Seung-Jun Lee
- Department of Pharmaceutical Science and Engineering, Seowon University, 377-3 Musimseoro, Seowon-gu, Cheong-ju City 28674, Republic of Korea
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28
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Forsyth JH, Barron NL, Scott L, Watson BNJ, Chisnall MAW, Meaden S, van Houte S, Raymond B. Decolonizing drug-resistant E. coli with phage and probiotics: breaking the frequency-dependent dominance of residents. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001352. [PMID: 37418300 PMCID: PMC10433417 DOI: 10.1099/mic.0.001352] [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: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Widespread antibiotic resistance in commensal bacteria creates a persistent challenge for human health. Resident drug-resistant microbes can prevent clinical interventions, colonize wounds post-surgery, pass resistance traits to pathogens or move to more harmful niches following routine interventions such as catheterization. Accelerating the removal of resistant bacteria or actively decolonizing particular lineages from hosts could therefore have a number of long-term benefits. However, removing resident bacteria via competition with probiotics, for example, poses a number of ecological challenges. Resident microbes are likely to have physiological and numerical advantages and competition based on bacteriocins or other secreted antagonists is expected to give advantages to the dominant partner, via positive frequency dependence. Since a narrow range of Escherichia coli genotypes (primarily those belonging to the clonal group ST131) cause a significant proportion of multidrug-resistant infections, this group presents a promising target for decolonization with bacteriophage, as narrow-host-range viral predation could lead to selective removal of particular genotypes. In this study we tested how a combination of an ST131-specific phage and competition from the well-known probiotic E. coli Nissle strain could displace E. coli ST131 under aerobic and anaerobic growth conditions in vitro. We showed that the addition of phage was able to break the frequency-dependent advantage of a numerically dominant ST131 isolate. Moreover, the addition of competing E. coli Nissle could improve the ability of phage to suppress ST131 by two orders of magnitude. Low-cost phage resistance evolved readily in these experiments and was not inhibited by the presence of a probiotic competitor. Nevertheless, combinations of phage and probiotic produced stable long-term suppression of ST131 over multiple transfers and under both aerobic and anaerobic growth conditions. Combinations of phage and probiotic therefore have real potential for accelerating the removal of drug-resistant commensal targets.
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Affiliation(s)
- Jessica H. Forsyth
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
- Present address: Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Natalie L. Barron
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Lucy Scott
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | | | | | - Sean Meaden
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
- Present address: Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Stineke van Houte
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
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29
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Loganathan K, Viswanathan B. Genome editing for phage design and uses for therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:203-224. [PMID: 37770172 DOI: 10.1016/bs.pmbts.2023.03.012] [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: 10/03/2023]
Abstract
The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.
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30
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Opperman CJ, Wojno J, Goosen W, Warren R. Phages for the treatment of Mycobacterium species. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:41-92. [PMID: 37770176 DOI: 10.1016/bs.pmbts.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Highly drug-resistant strains are not uncommon among the Mycobacterium genus, with patients requiring lengthy antibiotic treatment regimens with multiple drugs and harmful side effects. This alarming increase in antibiotic resistance globally has renewed the interest in mycobacteriophage therapy for both Mycobacterium tuberculosis complex and non-tuberculosis mycobacteria. With the increasing number of genetically well-characterized mycobacteriophages and robust engineering tools to convert temperate phages to obligate lytic phages, the phage cache against extensive drug-resistant mycobacteria is constantly expanding. Synergistic effects between phages and TB drugs are also a promising avenue to research, with mycobacteriophages having several additional advantages compared to traditional antibiotics due to their different modes of action. These advantages include less side effects, a narrow host spectrum, biofilm penetration, self-replication at the site of infection and the potential to be manufactured on a large scale. In addition, mycobacteriophage enzymes, not yet in clinical use, warrant further studies with their additional benefits for rupturing host bacteria thereby limiting resistance development as well as showing promise in vitro to act synergistically with TB drugs. Before mycobacteriophage therapy can be envisioned as part of routine care, several obstacles must be overcome to translate in vitro work into clinical practice. Strategies to target intracellular bacteria and selecting phage cocktails to limit cross-resistance remain important avenues to explore. However, insight into pathophysiological host-phage interactions on a molecular level and innovative solutions to transcend mycobacteriophage therapy impediments, offer sufficient encouragement to explore phage therapy. Recently, the first successful clinical studies were performed using a mycobacteriophage-constructed cocktail to treat non-tuberculosis mycobacteria, providing substantial insight into lessons learned and potential pitfalls to avoid in order to ensure favorable outcomes. However, due to mycobacterium strain variation, mycobacteriophage therapy remains personalized, only being utilized in compassionate care cases until there is further regulatory approval. Therefore, identifying the determinants that influence clinical outcomes that can expand the repertoire of mycobacteriophages for therapeutic benefit, remains key for their future application.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.
| | - Justyna Wojno
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa; Lancet Laboratories, Cape Town, South Africa
| | - Wynand Goosen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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31
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Ali Y, Inusa I, Sanghvi G, Mandaliya V, Bishoyi AK. The current status of phage therapy and its advancement towards establishing standard antimicrobials for combating multi drug-resistant bacterial pathogens. Microb Pathog 2023:106199. [PMID: 37336428 DOI: 10.1016/j.micpath.2023.106199] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
Phage therapy; a revived antimicrobial weapon, has great therapeutic advantages with the main ones being its ability to eradicate multidrug-resistant pathogens as well as selective toxicity, which ensures that beneficial microbiota is not harmed, unlike antibiotics. These therapeutic properties make phage therapy a novel approach for combating resistant pathogens. Since millions of people across the globe succumb to multidrug-resistant infections, the implementation of phage therapy as a standard antimicrobial could transform global medicine as it offers greater therapeutic advantages than conventional antibiotics. Although phage therapy has incomplete clinical data, such as a lack of standard dosage and the ideal mode of administration, the conducted clinical studies report its safety and efficacy in some case studies, and therefore, this could lessen the concerns of its skeptics. Since its discovery, the development of phage therapeutics has been in a smooth progression. Concerns about phage resistance in populations of pathogenic bacteria are raised when bacteria are exposed to phages. Bacteria can use restriction-modification, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) defense, or mutations in the phage receptors to prevent phage invasion. Phage resistance, however, is often costly for the bacteria and may lead to a reduction in its virulence. The ongoing competition between bacteria and phage, on the other hand, ensures the emergence of phage strains that have evolved to infect resistant bacteria. A phage can quickly adapt by altering one or more aspects of its mode of infection, evading a resistance mechanism through genetic modifications, or directly thwarting the CRISPR-Cas defense. Using phage-bacterium coevolution as a technique could be crucial in the development of phage therapy as well. Through its recent advancement, gene-editing tools such as CRISPR-Cas allow the bioengineering of phages to produce phage cocktails that have broad spectrum activities, which could maximize the treatment's efficacy. This review presents the current state of phage therapy and its progression toward establishing standard medicine for combating antibiotic resistance. Recent clinical trials of phage therapy, some important case studies, and other ongoing clinical studies of phage therapy are all presented in this review. Furthermore, the recent advancement in the development of phage therapeutics, its application in various sectors, and concerns regarding its implementation are also highlighted here. Phage therapy has great potential and could help the fight against drug-resistant bacterial pathogens.
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Affiliation(s)
- Yussuf Ali
- Department of Microbiology, Marwadi University, Gujarat, India
| | - Ibrahim Inusa
- Department of Information Technology, Marwadi University, Gujarat, India
| | - Gaurav Sanghvi
- Department of Microbiology, Marwadi University, Gujarat, India
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Naknaen A, Samernate T, Wannasrichan W, Surachat K, Nonejuie P, Chaikeeratisak V. Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria. Sci Rep 2023; 13:8921. [PMID: 37264114 DOI: 10.1038/s41598-023-36034-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Wichanan Wannasrichan
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Cell and Biomolecular Imaging Research Unit (CBIRU), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Samir S. Phages for treatment of Staphylococcus aureus infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:275-302. [PMID: 37739558 DOI: 10.1016/bs.pmbts.2023.03.027] [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
Combating multi-drug resistant bacterial infections should be a universal urgency. The gram- positive Staphylococcus aureus (S. aureus) bacteria are generally harmless; healthy people frequently have them on their skin and nose. These bacteria, for the most part, produce no difficulties or only minor skin diseases. Antibiotics and cleansing of the affected region are usually the treatments of choice. S. aureus can become virulent causing serious infections that may lead to pustules to sepsis or death. Normally, it is thought that antibiotics may solve problems concerning bacterial infection; but unfortunately, Staphylococci have evolved mechanisms to resist drugs. Methicillin-Resistant Staphylococcus aureus (MRSA); both in hospitals and in the community, infections are evolving into dangerous pathogens. Health care practitioners may need to use antibiotics with more adverse effects to treat antibiotic-resistant S. aureus infections. Amid existing efforts to resolve this problem, phage therapy proposes a hopeful alternate to face Staphylococcal infections. When the majority of antibiotics have failed to treat infections caused by multidrug-resistant bacteria, such as methicillin- and vancomycin-resistant S. aureus, phage therapy may be an option. Here, we appraise the potential efficacy, current knowledge on bacteriophages for S. aureus, experimental research and information on their clinical application, and limitations of phage therapy for S. aureus infections.
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Affiliation(s)
- Safia Samir
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt.
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Petrovic Fabijan A, Iredell J, Danis-Wlodarczyk K, Kebriaei R, Abedon ST. Translating phage therapy into the clinic: Recent accomplishments but continuing challenges. PLoS Biol 2023; 21:e3002119. [PMID: 37220114 PMCID: PMC10204993 DOI: 10.1371/journal.pbio.3002119] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Phage therapy is a medical form of biological control of bacterial infections, one that uses naturally occurring viruses, called bacteriophages or phages, as antibacterial agents. Pioneered over 100 years ago, phage therapy nonetheless is currently experiencing a resurgence in interest, with growing numbers of clinical case studies being published. This renewed enthusiasm is due in large part to phage therapy holding promise for providing safe and effective cures for bacterial infections that traditional antibiotics acting alone have been unable to clear. This Essay introduces basic phage biology, provides an outline of the long history of phage therapy, highlights some advantages of using phages as antibacterial agents, and provides an overview of recent phage therapy clinical successes. Although phage therapy has clear clinical potential, it faces biological, regulatory, and economic challenges to its further implementation and more mainstream acceptance.
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Affiliation(s)
- Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia
| | - Katarzyna Danis-Wlodarczyk
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Razieh Kebriaei
- P3 Research Laboratory, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, United States of America
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Hitchcock NM, Devequi Gomes Nunes D, Shiach J, Valeria Saraiva Hodel K, Dantas Viana Barbosa J, Alencar Pereira Rodrigues L, Coler BS, Botelho Pereira Soares M, Badaró R. Current Clinical Landscape and Global Potential of Bacteriophage Therapy. Viruses 2023; 15:v15041020. [PMID: 37113000 PMCID: PMC10146840 DOI: 10.3390/v15041020] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
In response to the global spread of antimicrobial resistance, there is an increased demand for novel and innovative antimicrobials. Bacteriophages have been known for their potential clinical utility in lysing bacteria for almost a century. Social pressures and the concomitant introduction of antibiotics in the mid-1900s hindered the widespread adoption of these naturally occurring bactericides. Recently, however, phage therapy has re-emerged as a promising strategy for combatting antimicrobial resistance. A unique mechanism of action and cost-effective production promotes phages as an ideal solution for addressing antibiotic-resistant bacterial infections, particularly in lower- and middle-income countries. As the number of phage-related research labs worldwide continues to grow, it will be increasingly important to encourage the expansion of well-developed clinical trials, the standardization of the production and storage of phage cocktails, and the advancement of international collaboration. In this review, we discuss the history, benefits, and limitations of bacteriophage research and its current role in the setting of addressing antimicrobial resistance with a specific focus on active clinical trials and case reports of phage therapy administration.
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Affiliation(s)
| | - Danielle Devequi Gomes Nunes
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40291-710, BA, Brazil
| | - Job Shiach
- School of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Katharine Valeria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | - Josiane Dantas Viana Barbosa
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
| | | | - Brahm Seymour Coler
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Milena Botelho Pereira Soares
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40291-710, BA, Brazil
| | - Roberto Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems, University Center SENAI/CIMATEC, Salvador 41650-010, BA, Brazil
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Abd-Allah IM, El-Housseiny GS, Al-Agamy MH, Radwan HH, Aboshanab KM, Hassouna NA. Statistical optimization of a podoviral anti-MRSA phage CCASU-L10 generated from an under sampled repository: Chicken rinse. Front Cell Infect Microbiol 2023; 13:1149848. [PMID: 37065190 PMCID: PMC10102507 DOI: 10.3389/fcimb.2023.1149848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionThe insurgence of antimicrobial resistance is an imminent health danger globally. A wide range of challenging diseases are attributed to methicillin-resistant Staphylococcus aureus (MRSA) as it is weaponized with a unique array of virulence factors, and most importantly, the resistance it develops to most of the antibiotics used clinically. On that account, the present study targeted the optimization of the production of a bacteriophage active against MRSA, and evaluating some of its characters.Methods and resultsThe bacteriophage originated from a quite peculiar environmental source, raw chicken rinse and was suggested to belong to Podoviridae, order Caudovirales. It withstood a variety of extreme conditions and yield optimization was accomplished via the D-optimal design by response surface methodology (RSM). A reduced quadratic model was generated, and the ideal production conditions recommended were pH 8, glycerol 0.9% v/v, peptone 0.08% w/v, and 107 CFU/ml as the host inoculum size. These conditions led to a two-log fold increase in the phage titer (1.17x10¹² PFU/ml), as compared to the regular conditions.DiscussionTo conclude, statistical optimization successfully enhanced the output of the podoviral phage titer by two-log fold and therefore, can be regarded as a potential scale-up strategy. The produced phage was able to tolerate extreme environmental condition making it suitable for topical pharmaceutical preparations. Further preclinical and clinical studies are required to ensure its suitability for use in human.
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Affiliation(s)
- Israa M. Abd-Allah
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abbassia, Cairo, Egypt
| | - Ghadir S. El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abbassia, Cairo, Egypt
- *Correspondence: Ghadir S. El-Housseiny, ; Khaled M. Aboshanab,
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Hesham H. Radwan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abbassia, Cairo, Egypt
- *Correspondence: Ghadir S. El-Housseiny, ; Khaled M. Aboshanab,
| | - Nadia A. Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abbassia, Cairo, Egypt
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Teklemariam AD, Al Hindi R, Qadri I, Alharbi MG, Hashem AM, Alrefaei AA, Basamad NA, Haque S, Alamri T, Harakeh S. Phage cocktails - an emerging approach for the control of bacterial infection with major emphasis on foodborne pathogens. Biotechnol Genet Eng Rev 2023:1-29. [PMID: 36927397 DOI: 10.1080/02648725.2023.2178870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Phage therapy has recently attracted a great deal of attention to counteract the rapid emergence of antibiotic-resistant bacteria. In comparison to monophage therapy, phage cocktails are typically used to treat individual and/or multi-bacterial infections since the bacterial agents are unlikely to become resistant as a result of exposure to multiple phages simultaneously. The bacteriolytic effect of phage cocktails may produce efficient killing effect in comparison to individual phage. However, multiple use of phages (complex cocktails) may lead to undesirable side effects such as dysbiosis, horizontal gene transfer, phage resistance, cross resistance, and/or higher cost of production. Cocktail formulation, therefore, representa compromise between limiting the complexity of the cocktail and achieving substantial bacterial load reduction towards the targeted host organisms. Despite some constraints, the applications of monophage therapy have been well documented in the literature. However, phage cocktails-based approaches and their role for the control of pathogens have not been well investigated. In this review, we discuss the principle of phage cocktail formulations, their optimization strategies, major phage cocktail preparations, and their efficacy in inactivating various food borne bacterial pathogens.
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Affiliation(s)
- Addisu D Teklemariam
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rashad Al Hindi
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona G Alharbi
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccine and Immunotherapy Unit, King Fahd Medical Research Center, Jeddah, Saudi Arabia
| | - Abdullah A Alrefaei
- Molecular Virology Department, King Fahad General Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Najlaa A Basamad
- Parasitology Department, King Fahad General Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia.,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese, American University, Beirut, Lebanon.,Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Turki Alamri
- Family and community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Topical phage therapy in a mouse model of Cutibacterium acnes-induced acne-like lesions. Nat Commun 2023; 14:1005. [PMID: 36813793 PMCID: PMC9947178 DOI: 10.1038/s41467-023-36694-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Acne vulgaris is a common neutrophil-driven inflammatory skin disorder in which Cutibacterium acnes (C. acnes) is known to play a key role. For decades, antibiotics have been widely employed to treat acne vulgaris, inevitably resulting in increased bacterial antibiotic resistance. Phage therapy is a promising strategy to combat the growing challenge of antibiotic-resistant bacteria, utilizing viruses that specifically lyse bacteria. Herein, we explore the feasibility of phage therapy against C. acnes. Eight novel phages, isolated in our laboratory, and commonly used antibiotics eradicate 100% of clinically isolated C. acnes strains. Topical phage therapy in a C. acnes-induced acne-like lesions mouse model affords significantly superior clinical and histological scores. Moreover, the decrease in inflammatory response was reflected by the reduced expression of chemokine CXCL2, neutrophil infiltration, and other inflammatory cytokines when compared with the infected-untreated group. Overall, these findings indicate the potential of phage therapy for acne vulgaris as an additional tool to conventional antibiotics.
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Wang M, Zhu H, Wei J, Jiang L, Jiang L, Liu Z, Li R, Wang Z. Uncovering the determinants of model Escherichia coli strain C600 susceptibility and resistance to lytic T4-like and T7-like phage. Virus Res 2023; 325:199048. [PMID: 36681192 DOI: 10.1016/j.virusres.2023.199048] [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: 08/11/2022] [Revised: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
As antimicrobial resistance (AMR) continues to increase, the therapeutic use of phages has re-emerged as an attractive alternative. However, knowledge of phage resistance development and bacterium-phage interaction complexity are still not fully interpreted. In this study, two lytic T4-like and T7-like phage infecting model Escherichia coli strain C600 are selected, and host genetic determinants involved in phage susceptibility and resistance are also identified using TraDIS strategy. Isolation and identification of the lytic T7-like show that though it belongs to the phage T7 family, genes encoding replication and transcription protein exhibit high differences. The TraDIS results identify a huge number of previously unidentified genes involved in phage infection, and a subset (six in susceptibility and nine in resistance) are shared under pressure of the two kinds of lytic phage. Susceptible gene wbbL has the highest value and implies the important role in phage susceptibility. Importantly, two susceptible genes QseE (QseE/QseF) and RstB (RstB/RstA), encoding the similar two-component system sensor histidine kinase (HKs), also identified. Conversely and strangely, outer membrane protein gene ompW, unlike the gene ompC encoding receptor protein of T4 phage, was shown to provide phage resistance. Overall, this study exploited a genome-wide fitness assay to uncover susceptibility and resistant genes, even the shared genes, important for the E. coli strain of both most popular high lytic T4-like and T7-like phages. This knowledge of the genetic determinants can be further used to analysis the behind function signatures to screen the potential agents to aid phage killing of MDR pathogens, which will greatly be valuable in improving the phage therapy outcome in fighting with microbial resistance.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China.
| | - Heng Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China; International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, Jiangsu 225009, China.
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Gaborieau B, Debarbieux L. The role of the animal host in the management of bacteriophage resistance during phage therapy. Curr Opin Virol 2023; 58:101290. [PMID: 36512896 DOI: 10.1016/j.coviro.2022.101290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/29/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022]
Abstract
Multi-drug-resistant bacteria are associated with significantly higher morbidity and mortality. The possibilities for discovering new antibiotics are limited, but phage therapy - the use of bacteriophages (viruses infecting bacteria) to cure infections - is now being investigated as an alternative or complementary treatment to antibiotics. However, one of the major limitations of this approach lies in the antagonistic coevolution between bacteria and bacteriophages, which determines the ultimate success or failure of phage therapy. Here, we review the possible influence of the animal host on phage resistance and its consequences for the efficacy of phage therapy. We also discuss the value of in vitro assays for anticipating the dynamics of phage resistance observed in vivo.
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Affiliation(s)
- Baptiste Gaborieau
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France; Université Paris Cité, INSERM UMR1137, IAME, Paris, France; APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France.
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Repetitive Exposure to Bacteriophage Cocktails against Pseudomonas aeruginosa or Escherichia coli Provokes Marginal Humoral Immunity in Naïve Mice. Viruses 2023; 15:v15020387. [PMID: 36851601 PMCID: PMC9964535 DOI: 10.3390/v15020387] [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: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Phage therapy of ventilator-associated pneumonia (VAP) is of great interest due to the rising incidence of multidrug-resistant bacterial pathogens. However, natural or therapy-induced immunity against therapeutic phages remains a potential concern. In this study, we investigated the innate and adaptive immune responses to two different phage cocktails targeting either Pseudomonas aeruginosa or Escherichia coli-two VAP-associated pathogens-in naïve mice without the confounding effects of a bacterial infection. Active or UV-inactivated phage cocktails or buffers were injected intraperitoneally daily for 7 days in C57BL/6J wild-type mice. Blood cell analysis, flow cytometry analysis, assessment of phage distribution and histopathological analysis of spleens were performed at 6 h, 10 days and 21 days after treatment start. Phages reached the lungs and although the phage cocktails were slightly immunogenic, phage injections were well tolerated without obvious adverse effects. No signs of activation of innate or adaptive immune cells were observed; however, both active phage cocktails elicited a minimal humoral response with secretion of phage-specific antibodies. Our findings show that even repetitive injections lead only to a minimal innate and adaptive immune response in naïve mice and suggest that systemic phage treatment is thus potentially suitable for treating bacterial lung infections.
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Akram F, Imtiaz M, Haq IU. Emergent crisis of antibiotic resistance: A silent pandemic threat to 21 st century. Microb Pathog 2023; 174:105923. [PMID: 36526035 DOI: 10.1016/j.micpath.2022.105923] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Antibiotic resistance has become an indispensably alarming menace to the global community. The primary factors are overuse and abuse of antibiotics, lack of novel medicines under development, the health care industry's focus on profit, and the absence of diagnostic testing prior to the prescription of antibiotics. Additionally, over the past few decades, the main factors contributing to the global spread of antibiotic resistance have been the overuse of antibiotics in livestock and other animals, drug efficacy, development of fewer new vaccines, environmental toxicity, transmission through travel, and lack of funding for healthcare research and development. These factors have accelerated resistance in microorganisms through structural and functional modifications in bacteria such as reduced drug permeability, increased efflux pumps, enzymatic antibiotic modification, and change in drug target, intracellular infection, and biofilm creation. There has been an increase in resistance during the pandemic and among cancer patients due to improper prescriptions. A number of modern therapeutic alternatives have been developed to curb widespread antibiotic resistance such as nanoparticle, bacteriophage, and antimicrobial biochemical approaches. It is high time to explore new alternatives to curtail enormous increase in resistant pathogens which could be an incurable global confrontation. This review highlights the complete insight on the global drivers of resistance along with the modes of action and impacts, finally discussing the latest therapeutic alternatives.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Memoona Imtiaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
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43
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Mitropoulou G, Koutsokera A, Csajka C, Blanchon S, Sauty A, Brunet JF, von Garnier C, Resch G, Guery B. Phage therapy for pulmonary infections: lessons from clinical experiences and key considerations. Eur Respir Rev 2022; 31:31/166/220121. [PMID: 36198417 DOI: 10.1183/16000617.0121-2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022] Open
Abstract
Lower respiratory tract infections lead to significant morbidity and mortality. They are increasingly caused by multidrug-resistant pathogens, notably in individuals with cystic fibrosis, hospital-acquired pneumonia and lung transplantation. The use of bacteriophages (phages) to treat bacterial infections is gaining growing attention, with numerous published cases of compassionate treatment over the last few years. Although the use of phages appears safe, the lack of standardisation, the significant heterogeneity of published studies and the paucity of robust efficacy data, alongside regulatory hurdles arising from the existing pharmaceutical legislation, are just some of the challenges phage therapy has to overcome. In this review, we discuss the lessons learned from recent clinical experiences of phage therapy for the treatment of pulmonary infections. We review the key aspects, opportunities and challenges of phage therapy regarding formulations and administration routes, interactions with antibiotics and the immune system, and phage resistance. Building upon the current knowledge base, future pre-clinical studies using emerging technologies and carefully designed clinical trials are expected to enhance our understanding and explore the therapeutic potential of phage therapy.
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Affiliation(s)
- Georgia Mitropoulou
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland .,University of Lausanne, Lausanne, Switzerland.,Shared first authorship
| | - Angela Koutsokera
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.,University of Lausanne, Lausanne, Switzerland.,Shared first authorship
| | - Chantal Csajka
- Centre for Research and Innovation in Clinical Pharmaceutical Sciences, Lausanne University Hospital, Lausanne, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, University of Lausanne, Geneva, Switzerland.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Sylvain Blanchon
- University of Lausanne, Lausanne, Switzerland.,Paediatric Pulmonology and Cystic Fibrosis Unit, Division of Paediatrics, Department of Woman-Mother-Child, Lausanne University Hospital, Lausanne, Switzerland
| | - Alain Sauty
- University of Lausanne, Lausanne, Switzerland.,Division of Pulmonology, Neuchâtel Hospital Network, Neuchâtel, Switzerland
| | - Jean-Francois Brunet
- University of Lausanne, Lausanne, Switzerland.,Cell Production Centre, Dept of Interdisciplinary Centres, Lausanne University Hospital, Lausanne, Switzerland
| | - Christophe von Garnier
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.,University of Lausanne, Lausanne, Switzerland
| | - Grégory Resch
- University of Lausanne, Lausanne, Switzerland.,Centre for Research and Innovation in Clinical Pharmaceutical Sciences, Lausanne University Hospital, Lausanne, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, University of Lausanne, Geneva, Switzerland.,Shared last authorship
| | - Benoit Guery
- University of Lausanne, Lausanne, Switzerland.,Service of Infectious Diseases, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.,Shared last authorship
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44
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Vallenas-Sánchez YPA, Bautista-Valles MF, Llaque-Chávarri F, Mendoza-Coello ME. Bacteriophage cocktail as a substitute for antimicrobials in companion animal dermatology. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090200097x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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45
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Vallenas-Sánchez YPA, Bautista-Valles MF, Llaque-Chávarri F, Mendoza-Coello ME. Cóctel de bacteriófagos como sustituto de antimicrobianos en dermatología de animales de compañía. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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46
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Daubie V, Chalhoub H, Blasdel B, Dahma H, Merabishvili M, Glonti T, De Vos N, Quintens J, Pirnay JP, Hallin M, Vandenberg O. Determination of phage susceptibility as a clinical diagnostic tool: A routine perspective. Front Cell Infect Microbiol 2022; 12:1000721. [PMID: 36211951 PMCID: PMC9532704 DOI: 10.3389/fcimb.2022.1000721] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.
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Affiliation(s)
- Valéry Daubie
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Houssein Chalhoub
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bob Blasdel
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Hafid Dahma
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Nathalie De Vos
- Department of Clinical Chemistry, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Johan Quintens
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- *Correspondence: Olivier Vandenberg,
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47
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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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48
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
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49
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Erol HB, Kaskatepe B, Ozturk S, Safi Oz Z. The comparison of lytic activity of isolated phage and commercial Intesti bacteriophage on ESBL producer E. coli and determination of Ec_P6 phage efficacy with in vivo Galleria mellonella larvae model. Microb Pathog 2022; 167:105563. [PMID: 35513294 DOI: 10.1016/j.micpath.2022.105563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Antibiotic resistance is one of the crucial public health challenges. As a result of rising resistance, as an alternative to antimicrobials, demands for bacteriophage therapy have increased significantly over the years. The objective of this study was to isolate and characterize potentially therapeutic phages active against Escherichia coli (E. coli) and compare the efficacy with commercial Intesti bacteriophage on the extended-spectrum beta-lactamase (ESBL) positive E. coli (ESBL-EC) and performed the effectiveness of bacteriophage using the Galleria mellonella (G. mellonella) larvae model. Intesti bacteriophage is a polyvalent bacteriophage-based drug. The isolated bacteriophages were obtained from the river and clinical isolates of E. coli were used for the enrichment of bacteriophage isolation. The phages were first screened based on plaque morphology and host ranges determined on clinical strains. The susceptibility of phages was determined against 50 clinical isolates of E. coli and eight different laboratory isolates using the spot test technique. E. coli lytic phage Ec_P6 was used to determine the therapeutic and preventive effects on the G. mellonella larvae model. The slides were prepared by G. mellonella hemolymph for cytologic examination, stained with May Grünwald Giemsa (MGG), and evaluated by light microscopy. The results of the activities revealed lytic spectra ranging from 24% to 97%. Overall strains were susceptible to one or more phages from the panel. It was proved that Intesti bacteriophage is very effective in a wide variety of strains of E. coli including test strains, also showed that isolated Ec_P6 phage is as effective as commercial phage. The best MOI of this phage was 0.01, and infectivity decreased above 60 °C. The results suggest that phage is stable at pH values ranging between 5.0 and 9.0. In vivo study was found that in E. coli infection to achieve a survival high rate the infected larvae should be after 2 hours treated with 0.01 MOI phage (10 μL, 106 PFU/mL) and colistin doses (10 μL, 2.5 mg/kg). It also prevented infection, increasing the survival of the larvae compared to the untreated control group. Ec_P6 phage was found to have a potential for the treatment of E. coli infections.
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Affiliation(s)
- Hilal Basak Erol
- Ankara University Faculty of Pharmacy, Department of Pharmaceutical Microbiology, 06100, Ankara, Turkey
| | - Banu Kaskatepe
- Ankara University Faculty of Pharmacy, Department of Pharmaceutical Microbiology, 06100, Ankara, Turkey.
| | - Sukran Ozturk
- Zonguldak Bulent Ecevit University, Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Zonguldak, Turkey
| | - Zehra Safi Oz
- Zonguldak Bulent Ecevit University, Faculty of Medicine, Department of Medical Biology, Zonguldak, Turkey
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50
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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