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Costa P, Pereira C, Romalde JL, Almeida A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 2024; 599:110209. [PMID: 39186863 DOI: 10.1016/j.virol.2024.110209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.
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Affiliation(s)
- Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS - Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain.
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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2
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Tan S, Chen H, Huang S, Zhu B, Wu J, Chen M, Zhang J, Wang J, Ding Y, Wu Q, Yang M. Characterization of the novel phage vB_BceP_LY3 and its potential role in controlling Bacillus cereus in milk and rice. Int J Food Microbiol 2024; 421:110778. [PMID: 38861847 DOI: 10.1016/j.ijfoodmicro.2024.110778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Bacillus cereus is a foodborne pathogen that induces vomiting and diarrhea in affected individuals. It exhibits resistance to traditional sterilization methods and has a high contamination rate in dairy products and rice. Therefore, the development of a new food safety controlling strategy is necessary. In this research, we isolated and identified a novel phage named vB_BceP_LY3, which belongs to a new genus of the subfamily Northropvirinae. This phage demonstrates a short latency period and remains stable over a wide range of temperatures (4-60 °C) and pH levels (4-11). The 28,124 bp genome of LY3 does not contain any antibiotic-resistance genes or virulence factors. With regards to its antibacterial properties, LY3 not only effectively inhibits the growth of B. cereus in TSB (tryptic soy broth), but also demonstrates significant inhibitory effects in various food matrices. Specifically, LY3 treatment at 4 °C with a high MOI (MOI = 10,000) can maintain B. cereus levels below the detection limit for up to 24 h in milk. LY3 represents a safe and promising biocontrol agent against B. cereus, possessing long-term antibacterial capabilities and stability.
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Affiliation(s)
- Shilin Tan
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Hanfang Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Shixuan Huang
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Bin Zhu
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Junquan Wu
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Moutong Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jumei Zhang
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yu Ding
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Qingping Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China.
| | - Meiyan Yang
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China.
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Li S, Wei B, Xu L, Cong C, Murtaza B, Wang L, Li X, Li J, Xu M, Yin J, Xu Y. A novel Saclayvirus Acinetobacter baumannii phage genomic analysis and effectiveness in preventing pneumonia. Appl Microbiol Biotechnol 2024; 108:428. [PMID: 39066795 PMCID: PMC11283397 DOI: 10.1007/s00253-024-13208-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/12/2024] [Accepted: 05/27/2024] [Indexed: 07/30/2024]
Abstract
Acinetobacter baumannii, which is resistant to multiple drugs, is an opportunistic pathogen responsible for severe nosocomial infections. With no antibiotics available, phages have obtained clinical attention. However, since immunocompromised patients are often susceptible to infection, the appropriate timing of administration is particularly important. During this research, we obtained a lytic phage vB_AbaM_P1 that specifically targets A. baumannii. We then assessed its potential as a prophylactic treatment for lung infections caused by clinical strains. The virus experiences a period of inactivity lasting 30 min and produces approximately 788 particles during an outbreak. Transmission electron microscopy shows that vB_AbaM_P1 was similar to the Saclayvirus. Based on the analysis of high-throughput sequencing and bioinformatics, vB_AbaM_P1 consists of 107537 bases with a G + C content of 37.68%. It contains a total of 177 open reading frames and 14 tRNAs. No antibiotic genes were detected. In vivo experiments, using a cyclophosphamide-induced neutrophil deficiency model, tested the protective effect of phage on neutrophil-deficient rats by prophylactic application of phage. The use of phages resulted in a decrease in rat mortality caused by A. baumannii and a reduction in the bacterial burden in the lungs. Histologic examination of lung tissue revealed a decrease in the presence of immune cells. The presence of phage vB_AbaM_P1 had a notable impact on preventing A. baumannii infection, as evidenced by the decrease in oxidative stress in lung tissue and cytokine levels in serum. Our research offers more robust evidence for the early utilization of bacteriophages to mitigate A. baumannii infection. KEY POINTS: •A novel Saclayvirus phage infecting A. baumannii was isolated from sewage. •The whole genome was determined, analyzed, and compared to other phages. •Assaying the effect of phage in preventing infection in neutrophil-deficient models.
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Affiliation(s)
- Shibin Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed Science, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Le Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Cong Cong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jibin Li
- Liaoning Innovation Center for Phage Application Professional Technology, Dalian, 116620, Liaoning, China
| | - Mu Xu
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, 116620, China
| | - Jiajun Yin
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116300, China.
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116300, China.
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Subramanian A. Emerging roles of bacteriophage-based therapeutics in combating antibiotic resistance. Front Microbiol 2024; 15:1384164. [PMID: 39035437 PMCID: PMC11257900 DOI: 10.3389/fmicb.2024.1384164] [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: 02/08/2024] [Accepted: 06/06/2024] [Indexed: 07/23/2024] Open
Abstract
Amid the growing challenge of antibiotic resistance on a global scale, there has been a notable resurgence in bacteriophage-based treatments, signaling a shift in our approach to managing infections. Bacteriophages (BPs), bacterial predators of nature, present a promising alternative for tackling infections caused by antibiotic-resistant pathogens. This review delves into the intricate relationship between bacteriophages and resistant bacteria, exploring various treatment strategies. Drawing upon both preclinical and clinical studies, the review highlights the effectiveness of bacteriophage therapy, particularly when integrated synergistically with conventional antibiotics. It discusses various treatment approaches for systemic and localized infections, demonstrating the adaptability of bacteriophage therapy across different clinical scenarios. Furthermore, the formulation and delivery of bacteriophages shed light on the various methods used to encapsulate and administer them effectively. It also acknowledges the challenge of bacterial resistance to bacteriophages and the ongoing efforts to overcome this hurdle. In addition, this review highlights the importance of the bacteriophage sensitivity profile (phagogram), which helps tailor treatment regimens to individual patients and specific pathogens. By surpassing the limitations of traditional antibiotics, bacteriophage-based therapies offer a personalized and potent solution against antibiotic resistance, promising to reshape the future of infectious disease management.
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Wei X, Qian S, Yang Y, Mo J. Microbiome-based therapies for periodontitis and peri-implantitis. Oral Dis 2024; 30:2838-2857. [PMID: 37890080 DOI: 10.1111/odi.14782] [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: 05/03/2023] [Revised: 09/16/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVES Periodontitis and peri-implantitis are oral infectious-inflammatory diseases associated with oral microbial dysbiosis. Microbiome-based therapies, characterized by manipulation of the microbiota, are emerging as promising therapeutic approaches to resolve the microbial dysbiosis and associated dysregulation of immune system. This review aims at summarizing recent progress on microbiome-based therapies in periodontitis and peri-implantitis, promoting a further understanding of the related therapeutic mechanisms. SUBJECTS AND METHODS Pertinent literatures focused on microbiome-based therapies for periodontitis and peri-implantitis are obtained from PubMed and Web of Science. RESULTS In this article, we review the roles and therapeutic mechanisms of four microbiome-based therapies, including probiotics, postbiotics, predatory bacteria and phages, and microbiota transplantation, in the management of periodontitis and peri-implantitis. Challenges facing this field are also discussed, highlighting the areas that require more attention and investigation. CONCLUSIONS Microbiome-based therapies may serve as effective treatment for periodontitis and peri-implantitis. This review presents a new viewpoint to this field.
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Affiliation(s)
- Xindi Wei
- Department of Oral and Maxillo-facial Implantology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Shujiao Qian
- Department of Oral and Maxillo-facial Implantology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yijie Yang
- Department of Oral and Maxillo-facial Implantology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiaji Mo
- Department of Oral and Maxillo-facial Implantology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
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Ragab S, Gouda SM, Abdelmoteleb M, El-Shibiny A. The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study. ENVIRONMENTAL TECHNOLOGY 2024; 45:3544-3558. [PMID: 37255221 DOI: 10.1080/09593330.2023.2220886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
The spread and development of Multi-Drug Resistant (MDR) bacteria in wastewater became beyond control and a global public health concern. The conventional disinfectants used in wastewater treatment methods have been becoming increasingly ineffective against a range of pathogenic and MDR bacteria. Bacteriophages are considered a novel approach to microbial control. Therefore, this study aims to explore the possibility of using phages against pathogenic and MDR Escherichia coli strains isolated from wastewater treatment plants. The wastewater samples were collected from two different treatment plants for E. coli isolation. The antibiotic sensitivity profile and occurrence of virulence and resistant genes were tested in 28 E. coli isolates. Phage ZCEC13 was selected based on its promising activity and host range to undergo identification and characterization. ZCEC13 was evaluated by transmission electron microscopy, genomic sequencing, in vitro lytic activity and tested for its stability under different conditions such as pH, Ultraviolet light exposure, and temperature. The results reported that ZCEC13 belongs to the Caudoviricetes class, with a high antibacterial dynamic. Phage ZCEC13 displayed high stability at different pH values ranging from 2 to 12, good tolerance to temperatures from -4 to 65°C, and high stability at UV exposure for 120 min. Respectively, the findings showed stability of the phage under several conditions and high efficiency in killing MDR bacteria isolated from the treatment plants. Further studies are encouraged to analyse the efficacy of phages as a microbial control agent in wastewater treatment plants.
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Affiliation(s)
- Samar Ragab
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Shrouk Mohamed Gouda
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | | | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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Raman SK, Siva Reddy DV, Jain V, Bajpai U, Misra A, Singh AK. Mycobacteriophages: therapeutic approach for mycobacterial infections. Drug Discov Today 2024; 29:104049. [PMID: 38830505 DOI: 10.1016/j.drudis.2024.104049] [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: 01/28/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Tuberculosis (TB) is a significant global health threat, and cases of infection with non-tuberculous mycobacteria (NTM) causing lung disease (NTM-LD) are rising. Bacteriophages and their gene products have garnered interest as potential therapeutic options for bacterial infections. Here, we have compiled information on bacteriophages and their products that can kill Mycobacterium tuberculosis or NTM. We summarize the mechanisms whereby viable phages can access macrophage-resident bacteria and not elicit immune responses, review methodologies of pharmaceutical product development containing mycobacteriophages and their gene products, mainly lysins, in the context of drug regulatory requirements and we discuss industrially relevant methods for producing pharmaceutical products comprising mycobacteriophages, emphasizing delivery of mycobacteriophages to the lungs. We conclude with an outline of some recent case studies on mycobacteriophage therapy.
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Affiliation(s)
- Sunil Kumar Raman
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - D V Siva Reddy
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji , New Delhi 110019, India
| | - Amit Misra
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra 282004, Uttar Pradesh, India.
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Madi N, Cato ET, Abu Sayeed M, Creasy-Marrazzo A, Cuénod A, Islam K, Khabir MIU, Bhuiyan MTR, Begum YA, Freeman E, Vustepalli A, Brinkley L, Kamat M, Bailey LS, Basso KB, Qadri F, Khan AI, Shapiro BJ, Nelson EJ. Phage predation, disease severity, and pathogen genetic diversity in cholera patients. Science 2024; 384:eadj3166. [PMID: 38669570 DOI: 10.1126/science.adj3166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/12/2024] [Indexed: 04/28/2024]
Abstract
Despite an increasingly detailed picture of the molecular mechanisms of bacteriophage (phage)-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. In this work, we report a year-long, nationwide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative polymerase chain reaction while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of antiphage defenses, predation was "effective," with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of antiphage defenses, predation was "ineffective," with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics.
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Affiliation(s)
- Naïma Madi
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Emilee T Cato
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Md Abu Sayeed
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Ashton Creasy-Marrazzo
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Aline Cuénod
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Kamrul Islam
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Imam Ul Khabir
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Taufiqur R Bhuiyan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Yasmin A Begum
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Emma Freeman
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Anirudh Vustepalli
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Lindsey Brinkley
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Manasi Kamat
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Firdausi Qadri
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful I Khan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - B Jesse Shapiro
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- McGill Centre for Microbiome Research, McGill University, Montréal, QC, Canada
| | - Eric J Nelson
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
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Liu Y, Lin Y, Zhu W. Systemic Effects of a Phage Cocktail on Healthy Weaned Piglets. BIOLOGY 2024; 13:271. [PMID: 38666883 PMCID: PMC11048100 DOI: 10.3390/biology13040271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
Numerous studies have demonstrated that bacteriophages (phages) can effectively treat intestinal bacterial infections. However, research on the impact of phages on overall body health once they enter the intestine is limited. This study utilized weaned piglets as subjects to evaluate the systemic effects of an orally administered phage cocktail on their health. Twelve 21-day-old weaned piglets were divided into control (CON) and phage gavage (Phages) groups. The phage cocktail consisted of five lytic phages, targeting Salmonella enterica serovar Choleraesuis (S. choleraesuis), Enteropathogenic Escherichia coli (EPEC), and Shiga tox-in-producing Escherichia coli (STEC). The phages group received 10 mL of phage cocktail orally for 20 consecutive days. The results show that the phage gavage did not affect the piglets' growth performance, serum biochemical indices, or most organ indices, except for the pancreas. However, the impact on the intestine was complex. Firstly, although the pancreatic index decreased, it did not affect the secretion of digestive enzymes in the intestine. Secondly, phages increased the pH of jejunum chyme and relative weight of the ileum, and enhanced intestinal barrier function without affecting the morphology of the intestine. Thirdly, phages did not proliferate in the intestine, but altered the intestinal microbiota structure and increased concentrations of microbial metabolites isobutyric acid and isovaleric acid in the colonic chyme. In addition, phages impacted the immune status, significantly increasing serum IgA, IgG, and IgM, as well as serum and intestinal mucosal IFN-γ, IL-1β, IL-17, and TGF-β, and decreasing IL-4 and IL-10. They also activated toll-like receptors TLR-4 and TLR-9. Apart from an increase in basophil numbers, the counts of other immune cells in the blood did not change. This study indicates that the impact of phages on body health is complex, especially regarding immune status, warranting further attention. Short-term phage gavage did not have significant negative effects on health but could enhance intestinal barrier function.
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Affiliation(s)
- Yankun Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
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Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley RA. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol 2024; 98:e0147623. [PMID: 38376991 PMCID: PMC10949491 DOI: 10.1128/jvi.01476-23] [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: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
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Affiliation(s)
- Luke Acton
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Hannah V. Pye
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Rafał Kolenda
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Michaela Matthews
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - A. Keith Turner
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Muhammad Yasir
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emma Holden
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Haider Al-Khanaq
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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11
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Madi N, Cato ET, Sayeed MA, Creasy-Marrazzo A, Cuénod A, Islam K, Khabir MIUL, Bhuiyan MTR, Begum YA, Freeman E, Vustepalli A, Brinkley L, Kamat M, Bailey LS, Basso KB, Qadri F, Khan AI, Shapiro BJ, Nelson EJ. Phage predation, disease severity and pathogen genetic diversity in cholera patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.14.544933. [PMID: 37398242 PMCID: PMC10312676 DOI: 10.1101/2023.06.14.544933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite an increasingly detailed picture of the molecular mechanisms of phage-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. Here we report a year-long, nation-wide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative PCR, while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of anti-phage defenses, predation was 'effective,' with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of anti-phage defenses, predation was 'ineffective,' with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics.
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Affiliation(s)
- Naïma Madi
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Emilee T. Cato
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Md. Abu Sayeed
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Ashton Creasy-Marrazzo
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Aline Cuénod
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Kamrul Islam
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md. Imam UL. Khabir
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md. Taufiqur R. Bhuiyan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Yasmin A. Begum
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Emma Freeman
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Anirudh Vustepalli
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Lindsey Brinkley
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Manasi Kamat
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura S. Bailey
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Firdausi Qadri
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful I. Khan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - B. Jesse Shapiro
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- McGill Centre for Microbiome Research, McGill University, Montréal, QC, Canada
| | - Eric J. Nelson
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
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12
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Schmitt DS, Siegel SD, Selle K. Applications of designer phage encoding recombinant gene payloads. Trends Biotechnol 2024; 42:326-338. [PMID: 37833198 DOI: 10.1016/j.tibtech.2023.09.008] [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: 06/23/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Advances in genetic engineering, synthetic biology, and DNA sequencing have transformed the re-emergent therapeutic bacteriophage field. The increasing rate of multidrug resistant (MDR) infections and the speed at which new bacteriophages can be isolated, sequenced, characterized, and engineered has reinvigorated phage therapy and unlocked new applications of phages for modulating bacteria. The methods used to genetically engineer bacteriophages are undergoing significant development, but identification of heterologous gene payloads with desirable activity and determination of their impact on bacteria or human cells in translationally relevant applications remain underexplored areas. Here, we discuss and categorize recombinant gene payloads for their potential outcome on phage-bacteria interactions when genetically engineered into phage genomes for expression in their bacterial hosts.
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Affiliation(s)
- Daniel S Schmitt
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA
| | - Sara D Siegel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA
| | - Kurt Selle
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, USA.
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13
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Dominguez SR, Doan PN, Rivera-Chávez F. The intersection between host-pathogen interactions and metabolism during Vibrio cholerae infection. Curr Opin Microbiol 2024; 77:102421. [PMID: 38215547 DOI: 10.1016/j.mib.2023.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Vibrio cholerae (V. cholerae), the etiological agent of cholera, uses cholera toxin (CT) to cause severe diarrheal disease. Cholera is still a significant cause of mortality worldwide with about half of all cholera cases and deaths occurring in children under five. Owing to the lack of cost-effective vaccination and poor vaccine efficacy in children, there is a need for alternative preventative and therapeutic strategies. Recent advances in our knowledge of the interplay between CT-induced disease and host-pathogen metabolism have opened the door for investigating how modulation of intestinal metabolism by V. cholerae during disease impacts host intestinal immunity, the gut microbiota, and pathogen-phage interactions. In this review article, we examine recent progress in our understanding of host-pathogen interactions during V. cholerae infection and discuss future work deciphering how modulation of gut metabolism during cholera intersects these processes to enable successful fecal-oral transmission of the pathogen.
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Affiliation(s)
- Sedelia R Dominguez
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Phillip N Doan
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Fabian Rivera-Chávez
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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14
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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15
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Emencheta SC, Olovo CV, Eze OC, Kalu CF, Berebon DP, Onuigbo EB, Vila MMDC, Balcão VM, Attama AA. The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health. Pharmaceutics 2023; 15:2416. [PMID: 37896176 PMCID: PMC10609668 DOI: 10.3390/pharmaceutics15102416] [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: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.
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Affiliation(s)
- Stephen C. Emencheta
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Chinasa V. Olovo
- Department of Microbiology, University of Nigeria, Nsukka 410001, Nigeria;
| | - Osita C. Eze
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Chisom F. Kalu
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Dinebari P. Berebon
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Ebele B. Onuigbo
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
| | - Anthony A. Attama
- Department of Pharmaceutics, University of Nigeria, Nsukka 410001, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka 410001, Nigeria
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16
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Mao X, Wu Y, Ma R, Li L, Wang L, Tan Y, Li Z, Liu H, Han K, Cao Y, Li Y, Peng H, Li X, Hu C, Wang X. Oral phage therapy with microencapsulated phage A221 against Escherichia coli infections in weaned piglets. BMC Vet Res 2023; 19:165. [PMID: 37730566 PMCID: PMC10510151 DOI: 10.1186/s12917-023-03724-y] [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: 03/01/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a common pathogen that often causes diarrhea in piglets. Since bacteria are becoming more and more resistant to antibiotics, phages have become a promising alternative therapy. However, the therapy of oral phage often fails to achieve the desired effect. A novel phage named A221 was isolated by using E. coli GXXW-1103 as host strain, characterized by electron microscopy, genomic sequencing and analyzed by measuring lysis ability in vitro. RESULTS Phage A221 was identified as a member of Ackermannviridae, Aglimvirinae, Agtrevirus with 153297 bp genome and effectively inhibited bacterial growth in vitro for 16 h. This study was conducted to evaluate the therapeutic effect of oral microencapsulated phage A221 on E. coli GXXW-1103 infections in weaned piglets. The protective effect of phage was evaluated by body weight analysis, bacterial load and histopathological changes. The results showed that with the treatment of phage A221, the body weight of piglets increased, the percentage of Enterobacteriaceae in duodenum decreased to 0.64%, the lesions in cecum and duodenum were alleviated, and the bacterial load in the jejunal lymph nodes, cecum and spleen were also significantly different with infected group (P < 0.001). CONCLUSIONS The results showed that phage A221 significantly increased the daily weight gain of piglets, reduced the bacterial load of tissues and the intestinal lesions, achieved the same therapeutic effect as antibiotic Florfenicol. Taken together, oral microencapsulated phage A221 has a good therapeutic effect on bacterial diarrhea of weaned piglets, which provides guidance for the clinical application of phage therapy in the future.
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Affiliation(s)
- Xinyu Mao
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yuxing Wu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Runwen Ma
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Lei Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Leping Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yizhou Tan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Ziyong Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Hui Liu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Kaiou Han
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yajie Cao
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yinan Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Hao Peng
- Guangxi Veterinary Research Institute, Nanning, 530004, Guangxi, China
| | - Xun Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Chuanhuo Hu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Xiaoye Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China.
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China.
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17
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Beckman DA, Waters CM. Vibrio cholerae phage ICP3 requires O1 antigen for infection. Infect Immun 2023; 91:e0002623. [PMID: 37594274 PMCID: PMC10501212 DOI: 10.1128/iai.00026-23] [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: 01/13/2023] [Accepted: 06/23/2023] [Indexed: 08/19/2023] Open
Abstract
In its natural aquatic environment, the bacterial pathogen Vibrio cholerae, the causative agent of the enteric disease cholera, is in constant competition with bacterial viruses known as phages. Following ICP3 infection, V. cholerae cultures that exhibited phage killing always recovered overnight, and clones isolated from these regrowth populations exhibited complete resistance to subsequent infections. Whole-genome sequencing of these resistant mutants revealed seven distinct mutations in genes encoding for enzymes involved in O1 antigen biosynthesis, demonstrating that the O1 antigen is a previously uncharacterized putative receptor of ICP3. To further elucidate the specificity of the resistance conferred by these mutations, they were challenged with the V. cholerae-specific phages ICP1 and ICP2. All seven O1 antigen mutants demonstrated pan-resistance to ICP1 but not ICP2, which utilizes the OmpU outer membrane protein as a receptor. We show that resistant mutations to ICP1 and ICP3 evolve at a significantly higher frequency than ICP2, but these mutations have a significant fitness tradeoff to V. cholerae and are unable to evolve in the presence of an antimicrobial that mimics host cell defensins.
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Affiliation(s)
- Drew A. Beckman
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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18
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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: 3] [Impact Index Per Article: 3.0] [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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19
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Beckman DA, Waters CM. Vibrio cholerae phage ICP3 requires O1 antigen for infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526503. [PMID: 36778411 PMCID: PMC9915646 DOI: 10.1101/2023.01.31.526503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In its natural aquatic environment, the bacterial pathogen Vibrio cholerae, the causative agent of the enteric disease cholera, is in constant competition with bacterial viruses known as phages. Following ICP3 infection, V. cholerae cultures that exhibited phage killing always recovered overnight, and clones isolated from these regrowth populations exhibited complete resistance to subsequent infections. Whole genome sequencing of these resistant mutants revealed seven distinct mutations in genes encoding for enzymes involved in O1 antigen biosynthesis, demonstrating that the O1 antigen is a previously uncharacterized putative receptor of ICP3. To further elucidate the specificity of the resistance conferred by these mutations, they were challenged with the V. cholerae-specific phages ICP1 and ICP2. All seven O1 antigen mutants demonstrated pan-resistance to ICP1 but not ICP2, which utilizes the OmpU outer membrane protein as a receptor. We show that resistant mutations to ICP1 and ICP3 evolve at a significantly higher frequency than ICP2, but these mutations have a significant fitness tradeoff to V. cholerae and are unable to evolve in the presence of an antimicrobial that mimics host cell defensins.
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20
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Chaudhary N, Mohan B, Kaur H, Modgil V, Kant V, Bhatia A, Taneja N. Vibrio Phage VMJ710 Can Prevent and Treat Disease Caused by Pathogenic MDR V. cholerae O1 in an Infant Mouse Model. Antibiotics (Basel) 2023; 12:1046. [PMID: 37370365 DOI: 10.3390/antibiotics12061046] [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: 05/28/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Cholera, a disease of antiquity, is still festering in developing countries that lack safe drinking water and sewage disposal. Vibrio cholerae, the causative agent of cholera, has developed multi-drug resistance to many antimicrobial agents. In aquatic habitats, phages are known to influence the occurrence and dispersion of pathogenic V. cholerae. We isolated Vibrio phage VMJ710 from a community sewage water sample of Manimajra, Chandigarh, in 2015 during an outbreak of cholera. It lysed 46% of multidrug-resistant V. cholerae O1 strains. It had significantly reduced the bacterial density within the first 4-6 h of treatment at the three multiplicity of infection (MOI 0.01, 0.1, and 1.0) values used. No bacterial resistance was observed against phage VMJ710 for 20 h in the time-kill assay. It is nearest to an ICP1 phage, i.e., Vibrio phage ICP1_2012 (MH310936.1), belonging to the class Caudoviricetes. ICP1 phages have been the dominant bacteriophages found in cholera patients' stools since 2001. Comparative genome analysis of phage VMJ710 and related phages indicated a high level of genetic conservation. The phage was stable over a wide range of temperatures and pH, which will be an advantage for applications in different environmental settings. The phage VMJ710 showed a reduction in biofilm mass growth, bacterial dispersal, and a clear disruption of bacterial biofilm structure. We further tested the phage VMJ710 for its potential therapeutic and prophylactic properties using infant BALB/c mice. Bacterial counts were reduced significantly when phages were administered before and after the challenge of orogastric inoculation with V. cholerae serotype O1. A comprehensive whole genome study revealed no indication of lysogenic genes, genes associated with possible virulence factors, or antibiotic resistance. Based on all these properties, phage VMJ710 can be a suitable candidate for oral phage administration and could be a viable method of combatting cholera infection caused by MDR V. cholerae pathogenic strains.
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Affiliation(s)
- Naveen Chaudhary
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Vinay Modgil
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Vishal Kant
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Alka Bhatia
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
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21
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Cai L, Tian Y, Li Z, Yang Y, Ai C, Zhang R. A broad-host-range lytic phage vB_VhaS-R18L as a candidate against vibriosis. Front Microbiol 2023; 14:1191157. [PMID: 37333633 PMCID: PMC10272388 DOI: 10.3389/fmicb.2023.1191157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Vibriosis is one of the most common bacterial diseases that cause high rates of mortality and considerable economic losses in aquaculture. Phage therapy has been considered as a promising alternative method to antibiotics in the biocontrol of infectious diseases. Genome sequencing and characterization of the phage candidates are prerequisites before field applications to ensure environmental safety. In this study, a lytic phage, named vB_VhaS-R18L (R18L), was isolated from the coastal seawater of Dongshan Island, China. The phage was characterized in terms of morphology, genetic content, infection kinetics, lytic profile, and virion stability. Transmission electronic microscopy indicated that R18L is siphovirus-like, comprising an icosahedral head (diameter 88.6 ± 2.2 nm) and a long noncontractile tail (225 × 11 nm). Genome analysis indicated R18L to be a double-stranded DNA virus with a genome size of 80,965 bp and a G + C content of 44.96%. No genes that encode known toxins or genes implicated in lysogeny control were found in R18L. A one-step growth experiment showed that R18L had a latent period of approximately 40 min and a burst size of 54 phage particles per infected cell. R18L showed lytic activity against a wide range of at least five Vibrio species (V. alginolyticus, V. cholerae, V. harveyi, V. parahemolyticus, and V. proteolyticus). R18L was relatively stable at pH 6-11 and at temperatures ranging from 4°C to 50°C. The broad lytic activity across Vibrio species and the stability in the environment make R18L a potential candidate for phage therapy in controlling vibriosis in aquaculture systems.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ziqiang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunxiang Ai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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22
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Chen L, Hou X, Chu H. The Novel Role of Phage Particles in Chronic Liver Diseases. Microorganisms 2023; 11:1181. [PMID: 37317156 DOI: 10.3390/microorganisms11051181] [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: 03/20/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 06/16/2023] Open
Abstract
The gut microbiome is made up of bacteria, fungi, viruses and archaea, all of which are closely related with human health. As the main component of enterovirus, the role of bacteriophages (phages) in chronic liver disease has been gradually recognized. Chronic liver diseases, including alcohol-related liver disease and nonalcoholic fatty liver disease, exhibit alterations of the enteric phages. Phages shape intestinal bacterial colonization and regulate bacterial metabolism. Phages adjoining to intestinal epithelial cells prevent bacteria from invading the intestinal barrier, and mediate intestinal inflammatory response. Phages are also observed increasing intestinal permeability and migrating to peripheral blood and organs, likely contributing to inflammatory injury in chronic liver diseases. By preying on harmful bacteria, phages can improve the gut microbiome of patients with chronic liver disease and thus act as an effective treatment method.
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Affiliation(s)
- Liuying Chen
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
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23
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Mittal M, Tripathi S, Saini A, Mani I. Phage for treatment of Vibrio cholerae infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:21-39. [PMID: 37770173 DOI: 10.1016/bs.pmbts.2023.03.021] [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
Bacteriophages (or "phages") are ubiquitous and the amplest biological entities on our planet. It is a natural enemy of bacteria. Cholera is one of the most known diseases to cause multiple pandemics around the world, killing millions of people. The pathogen of cholera is Vibrio species. Up until the emergence of multidrug resistance, preventive therapeutics like antibiotics were the most effective means of battling bacteria. Globally, one of the most significant challenges in treating microbial infections is the development of drug-resistant strains. Based on their antibacterial properties and unique characteristics, phages are being comprehensively evaluated taxonomically. Moreover, phage-based vaccination is evolving as one of the most encouraging preventive approaches. Due to this, its related research got remarkable recognition. However, due to the rapid emergence of bacterial resistance to antibiotics, the use of phages (phage therapy) could be a major motive for research because the most promising solution lies in bacteriophages. This chapter briefly highlights the promising use of bacteriophages to combat Vibrio-related infectious diseases.
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Affiliation(s)
- Milky Mittal
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Surbhi Tripathi
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Ashok Saini
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India.
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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24
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Williams J, Burton N, Dhanoa G, Sagona AP. Host-phage interactions and modeling for therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:127-158. [PMID: 37739552 DOI: 10.1016/bs.pmbts.2023.03.010] [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
Phage are drivers of numerous ecological processes on the planet and have the potential to be developed into a therapy alternative to antibiotics. Phage at all points of their life cycle, from initiation of infection to their release, interact with their host in some manner. More importantly, to harness their antimicrobial potential it is vital to understand how phage interact with the eukaryotic environment in the context of applying phage for therapy. In this chapter, the various mechanisms of phage interplay with their hosts as part of their natural life cycle are discussed in depth for Gram-positive and negative bacteria. Further, the literature surrounding the various models utilized to develop phage as a therapeutic are examined, and how these models may improve our understanding of phage-host interactions and current progress in utilizing phage for therapy in the clinical environment.
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Affiliation(s)
- Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Nathan Burton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gurneet Dhanoa
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.
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25
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Mehmood Khan F, Manohar P, Singh Gondil V, Mehra N, Kayode Oyejobi G, Odiwuor N, Ahmad T, Huang G. The applications of animal models in phage therapy: An update. Hum Vaccin Immunother 2023; 19:2175519. [PMID: 36935353 PMCID: PMC10072079 DOI: 10.1080/21645515.2023.2175519] [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: 03/21/2023] Open
Abstract
The rapid increase in antibiotic resistance presents a dire situation necessitating the need for alternative therapeutic agents. Among the current alternative therapies, phage therapy (PT) is promising. This review extensively summarizes preclinical PT approaches in various in-vivo models. PT has been evaluated in several recent clinical trials. However, there are still several unanswered concerns due to a lack of appropriate regulation and pharmacokinetic data regarding the application of phages in human therapeutic procedures. In this review, we also presented the current state of PT and considered how animal models can be used to adapt these therapies for humans. The development of realistic solutions to circumvent these constraints is critical for advancing this technology.
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Affiliation(s)
- Fazal Mehmood Khan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China.,Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Prasanth Manohar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Vijay Singh Gondil
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Nancy Mehra
- Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology, Osun State University, Osogbo, Nigeria.,School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Nelson Odiwuor
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Microbiology, Sino-Africa Joint Research Centre, Nairobi, Kenya
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guangtao Huang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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26
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Behera BK, Patra B, Chakraborty HJ, Rout AK, Dixit S, Rai A, Das BK, Mohapatra T. Bacteriophages diversity in India's major river Ganga: a repository to regulate pathogenic bacteria in the aquatic environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:34101-34114. [PMID: 36508095 DOI: 10.1007/s11356-022-24637-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/03/2022] [Indexed: 06/18/2023]
Abstract
Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
| | - Biswanath Patra
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
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27
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Shivaram KB, Bhatt P, Applegate B, Simsek H. Bacteriophage-based biocontrol technology to enhance the efficiency of wastewater treatment and reduce targeted bacterial biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160723. [PMID: 36496019 DOI: 10.1016/j.scitotenv.2022.160723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/13/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Wastewater treatment is an essential process for public health and a sustainable ecosystem. Inadequate wastewater treatment can lead to the release of organic and inorganic pollutants and pathogenic bacteria into the receiving waters which could be further utilized for recreation purposes. The interaction between bacteriophage and bacteria in a wastewater treatment plant plays a major role in maintaining the treatment process. Phage therapy has been proposed as an alternative to conventional treatment methods as bacteriophages can be used on specific targets and leave useful bacteria unharmed. The bacterial species, which are responsible for bulking, foaming, and biofilm formation in a wastewater treatment plant (WWTP) have been identified and their respective phages are isolated to control their growth. Phages with lytic life cycles are preferred to lysogenic. Lytic phages can kill the specific target as they lyse the cell, infect most of the hosts, and have an immediate effect on controlling problems caused by bacteria in a WWTP. The bacteriophages such as T7, SPI1, GTE7, PhaxI, MAG1, MAG2, ϕPh_Se01, ϕPh_Se02, and Bxb1 have been investigated for the removal of bacterial biofilms from wastewater. Novel experimental setups have improved the efficiency of phage therapy in small-scale and pilot-scale experiments. Much more in-depth knowledge of the microbial community and their interaction would help promote the usage of phage therapy in large-scale wastewater treatments. This paper has covered the recent advancements in phage therapy as an effective biocontrol of pathogenic bacteria in the wastewater treatment process and has looked at certain shortcomings that have to be improved.
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Affiliation(s)
- Karthik Basthi Shivaram
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Bruce Applegate
- Department of Food Science, Purdue University, West Lafayette, IN 47906, USA
| | - Halis Simsek
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA.
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28
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Yang Y, Du H, Zou G, Song Z, Zhou Y, Li H, Tan C, Chen H, Fischetti VA, Li J. Encapsulation and delivery of phage as a novel method for gut flora manipulation in situ: A review. J Control Release 2023; 353:634-649. [PMID: 36464065 DOI: 10.1016/j.jconrel.2022.11.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
Intestinal flora regulation is an effective method to intervene and treat diseases associated with microbiome imbalance. In addition to conventional probiotic supplement, phage delivery has recently exhibited great prospect in modifying gut flora composition and regulating certain gene expression of gut bacteria. However, the protein structure of phage is vulnerable to external factors during storage and delivery, which leads to the loss of infection ability and flora regulation function. Encapsulation strategy provides an effective solution for improving phage stability and precisely controlling delivery dosage. Different functional materials including enzyme-responsive and pH-responsive polymers have been used to construct encapsulation carriers to protect phages from harsh conditions and release them in the colon. Meanwhile, diverse carriers showed different characteristics in structure and function, which influenced their protective effect and delivery efficiency. This review systematically summarizes recent research progress on the phage encapsulation and delivery, with an emphasis on function properties of carrier systems in the protection effect and colon-targeted delivery. The present review may provide a theoretical reference for the encapsulation and delivery of phage as microbiota modulator, so as to expedite the development of functional material and delivery carrier, as well as the advances in practical application of intestinal flora regulation.
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Affiliation(s)
- Yufan Yang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Du
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Song
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Li
- Faculty of Bioscience Engineering, Ghent University, Gent 9000, Belgium
| | - Chen Tan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York 10065, USA
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York 10065, USA; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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29
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Molina-Quiroz RC, Camilli A, Silva-Valenzuela CA. Role of Bacteriophages in the Evolution of Pathogenic Vibrios and Lessons for Phage Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:149-173. [PMID: 36792875 PMCID: PMC10587905 DOI: 10.1007/978-3-031-22997-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Viruses of bacteria, i.e., bacteriophages (or phages for short), were discovered over a century ago and have played a major role as a model system for the establishment of the fields of microbial genetics and molecular biology. Despite the relative simplicity of phages, microbiologists are continually discovering new aspects of their biology including mechanisms for battling host defenses. In turn, novel mechanisms of host defense against phages are being discovered at a rapid clip. A deeper understanding of the arms race between bacteria and phages will continue to reveal novel molecular mechanisms and will be important for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections, respectively. Here we delve into the molecular interactions of Vibrio species and phages.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, MA, USA
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30
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Kuźmińska-Bajor M, Śliwka P, Korzeniowski P, Kuczkowski M, Moreno DS, Woźniak-Biel A, Śliwińska E, Grzymajło K. Effective reduction of Salmonella Enteritidis in broiler chickens using the UPWr_S134 phage cocktail. Front Microbiol 2023; 14:1136261. [PMID: 37180264 PMCID: PMC10174237 DOI: 10.3389/fmicb.2023.1136261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Salmonella is a poultry-associated pathogen that is considered one of the most important zoonotic bacterial agents of contaminated food of animal origin including poultry products. Many efforts are taken to eliminate it from the food chain, and phages are one of the most promising tools to control Salmonella in poultry production. We investigated the usefulness of the UPWr_S134 phage cocktail in reducing Salmonella in broiler chickens. For this purpose, we analyzed the survivability of phages in the harsh environment encountered in the chicken gastrointestinal tract, which has low pH, high temperatures, and digestive activity. Phages in the cocktail UPWr_S134 showed the ability to remain active after storage at temperatures ranging from 4 to 42°C, reflecting temperatures of storage conditions, broiler handling, and the chicken body, and exhibited robust pH stability. We found that although simulated gastric fluids (SGF) caused phage inactivation, the addition of feed to gastric juice allows maintenance of UPWr_S134 phage cocktail activity. Further, we analyzed UPWr_S134 phage cocktail anti-Salmonella activity in live animals such as mice and broilers. In an acute infection model in mice, the application of doses of 107 and 1014 PFU/ml UPWr_S134 phage cocktail resulted in delaying symptoms of intrinsic infection in all analyzed treatment schedules. In Salmonella-infected chickens orally treated with the UPWr_S134 phage cocktail the number of pathogens in internal organs in comparison to untreated birds was significantly lower. Therefore we concluded that the UPWr_S134 phage cocktail could be an effective tool against this pathogen in the poultry industry.
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Affiliation(s)
- Marta Kuźmińska-Bajor
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- *Correspondence: Marta Kuźmińska-Bajor,
| | - Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paweł Korzeniowski
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Maciej Kuczkowski
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - David Sáez Moreno
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS Associate Laboratory, Guimarães, Braga, Portugal
| | - Anna Woźniak-Biel
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Emilia Śliwińska
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Krzysztof Grzymajło
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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31
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Ping L, Zhuoya L, Pei J, Jingchao C, Yi L, Guosheng L, Hailei W. Editing of a Specific Strain of Escherichia coli in the Mouse Gut Using Native Phages. Microbiol Spectr 2022; 10:e0180422. [PMID: 36301104 PMCID: PMC9770003 DOI: 10.1128/spectrum.01804-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/20/2022] [Indexed: 01/05/2023] Open
Abstract
There is a lack of methodological investigation of the in situ functions of bacterial species in microecosystems. Here, we used native phages as a microbial editing tool for eliminating Escherichia coli strain MG1655 labeled with green fluorescent protein (GFP) in the mouse gut. The virulent phages (W1 and W3) possessed host specificity at both the genus and species levels, resulting in an 8.8-log10 difference in the titer of viable bacteria after 12 h of phage treatment compared with that in the phage-free control in an in vitro test. In vivo, they reduced strain MG1655 colonizing the mouse gut at concentrations of 106 to 108 CFU g-1 to a 102 CFU g-1 level, which is almost undetectable by the plate colony-counting method. Moreover, the impact of phage treatment on the microbial community structure of the mouse gut was not significant (P > 0.05), indicating that native phages can effectively edit a target bacterium, with limited perturbation of microbial diversity and relative abundance. Therefore, we developed an engineering technique for investigation of the functions of a specific bacterium by depleting its abundance in microecosystems. IMPORTANCE This report describes a gut engineering technique for investigation of the functions of a specific bacterium. Native phages with host specificity can knock down the corresponding E. coli strain in the mouse gut with limited perturbation of microbial diversity and relative abundance, indicating that they, as a microbial editing tool, can effectively edit the abundance of a target bacterium. Such an approach is undoubtedly of interest in the context of lack of knowledge of how to methodologically study the in situ function of a specific species in a complex microecosystem.
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Affiliation(s)
- Li Ping
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Zhuoya
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Jia Pei
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chen Jingchao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Yi
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Liu Guosheng
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wang Hailei
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Advanced Environmental Biotechnology Center, Nanyang Technological University, Singapore, Singapore
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Habees AA, Aldabbas E, Bragazzi NL, Kong JD. Bacteria-bacteriophage cycles facilitate Cholera outbreak cycles: an indirect Susceptible-Infected-Recovered-Bacteria- Phage (iSIRBP) model-based mathematical study. JOURNAL OF BIOLOGICAL DYNAMICS 2022; 16:29-43. [PMID: 34994295 DOI: 10.1080/17513758.2021.2017032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Cholera is an acute enteric infectious disease caused by the Gram-negative bacterium Vibrio cholerae. Despite a huge body of research, the precise nature of its transmission dynamics has yet to be fully elucidated. Mathematical models can be useful to better understand how an infectious agent can spread and be properly controlled. We develop a compartmental model describing a human population, a bacterial population as well as a phage population. We show that there might be eight equilibrium points, one of which is a disease free equilibrium point. We carry out numerical simulations and sensitivity analyses and we show that the presence of phage can reduce the number of infectious individuals. Moreover, we discuss the main implications in terms of public health management and control strategies.
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Affiliation(s)
- Asma Al Habees
- Department of Mathematics, The University of Jordan, Amman, Jordan
| | - Eman Aldabbas
- Department of Mathematics, The University of Jordan, Amman, Jordan
| | - Nicola L Bragazzi
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Jude D Kong
- Department of Mathematics and Statistics, York University, Toronto, Canada
- Canadian Center for Diseases Modeling (CDM), York University, Toronto, Canada
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33
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Anyaegbunam NJ, Anekpo CC, Anyaegbunam ZKG, Doowuese Y, Chinaka CB, Odo OJ, Sharndama HC, Okeke OP, Mba IE. The resurgence of phage-based therapy in the era of increasing antibiotic resistance: From research progress to challenges and prospects. Microbiol Res 2022; 264:127155. [PMID: 35969943 DOI: 10.1016/j.micres.2022.127155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/23/2022]
Abstract
Phage therapy was implemented almost a century ago but was subsequently abandoned when antibiotics emerged. However, the rapid emergence of drug-resistant, which has brought to the limelight situation reminiscent of the pre-antibiotic era, coupled with the unavailability of new drugs, has triggered the quest for an alternative therapeutic approach, and this has led to the rebirth of phage-derived therapy. Phages are viruses that infect and replicate in bacterial cells. Phage therapy, especially phage-derived proteins, is being given considerable attention among scientists as an antimicrobial agent. They are used alone or in combination with other biomaterials for improved biological activity. Over the years, much has been learned about the genetics and diversity of bacteriophages. Phage cocktails are currently being exploited for treating several infectious diseases as preliminary studies involving animal models and clinical trials show promising therapeutic efficacy. However, despite its numerous advantages, this approach has several challenges and unaddressed limitations. Addressing these issues requires lots of creativity and innovative ideas from interdisciplinary fields. However, with all available indications, phage therapy could hold the solution in this era of increasing antibiotic resistance. This review discussed the potential use of phages and phage-derived proteins in treating drug-resistant bacterial infections. Finally, we highlight the progress, challenges, and knowledge gaps and evaluate key questions requiring prompt attention for the full clinical application of phage therapy.
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Affiliation(s)
| | - Chijioke Chinedu Anekpo
- Department of Ear Nose and Throat (ENT), College of Medicine, Enugu state University of Science and Technology, Enugu, Nigeria
| | - Zikora Kizito Glory Anyaegbunam
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria Nsukka, Nigeria; Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Yandev Doowuese
- Department of Microbiology, Federal University of Health Sciences, Otukpo, Nigeria
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34
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Yun YB, Um Y, Kim YK. Optimization of the Bacteriophage Cocktail for the Prevention of Brown Blotch Disease Caused by Pseudomonas tolaasii. THE PLANT PATHOLOGY JOURNAL 2022; 38:472-481. [PMID: 36221919 PMCID: PMC9561164 DOI: 10.5423/ppj.oa.03.2022.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Brown blotch disease, caused by Pseudomonas tolaasii, is one of the most serious diseases in mushroom cultivation, and its control remains an important issue. This study isolated and evaluated pathogen-specific bacteriophages for the biological control of the disease. In previous studies, 23 varieties of P. tolaasii were isolated from infected mushrooms with disease symptoms and classified into three subtypes, Ptα, Ptβ, and Ptγ, based on their 16S rRNA gene sequences analysis and pathogenic characters. In this study, 42 virulent bacteriophages were isolated against these pathogens and tested for their host range. Some phages could lyse more than two pathogens only within the corresponding subtype, and no phage exhibited a wide host range across different pathogen subtypes. To eliminate all pathogens of the Ptα, Ptβ, and Ptγ subtype, corresponding phages of one, six, and one strains were required, respectively. These phages were able to suppress the disease completely, as confirmed by the field-scale on-farm cultivation experiments. These results suggested that a cocktail of these eight phages is sufficient to control the disease induced by all 23 P. tolaasii pathogens. Additionally, the antibacterial effect of this phage cocktail persisted in the second cycle of mushroom growth on the cultivation bed.
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Affiliation(s)
- Yeong-Bae Yun
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644,
Korea
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040,
Korea
| | - Yurry Um
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040,
Korea
| | - Young-Kee Kim
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644,
Korea
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35
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Zang Z, Park KJ, Gerdt JP. A Metabolite Produced by Gut Microbes Represses Phage Infections in Vibrio cholerae. ACS Chem Biol 2022; 17:2396-2403. [PMID: 35960903 PMCID: PMC10981169 DOI: 10.1021/acschembio.2c00422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. Bacteriophages that prey on V. cholerae may be employed as phage therapy against cholera. However, the influence of the chemical environment on the infectivity of vibriophages has been unexplored. Here, we discovered that a common metabolite produced by gut microbes─linear enterobactin (LinEnt), represses vibriophage proliferation. We found that the antiphage effect by LinEnt is due to iron sequestration and that multiple forms of iron sequestration can protect V. cholerae from phage predation. This discovery emphasizes the significance that the chemical environment can have on natural phage infectivity and phage-based interventions.
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Affiliation(s)
- Zhiyu Zang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Kyoung Jin Park
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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36
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Abstract
EMBL-EBI The European Bioinformatics Institute; E. coli Escherichia coli; E. faecalis Enterobacter faecalis; B. fragilis Bacteroides fragilis; B. vulgatus Bacteroides vulgatus; SaPIs Staphylococcus aureus pathogenicity islands; ARGs Antibiotic resistance genes; STEC Shiga toxigenic E. coli; Stx Shiga toxin; BLAST Basic Local Alignment Search Tool; TSST-1 Toxic shock toxin 1; RBPs Receptor-binding proteins; LPS lipopolysaccharide; OMVs Outer membrane vesicles; PT Phosphorothioate; BREX Bacteriophage exclusion; OCR Overcome classical restriction; Pgl Phage growth limitation; DISARM Defense island system associated with restrictionmodification; R-M system Restriction-modification system; BREX system Bacteriophage exclusion system; CRISPR Clustered regularly interspaced short palindromic repeats; Cas CRISPR-associated; PAMs Prospacer adjacent motifs; crRNA CRISPR RNA; SIE; OMPs; Superinfection exclusion; Outer membrane proteins; Abi Abortive infection; TA Toxin-antitoxin; TLR Toll-like receptor; APCs Antigen-presenting cells; DSS Dextran sulfate sodium; IELs Intraepithelial lymphocytes; FMT Fecal microbiota transfer; IFN-γ Interferon-gamma; IBD Inflammatory bowel disease; AgNPs Silver nanoparticles; MDSC Myeloid-derived suppressor cell; CRC Colorectal cancer; VLPs Virus-like particles; TMP Tape measure protein; PSMB4 Proteasome subunit beta type-4; ALD Alcohol-related liver disease; GVHD Graft-versus-host disease; ROS Reactive oxygen species; RA Rheumatoid arthritis; CCP Cyclic citrullinated protein; AMGs Accessory metabolic genes; T1DM Type 1 diabetes mellitus; T2DM Type 2 diabetes mellitus; SCFAs Short-chain fatty acids; GLP-1 Glucagon-like peptide-1; A. baumannii Acinetobacter baumannii; CpG Deoxycytidylinate-phosphodeoxyguanosine; PEG Polyethylene glycol; MetS Metabolic syndrome; OprM Outer membrane porin M.
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Affiliation(s)
- Han Shuwen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Medical Oncology, Huzhou Central Hospital, Huzhou, China
| | - Ding Kefeng
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Colorectal Surgery and Oncology, Cancer Center Zhejiang University, Hangzhou, China,CONTACT Ding Kefeng Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Building 6 room 2018, Hangzhou, Zhejiang310009, China
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37
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Noor Mohammadi T, Shen C, Li Y, Zayda MG, Sato J, Masuda Y, Honjoh KI, Miyamoto T. Characterization and optimization of bacteriophage cocktails to control Clostridium perfringens in vitro and in curry roux. Int J Food Microbiol 2022; 380:109886. [PMID: 36027839 DOI: 10.1016/j.ijfoodmicro.2022.109886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 10/31/2022]
Abstract
Clostridium perfringens is a major cause of foodborne disease in developed countries. The aim of this study was to isolate and characterize phages specific to C. perfringens to evaluate the most efficient phage cocktail for the biocontrol of C. perfringens, both in vitro and in curry roux. In this study, four phages were isolated from chicken meat and were morphologically and genetically characterized along with two phages previously isolated in our laboratory that display different host lysis spectra. Phage cocktail CP11, consisting of phages CPQ3, 7, 8, and 10, showed the broadest host range. Electron micrograph images suggested that all four phages belong to the Podoviridae family, and none of them carry any antibiotic resistance or toxin genes. Notably, the phages were stable at various pH values and in curry roux. Cocktails consisting of six, five, and four phages at the same concentrations were examined to determine the most effective phage cocktail. Phage cocktail PC11 significantly decreased the viable count of C. perfringens to a value less than the lower detection limit up to 48 h at both 8 and 37 °C in broth and at 24 °C in the curry roux. These results suggest that phage cocktail PC11 is a promising natural biocontrol agent against C. perfringens in vitro and in curry roux.
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Affiliation(s)
- Tahir Noor Mohammadi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Cunkuan Shen
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuncheng Li
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mahmoud Gamaleldin Zayda
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Monofiya Governorate, Egypt
| | - Jun Sato
- Safety Science Research, R&D, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi 321-3497, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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38
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Hsueh BY, Severin GB, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol 2022; 7:1210-1220. [PMID: 35817890 PMCID: PMC9830645 DOI: 10.1038/s41564-022-01162-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/24/2022] [Indexed: 02/03/2023]
Abstract
Vibrio cholerae biotype El Tor is perpetuating the longest cholera pandemic in recorded history. The genomic islands VSP-1 and VSP-2 distinguish El Tor from previous pandemic V. cholerae strains. Using a co-occurrence analysis of VSP genes in >200,000 bacterial genomes we built gene networks to infer biological functions encoded in these islands. This revealed that dncV, a component of the cyclic-oligonucleotide-based anti-phage signalling system (CBASS) anti-phage defence system, co-occurs with an uncharacterized gene vc0175 that we rename avcD for anti-viral cytodine deaminase. We show that AvcD is a deoxycytidylate deaminase and that its activity is post-translationally inhibited by a non-coding RNA named AvcI. AvcID and bacterial homologues protect bacterial populations against phage invasion by depleting free deoxycytidine nucleotides during infection, thereby decreasing phage replication. Homologues of avcD exist in all three domains of life, and bacterial AvcID defends against phage infection by combining traits of two eukaryotic innate viral immunity proteins, APOBEC and SAMHD1.
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Affiliation(s)
- Brian Y Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Geoffrey B Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Clinton A Elg
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Evan J Waldron
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Abhiruchi Kant
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Alex J Wessel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Christopher R Rhoades
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Benjamin J Ridenhour
- Department of Mathematics and Statistical Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Janani Ravi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Eva M Top
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences, Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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39
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Development of a Monoclonal Antibody to a Vibriophage as a Proxy for Vibrio cholerae Detection. Infect Immun 2022; 90:e0016122. [PMID: 35862704 PMCID: PMC9387236 DOI: 10.1128/iai.00161-22] [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] [Indexed: 11/24/2022] Open
Abstract
Cholera is an acute watery, diarrheal disease that causes high rates of morbidity and mortality without treatment. Early detection of the etiologic agent of toxigenic Vibrio cholerae is important to mobilize treatment and mitigate outbreaks. Monoclonal antibody (mAb) based rapid diagnostic tests (RDTs) enable early detection in settings without laboratory capacity. However, the odds of an RDT testing positive are reduced by nearly 90% when the common virulent bacteriophage ICP1 is present. We hypothesize that adding a mAb for the common, and specific, virulent bacteriophage ICP1 as a proxy for V. cholerae to an RDT will increase diagnostic sensitivity when virulent ICP1 phage is present. In this study, we used an in-silico approach to identify immunogenic ICP1 protein targets that were conserved across disparate time periods and locations. Specificity of targets to cholera patients with known ICP1 was determined, and specific targets were used to produce mAbs in a murine model. Candidate mAbs to the head protein demonstrated specificity to ICP1 by Enzyme linked immunosorbent assay (ELISA) and an ICP1 phage neutralization assay. The limit of detection of the final mAb candidate for ICP1 phage particles spiked into cholera stool matrix was 8 × 105 PFU by Western blotting analysis. This mAb will be incorporated into a RDT prototype for evaluation in a future diagnostic study to test the guiding hypothesis behind this study.
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40
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Aaron J, van Zyl LJ, Dicks LMT. Isolation and Characterization of Lytic Proteus Virus 309. Viruses 2022; 14:1309. [PMID: 35746779 PMCID: PMC9229222 DOI: 10.3390/v14061309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Proteus mirabilis is frequently associated with complicated urinary tract infections (UTIs) and is the main cause of catheter-associated urinary tract infections (CAUTIs). Treatment of such infections is complicated and challenging due to the biofilm forming abilities of P. mirabilis. If neglected or mistreated, infections may lead to life-threating conditions such as cystitis, pyelonephritis, kidney failure, and bacteremia that may progress to urosepsis. Treatment with antibiotics, especially in cases of recurring and persistent infections, leads to the development of resistant strains. Recent insights into phage therapy and using phages to coat catheters have been evaluated with many studies showing promising results. Here, we describe a highly lytic bacteriophage, Proteus_virus_309 (41,740 bp), isolated from a wastewater treatment facility in Cape Town, South Africa. According to guidelines of the International Committee on Taxonomy of Viruses (ICTV), bacteriophage 309 is a species within the genus Novosibovirus. Similar to most members of the genus, bacteriophage 309 is strain-specific and lyse P. mirabilis in less than 20 min.
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Affiliation(s)
- Joshua Aaron
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville 7535, South Africa;
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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41
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Oyejobi GK, Sule WF, Akinde SB, Khan FM, Ogolla F. Multidrug-resistant enteric bacteria in Nigeria and potential use of bacteriophages as biocontrol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153842. [PMID: 35183626 DOI: 10.1016/j.scitotenv.2022.153842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Enteric bacterial pathogens have been implicated in many cases of gastroenteritis in Nigeria, a West African country. This situation is worsened by some reports of the high prevalence of multidrug-resistant enteric bacteria. To better prepare for situations in which even antibiotics of last resort would fail to treat infections caused by these pathogens, attention should be paid to alternative antimicrobial strategies. Here, we summarize existing reports of multidrug-resistant enteric bacterial infections in Nigeria, and importantly present the use of bacteriophages (viruses of bacteria) as an attractive antimicrobial alternative to combat these pathogens. It is hoped that this review will encourage research into the use of lytic bacteriophages against multidrug-resistant enteric bacteria in Nigeria.
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Affiliation(s)
- Greater Kayode Oyejobi
- Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo 230212, Osun State, Nigeria; Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; International College, University of Chinese Academy of Sciences, Beijing, China; Organization of African Academic Doctors, Off Kamiti Road, P.O. Box 25305-00100, Nairobi, Kenya.
| | - Waidi Folorunso Sule
- Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo 230212, Osun State, Nigeria
| | - Sunday Babatunde Akinde
- Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo 230212, Osun State, Nigeria
| | - Fazal Mehmood Khan
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Faith Ogolla
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China; International College, University of Chinese Academy of Sciences, Beijing, China; Organization of African Academic Doctors, Off Kamiti Road, P.O. Box 25305-00100, Nairobi, Kenya; Sino-Africa Joint Research Center, Nairobi, Kenya
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42
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Zhang M, Qian J, Xu X, Ahmed T, Yang Y, Yan C, Elsharkawy MM, Hassan MM, Alorabi JA, Chen J, Li B. Resistance of Xanthomonas oryzae pv. oryzae to Lytic Phage X2 by Spontaneous Mutation of Lipopolysaccharide Synthesis-Related Glycosyltransferase. Viruses 2022; 14:1088. [PMID: 35632829 PMCID: PMC9143033 DOI: 10.3390/v14051088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Phage therapy is a promising biocontrol management on plant diseases caused by bacterial pathogens due to its specificity, efficiency and environmental friendliness. The emergence of natural phage-resistant bacteria hinders the application of phage therapy. Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of the devastating bacterial leaf blight disease of rice. Here, we obtained a spontaneous mutant C2R of an Xoo strain C2 showing strong resistance to the lytic phage X2. Analysis of the C2R genome found that the CDS2289 gene encoding glycosyltransferase acquired a frameshift mutation at the 180th nucleotide site, which also leads to a premature stop mutation at the 142nd amino acid. This mutation confers the inhibition of phage adsorption through the changes in lipopolysaccharide production and structure and bacterial surface morphology. Interestingly, glycosyltransferase-deficient C2R and an insertional mutant k2289 also showed reduced virulence, suggesting the trade-off costs of phage resistance. In summary, this study highlights the role of glycosyltransferase in interactions among pathogenic bacteria, phages and plant hosts, which provide insights into balanced coevolution from environmental perspectives.
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Affiliation(s)
- Muchen Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.Z.); (J.Q.); (X.X.); (T.A.)
| | - Jiahui Qian
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.Z.); (J.Q.); (X.X.); (T.A.)
| | - Xinyan Xu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.Z.); (J.Q.); (X.X.); (T.A.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.Z.); (J.Q.); (X.X.); (T.A.)
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
| | - Chenqi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Mohsen Mohamed Elsharkawy
- Agricultural Botany Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt;
| | - Mohamed M. Hassan
- Department of Biology, College of Science, Taif University, Taif P.O. Box 21974, Saudi Arabia; (M.M.H.); (J.A.A.)
| | - Jamal A. Alorabi
- Department of Biology, College of Science, Taif University, Taif P.O. Box 21974, Saudi Arabia; (M.M.H.); (J.A.A.)
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.Z.); (J.Q.); (X.X.); (T.A.)
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43
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Biocontrol of bacterial wilt in tomato with a cocktail of lytic bacteriophages. Appl Microbiol Biotechnol 2022; 106:3837-3848. [PMID: 35562488 DOI: 10.1007/s00253-022-11962-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/02/2022]
Abstract
Bacteriophages (phages) have been proposed as promising alternative pesticides against various bacterial diseases of crops. However, the efficacy of phages in managing plant bacterial diseases is variable and poorly understood in natural settings. In this study, two lytic phages, RpT1 and RpY2, were investigated for their biocontrol potential against bacterial wilt by Ralstonia pseudosolanacearum invasion in tomato plants. The two phages possess similar morphology and genome organization to those of the Autographiviridae family with a broad host range. Treatment with the two phages (alone or in combination) resulted in a significant reduction in bacterial wilt incidence. Three days post-treatment with phages, which was performed after R. pseudosolanacearum inoculation with a specified density of 108 PFU (plaque forming units)/g of soil, led to the most effective biocontrol activity compared to other treatments and a lower density of phage. A phage cocktail containing both RpT1 and RpY2 suppressed disease symptoms in agricultural soils, mimicking their ability to control diseases in natural settings. Furthermore, supplementation with specific adjuvants enhanced the biocontrol potential of both phages. The persistence of the two phages under various environmental conditions indicates their stable activity in soils. Consequently, the consistent biocontrol activity of these phages provides insights into the proper application, timing, and density of phages for effective phage therapy in bacterial wilt control in tomato. KEY POINTS: • Biocontrol potential of phages in natural settings individually and as a cocktail. • Apparent long-term persistence of phages in natural soils, various temperatures, and pH. • An effective approach for developing phages for biocontrol.
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Chen LK, Chang JC, Chu HT, Chen YT, Jiang HL, Wang LS, Teh SH, Yang HH, Chen DS, Li YZ, Chang CC, Sankhla D, Tseng CC. Preoptimized phage cocktail for use in aerosols against nosocomial transmission of carbapenem-resistant Acinetobacter baumannii: A 3-year prospective intervention study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 236:113476. [PMID: 35367880 DOI: 10.1016/j.ecoenv.2022.113476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Using bacteriophages (phages) as environmental sanitizers has been recognized as a potential alternative method to remove bacterial contamination in vitro; however, very few studies are available on the application of phages for infection control in hospitals. Here, we performed a 3-year prospective intervention study using aerosolized phage cocktails as biocontrol agents against carbapenem-resistant Acinetobacter baumannii (CRAB) infection in the hospital. When a CRAB-infected patient was identified in an intensive care unit (ICU), their surrounding environment was chosen for phage aerosol decontamination. Before decontamination, 501 clinical specimens from the patients were subjected to antibiotic resistance analysis and phage typing. The optimal phage cocktails were a combination of different phage families or were constructed by next-evolutionary phage typing with the highest score for the host lysis zone to prevent the development of environmental CRAB phage resistance. The phage infection percentage of the antibiotic-resistant A. baumannii strains was 97.1%, whereas the infection percentage in the antibiotic-susceptible strains was 79.3%. During the phage decontamination periods from 2017 to 2019, the percentage of carbapenem-resistant A. baumannii in test ICUs decreased significantly from 65.3% to 55%. The rate of new acquisitions of CRAB infection over the three years was 4.4 per 1000 patient-days, which was significantly lower than that in the control wards (8.9 per 1000 patient-days) where phage decontamination had never been performed. In conclusion, our results support the potential of phage cocktails to decrease CRAB infection rates, and the aerosol generation process may make this approach more comprehensive and time-saving.
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Affiliation(s)
- Li-Kuang Chen
- Institute of Medical Sciences, Department of Laboratory Diagnostic, College of Medicine, Tzu Chi University, Hualien, Taiwan; Branch of Clinical Pathology, Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Jui-Chih Chang
- Department of Surgery, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Section 3, Zhongyang Rd., Hualien, Taiwan; Department of Surgery, School of Medicine, Tzu Chi University, No. 701, Section 3, Zhongyang Rd., Hualien, Taiwan.
| | - Hsiu-Tzu Chu
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan; Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
| | - Yi-Ting Chen
- Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
| | - Hui-Li Jiang
- Unit of Infection Control and Management, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Lih-Shinn Wang
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Soon-Hian Teh
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Hui-Hua Yang
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
| | - Dar-Sen Chen
- School of Pharmacy, China Medical University, Taiwan.
| | - Yu-Zhong Li
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Chin-Cheng Chang
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Debangana Sankhla
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Chun-Chieh Tseng
- Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
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Barman RK, Chakrabarti AK, Dutta S. Screening of Potential Vibrio cholerae Bacteriophages for Cholera Therapy: A Comparative Genomic Approach. Front Microbiol 2022; 13:803933. [PMID: 35422793 PMCID: PMC9002330 DOI: 10.3389/fmicb.2022.803933] [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: 10/28/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Cholera continues to be a major burden for developing nations, especially where sanitation, quality of water supply, and hospitalization have remained an issue. Recently, growing antimicrobial-resistant strains of Vibrio cholerae underscores alternative therapeutic strategies for cholera. Bacteriophage therapy is considered one of the best alternatives for antibiotic treatment. For the identification of potential therapeutic phages for cholera, we have introduced a comprehensive comparative analysis of whole-genome sequences of 86 Vibrio cholerae phages. We have witnessed extensive variation in genome size (ranging from 33 to 148 kbp), GC (G + C) content (varies from 34.5 to 50.8%), and the number of proteins (ranging from 15 to 232). We have identified nine clusters and three singletons using BLASTn, confirmed by nucleotide dot plot and sequence identity. A high degree of sequence and functional similarities in both the genomic and proteomic levels have been observed within the clusters. Evolutionary analysis confirms that phages are conserved within the clusters but diverse between the clusters. For each therapeutic phage, the top 2 closest phages have been identified using a system biology approach and proposed as potential therapeutic phages for cholera. This method can be applied for the classification of the newly isolated Vibrio cholerae phage. Furthermore, this systematic approach might be useful as a model for screening potential therapeutic phages for other bacterial diseases.
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Affiliation(s)
- Ranjan Kumar Barman
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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46
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Zhang X, Wang S, Zhang Q, Zhang K, Liu W, Zhang R, Zhang Z. The Expansion of a Single Bacteriophage Leads to Bacterial Disturbance in Gut and Reduction of Larval Growth in Musca domestica. Front Immunol 2022; 13:885722. [PMID: 35464464 PMCID: PMC9019163 DOI: 10.3389/fimmu.2022.885722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022] Open
Abstract
The housefly larvae gut microbiota influences larval health and has become an important model to study the ecology and evolution of microbiota-host interactions. However, little is known about the phage community associated with the housefly larval gut, although bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact insect health remains unclear. We noticed that treating 1-day-old housefly larvae with ~107, ~109, and ~1011 phage particles per ml of bacteriophages led to changes in the growth and development of housefly larvae. Additionally, treating housefly larvae with bacteriophages led to bacterial composition changes in the gut. Changes in the compositions of these gut bacteria are mainly manifested in the increase in harmful bacteria, including Pseudomonas and Providencia and the decrease in beneficial bacteria, including Enterobacter and Klebsiella, after different growth and development periods. The alterations in gut microbiota further influenced the larval growth and development. Collectively, these results indicate that bacteriophages can perturb the intestinal microbiome and impact insect health.
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Affiliation(s)
- Xinyu Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Shumin Wang
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Qian Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Kexin Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Wenjuan Liu
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Ruiling Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
| | - Zhong Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, China
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Castledine M, Sierocinski P, Inglis M, Kay S, Hayward A, Buckling A, Padfield D. Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution. Front Cell Infect Microbiol 2022; 12:834406. [PMID: 35310856 PMCID: PMC8931298 DOI: 10.3389/fcimb.2022.834406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and evolution. The dynamics of coevolution—notably whether host or parasite has an evolutionary advantage—is greatly affected by the relative amount of genetic variation in host resistance and parasite infectivity traits. While studies have manipulated genetic diversity during coevolution, such as by increasing mutation rates, it is unclear how starting genetic diversity affects host–parasite coevolution. Here, we (co)evolved the bacterium Pseudomonas fluorescens SBW25 and two bacteriophage genotypes of its lytic phage SBW25ɸ2 in isolation (one phage genotype) and together (two phage genotypes). Bacterial populations rapidly evolved phage resistance, and phage reciprocally increased their infectivity in response. When phage populations were evolved with bacteria in isolation, bacterial resistance and phage infectivity increased through time, indicative of arms-race coevolution. In contrast, when both phage genotypes were together, bacteria did not increase their resistance in response to increasing phage infectivity. This was likely due to bacteria being unable to evolve resistance to both phage via the same mutations. These results suggest that increasing initial parasite genotypic diversity can give parasites an evolutionary advantage that arrests long-term coevolution. This study has important implications for the applied use of phage in phage therapy and in understanding host–parasite dynamics in broader ecological and evolutionary theory.
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Duan Y, Young R, Schnabl B. Bacteriophages and their potential for treatment of gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2022; 19:135-144. [PMID: 34782783 PMCID: PMC8966578 DOI: 10.1038/s41575-021-00536-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 02/08/2023]
Abstract
Although bacteriophages have been overshadowed as therapeutic agents by antibiotics for decades, the emergence of multidrug-resistant bacteria and a better understanding of the role of the gut microbiota in human health and disease have brought them back into focus. In this Perspective, we briefly introduce basic phage biology and summarize recent discoveries about phages in relation to their role in the gut microbiota and gastrointestinal diseases, such as inflammatory bowel disease and chronic liver disease. In addition, we review preclinical studies and clinical trials of phage therapy for enteric disease and explore current challenges and potential future directions.
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Affiliation(s)
- Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Center for Phage Technology, Texas A&M AgriLife Research and Texas A&M University, College Station, TX, USA
- Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
- Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA.
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49
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Jones IJ, Sokolow SH, De Leo GA. Three reasons why expanded use of natural enemy solutions may offer sustainable control of human infections. PEOPLE AND NATURE 2022; 4:32-43. [PMID: 35450207 PMCID: PMC9017516 DOI: 10.1002/pan3.10264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
1. Many infectious pathogens spend a significant portion of their life cycles in the environment or in animal hosts, where ecological interactions with natural enemies may influence pathogen transmission to people. Yet, our understanding of natural enemy opportunities for human disease control is lacking, despite widespread uptake and success of natural enemy solutions for pest and parasite management in agriculture. 2. Here we explore three reasons why conserving, restoring, or augmenting specific natural enemies in the environment could offer a promising complement to conventional clinical strategies to fight environmentally mediated pathogens and parasites. (1) Natural enemies of human infections abound in nature, largely understudied and undiscovered. (2) Natural enemy solutions could provide ecological options for infectious disease control where conventional interventions are lacking. And, (3) Many natural enemy solutions could provide important co-benefits for conservation and human well-being. 3. We illustrate these three arguments with a broad set of examples whereby natural enemies of human infections have been used or proposed to curb human disease burden, with some clear successes. However, the evidence base for most proposed solutions is sparse, and many opportunities likely remain undiscovered, highlighting opportunities for future research.
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Affiliation(s)
- IJ Jones
- Hopkins Marine Station of Stanford University, Pacific Grove, CA, 93950,Corresponding Author: Isabel J. Jones, , 415-309-3125
| | - SH Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, CA, 94305,Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA 93106
| | - GA De Leo
- Hopkins Marine Station of Stanford University, Pacific Grove, CA, 93950,Woods Institute for the Environment, Stanford University, Stanford, CA, 94305
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50
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Sit B, Fakoya B, Waldor MK. Animal models for dissecting Vibrio cholerae intestinal pathogenesis and immunity. Curr Opin Microbiol 2022; 65:1-7. [PMID: 34695646 PMCID: PMC8792189 DOI: 10.1016/j.mib.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023]
Abstract
The human diarrheal disease cholera is caused by the bacterium Vibrio cholerae. Efforts to develop animal models that closely mimic cholera to study the pathogenesis of this disease began >125 years ago. Here, we review currently used non-surgical, oral inoculation-based animal models for investigation of V. cholerae intestinal colonization and disease and highlight recent discoveries that have illuminated mechanisms of cholera pathogenesis and immunity, particularly in the area of how V. cholerae interacts with the gut microbiome to influence infection. The emergence of high-throughput tools for studies of pathogen-host interactions, along with continued advances in host genetic engineering and manipulation in animal models of V. cholerae will deepen understanding of cholera pathogenesis, uncovering knowledge important for control of this globally important bacterial pathogen.
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Affiliation(s)
- Brandon Sit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Bolutife Fakoya
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Massachusetts, USA,Howard Hughes Medical Institute, Bethesda, Maryland, USA,corresponding author: , Phone: 6175254646, Address: MCP-759, 181 Longwood Avenue, Boston, Massachusetts, USA 02115
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