1
|
Choudhary A, Midha T, Gulati I, Baranwal S. Isolation, Genomic Characterization of Shigella prophage fPSFA that effectively infects multi-drug resistant Shigella isolates from the Indian Poultry Sector. Microb Pathog 2024; 188:106538. [PMID: 38184177 DOI: 10.1016/j.micpath.2024.106538] [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: 10/25/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/08/2024]
Abstract
Because of uncontrolled use of antibiotics, emergence of multidrug-resistant Shigella species poses a huge potential of zoonotic transfer from poultry sector. With increasing resistance to current antibiotics, there is a critical need to explore antibiotic alternatives. Using a Shigella flexneri reference strain, we isolated a novel fPSFA phage after inducing with mitomycin C. The phage was found to be stable for wide ranges of temperature -20 °C-65 °C and pH 3 to 11. fPSFA shows a latent period that ranges from 20 to 30 min and generation times of 50-60 min. The genome analysis of phage reveals two major contigs of 23788 bp and 23285 bp with 50.16 % and 39.33 % G + C content containing a total of 80 CDS and 2 tRNA genes. The phage belongs to Straboviridae family and lacks any virulence or antimicrobial resistance gene, thus making it a suitable candidate for treatment of drug-resistant infections. To confirm lytic ability of novel phage, we isolated 54 multidrug-resistant Shigella species from thirty-five poultry fecal samples that shows multiple antibiotic resistance index ranging from 0.15 to 0.75 (from 3 Indian states). The fPSFA showed lytic activity against multidrug-resistant Shigella isolates (73.08 %) (MARI≥0.50). The wide host ranges of fPSFA phage demonstrate its potential to be used as a biocontrol agent.
Collapse
Affiliation(s)
- Aaina Choudhary
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Tushar Midha
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Ishita Gulati
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Somesh Baranwal
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India.
| |
Collapse
|
2
|
Martínez-Gallardo MJ, Villicaña C, Yocupicio-Monroy M, Alcaraz-Estrada SL, León-Félix J. Current knowledge in the use of bacteriophages to combat infections caused by Pseudomonas aeruginosa in cystic fibrosis. Folia Microbiol (Praha) 2023; 68:1-16. [PMID: 35931928 DOI: 10.1007/s12223-022-00990-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/02/2022] [Indexed: 11/04/2022]
Abstract
Pseudomonas aeruginosa (PA) is considered the first causal agent of morbidity and mortality in people with cystic fibrosis (CF) disease. Multi-resistant strains have emerged due to prolonged treatment with specific antibiotics, so new alternatives have been sought for their control. In this context, there is a renewed interest in therapies based on bacteriophages (phages) supported by several studies suggesting that therapy based on lytic phages and biofilm degraders may be promising for the treatment of lung infections in CF patients. However, there is little clinical data about phage studies in CF and the effectiveness and safety in patients with this disease has not been clear. Therefore, studies regarding on phage characterization, selection, and evaluation in vitro and in vivo models will provide reliable information for designing effective cocktails, either using mixed phages or in combination with antibiotics, making a great progress in clinical research. Hence, this review focuses on the most relevant and recent findings on the activity of lytic phages against PA strains isolated from CF patients and hospital environments, and discusses perspectives on the use of phage therapy on the treatment of PA in CF patients.
Collapse
Affiliation(s)
- María José Martínez-Gallardo
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Sinaloa, A.C. (CIAD), Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Martha Yocupicio-Monroy
- Postgraduate in Genomic Sciences, Universidad Autónoma de la Ciudad de México (UACM), Mexico City, Mexico
| | | | - Josefina León-Félix
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Sinaloa, A.C. (CIAD), Mexico.
| |
Collapse
|
3
|
Zhu Y, Shang J, Peng C, Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front Microbiol 2022; 13:1032186. [PMID: 36590402 PMCID: PMC9800612 DOI: 10.3389/fmicb.2022.1032186] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.
Collapse
|
4
|
Allué-Guardia A, Saranathan R, Chan J, Torrelles JB. Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis. Int J Mol Sci 2021; 22:ijms22020735. [PMID: 33450990 PMCID: PMC7828454 DOI: 10.3390/ijms22020735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/21/2023] Open
Abstract
The current emergence of multi-, extensively-, extremely-, and total-drug resistant strains of Mycobacterium tuberculosis poses a major health, social, and economic threat, and stresses the need to develop new therapeutic strategies. The notion of phage therapy against bacteria has been around for more than a century and, although its implementation was abandoned after the introduction of drugs, it is now making a comeback and gaining renewed interest in Western medicine as an alternative to treat drug-resistant pathogens. Mycobacteriophages are genetically diverse viruses that specifically infect mycobacterial hosts, including members of the M. tuberculosis complex. This review describes general features of mycobacteriophages and their mechanisms of killing M. tuberculosis, as well as their advantages and limitations as therapeutic and prophylactic agents against drug-resistant M. tuberculosis strains. This review also discusses the role of human lung micro-environments in shaping the availability of mycobacteriophage receptors on the M. tuberculosis cell envelope surface, the risk of potential development of bacterial resistance to mycobacteriophages, and the interactions with the mammalian host immune system. Finally, it summarizes the knowledge gaps and defines key questions to be addressed regarding the clinical application of phage therapy for the treatment of drug-resistant tuberculosis.
Collapse
Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - Jordi B. Torrelles
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
| |
Collapse
|
5
|
Yang Y, Fan C, Zhao Q. Recent Advances on the Machine Learning Methods in Identifying Phage Virion Proteins. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191203155511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the field of bioinformatics, the prediction of phage virion proteins helps us understand
the interaction between phage and its host cells and promotes the development of new antibacterial
drugs. However, traditional experimental methods to identify phage virion proteins are expensive
and inefficient, more researchers are working to develop new computational methods. In this review,
we summarized the machine learning methods for predicting phage virion proteins during recent
years, and briefly described their advantages and limitations. Finally, some research directions
related to phage virion proteins are listed.
Collapse
Affiliation(s)
- Yingjuan Yang
- School of Mathematics, Liaoning University, Shenyang, 110036, China
| | - Chunlong Fan
- College of Computer Science, Shenyang Aerospace University, Shenyang, 110136, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| |
Collapse
|
6
|
Rahimzadeh G, Saeedi M, Nokhodchi A, Moosazadeh M, Ghasemi M, Rostamkalaei SS, Mortazavi P, Eghbali M, Pourbakhshian R, Rezai MS, Nemati Hevelaee E. Evaluation of in-situ gel-forming eye drop containing bacteriophage against Pseudomonas aeruginosa keratoconjunctivitis in vivo. BIOIMPACTS : BI 2020; 11:281-287. [PMID: 34631490 PMCID: PMC8494255 DOI: 10.34172/bi.2021.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/20/2023]
Abstract
Introduction: Eradication of Pseudomonas aeruginosa has become increasingly difficult due to its remarkable capacity to resist antibiotics. Bacteriophages have been suggested as an alternative treatment for bacterial infections. Methods: In-situ gel-forming eye drop containing phage against P. aeruginosa keratoconjunctivitis was prepared. The Cystoviridae phage was formulated as in-situ gel-forming formulation which is a solution formulation but turns into gel when it contacts the eye. Therapeutic effectiveness of the in-situ gel forming formulation was evaluated by histological examination on day 12 post-infection. Results: The viscosity of selected formulation increased when it was instilled into the eye. The histological results showed edema, abscesses, and destruction of the stromal structure of cornea in groups where no in-situ gel-forming formulation was used. In the group where in-situ gel forming formulation was used, re-epithelialization and normal corneal structure were observed. Conclusion: In-situ gel-forming ophthalmic formulation containing phage can be effective in the treatment of P. aeruginosa keratoconjunctivitis.
Collapse
Affiliation(s)
- Golnar Rahimzadeh
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali Nokhodchi
- Pharmaceutics Research Lab, School of Life Sciences, University of Sussex, Brighton, UK
| | - Mahmood Moosazadeh
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Ghasemi
- Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyyed Sohrab Rostamkalaei
- Department of Pharmaceutics, Faculty of Pharmacy, Islamic Azad University, Ayatollah Amoli Branch, Amol, Iran
| | - Parham Mortazavi
- Student Research Committee, School of pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Eghbali
- Student Research Committee, School of pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Pourbakhshian
- Student Research Committee, School of pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Sadegh Rezai
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ebrahim Nemati Hevelaee
- Laboratory of Microbiology, Bouali Sina Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| |
Collapse
|
7
|
Xu J, Li X, Kang G, Bai L, Wang P, Huang H. Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules. Viruses 2020; 12:v12020205. [PMID: 32059512 PMCID: PMC7077233 DOI: 10.3390/v12020205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/29/2022] Open
Abstract
A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.
Collapse
Affiliation(s)
- Jingzhi Xu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xiaobo Li
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Liang Bai
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ping Wang
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
| |
Collapse
|
8
|
Abedon ST. Use of phage therapy to treat long-standing, persistent, or chronic bacterial infections. Adv Drug Deliv Rev 2019; 145:18-39. [PMID: 31708017 DOI: 10.1016/j.addr.2018.06.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/10/2018] [Accepted: 06/23/2018] [Indexed: 01/01/2023]
Abstract
Viruses of bacteria - known as bacteriophages or phages - have been used clinically as antibacterial agents for nearly 100 years. Often this phage therapy is of long-standing, persistent, or chronic bacterial infections, and this can be particularly so given prior but insufficiently effective infection treatment using standard antibiotics. Such infections, in turn, often have a biofilm component. Phages in modern medicine thus are envisaged to serve especially as anti-biofilm/anti-persistent infection agents. Here I review the English-language literature concerning in vivo experimental and clinical phage treatment of longer-lived bacterial infections. Overall, published data appears to be supportive of a relatively high potential for phages to cure infections which are long standing and which otherwise have resisted treatment with antibieiotics.
Collapse
|
9
|
Agarwal R, Johnson CT, Imhoff BR, Donlan RM, McCarty NA, García AJ. Inhaled bacteriophage-loaded polymeric microparticles ameliorate acute lung infections. Nat Biomed Eng 2018; 2:841-849. [PMID: 30854250 PMCID: PMC6408147 DOI: 10.1038/s41551-018-0263-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rachit Agarwal
- Woodruff School of Mechanical Engineering , Georgia Institute of Technology, Atlanta, GA, USA.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.,Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Christopher T Johnson
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.,Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Barry R Imhoff
- Department of Pediatrics , Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA.,Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Rodney M Donlan
- Biofilm Laboratory, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nael A McCarty
- Department of Pediatrics , Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA.,Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Andrés J García
- Woodruff School of Mechanical Engineering , Georgia Institute of Technology, Atlanta, GA, USA. .,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
10
|
Dufour N, Debarbieux L. [Phage therapy: a realistic weapon against multidrug resistant bacteria]. Med Sci (Paris) 2017; 33:410-416. [PMID: 28497737 DOI: 10.1051/medsci/20173304011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The continuous increase in antibiotic resistance among bacteria in infectious diseases associated with the lack of new antibiotics able to circumvent them are urging physicians, researchers and politicians to look for others options for treatments. Among those, phage therapy (use of natural viruses that infect bacteria, called bacteriophages) is one of the most promising approaches. In this review, we first focus on the problematic raised by multidrug resistant bacteria before addressing the main biological characteristics of bacteriophages, as well as the credibility and the relevance of phage therapy. We then introduce human applications, their potentials and limits.
Collapse
Affiliation(s)
- Nicolas Dufour
- Institut Pasteur, groupe interactions bactériophages bactéries chez l'animal, département de microbiologie, 25, rue du Docteur Roux, 75015 Paris, France - Centre hospitalier René Dubos, Service de réanimation médico-chirurgicale, 95500 Pontoise, France
| | - Laurent Debarbieux
- Institut Pasteur, groupe interactions bactériophages bactéries chez l'animal, département de microbiologie, 25, rue du Docteur Roux, 75015 Paris, France
| |
Collapse
|
11
|
Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa. Sci Rep 2016; 6:38795. [PMID: 27934909 PMCID: PMC5146939 DOI: 10.1038/srep38795] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022] Open
Abstract
Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are currently deposited in NCBI, but only 6 dsRNA bacteriophages and 12 ssRNA bacteriophages genome sequences are reported. The 6 dsRNA bacteriophages were isolated from legume samples or lakes with Pseudomonas syringae as the host. Here, we report the first Pseudomonas aeruginosa phage phiYY with a three-segmented dsRNA genome. phiYY was isolated from hospital sewage in China with the clinical P. aeruginosa strain, PAO38, as a host. Moreover, the dsRNA phage phiYY has a broad host range, which infects 99 out of 233 clinical P. aeruginosa strains isolated from four provinces in China. This work presented a detailed characterization of the dsRNA bacteriophage infecting P. aeruginosa.
Collapse
|
12
|
Jeon J, D'Souza R, Pinto N, Ryu C, Park J, Yong D, Lee K. Characterization and complete genome sequence analysis of two
Myoviral
bacteriophages infecting clinical carbapenem‐resistant
Acinetobacter baumannii
isolates. J Appl Microbiol 2016; 121:68-77. [DOI: 10.1111/jam.13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/16/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- J. Jeon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - R. D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - N. Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - C.‐M. Ryu
- Molecular Phytobacteriology Laboratory KRIBB Daejeon Korea
- Biosystems and Bioengineering Program School of Science University of Science and Technology (UST) Daejeon Korea
| | - J. Park
- Laboratory Animal Medicine College of Veterinary Medicine Chonnam National University Gwang‐ju Korea
| | - D. Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - K. Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| |
Collapse
|
13
|
Roach DR, Donovan DM. Antimicrobial bacteriophage-derived proteins and therapeutic applications. BACTERIOPHAGE 2015; 5:e1062590. [PMID: 26442196 DOI: 10.1080/21597081.2015.1062590] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 02/07/2023]
Abstract
Antibiotics have the remarkable power to control bacterial infections. Unfortunately, widespread use, whether regarded as prudent or not, has favored the emergence and persistence of antibiotic resistant strains of human pathogenic bacteria, resulting in a global health threat. Bacteriophages (phages) are parasites that invade the cells of virtually all known bacteria. Phages reproduce by utilizing the host cell's machinery to replicate viral proteins and genomic material, generally damaging and killing the cell in the process. Thus, phage can be exploited therapeutically as bacteriolytic agents against bacteria. Furthermore, understanding of the molecular processes involved in the viral life cycle, particularly the entry and cell lysis steps, has led to the development of viral proteins as antibacterial agents. Here we review the current preclinical state of using phage-derived endolysins, virion-associated peptidoglycan hydrolases, polysaccharide depolymerases, and holins for the treatment of bacterial infection. The scope of this review is a focus on the viral proteins that have been assessed for protective effects against human pathogenic bacteria in animal models of infection and disease.
Collapse
Affiliation(s)
- Dwayne R Roach
- Molecular Biology of the Genes in Extremophiles; Department of Microbiology; Institute Pasteur ; Paris, France
| | - David M Donovan
- Animal Biosciences and Biotechnology Laboratory; NEA; Agricultural Research Service; US Department of Agriculture ; Beltsville, MD USA
| |
Collapse
|
14
|
Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One 2015; 10:e0117163. [PMID: 25629728 PMCID: PMC4309531 DOI: 10.1371/journal.pone.0117163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/19/2014] [Indexed: 11/18/2022] Open
Abstract
In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.
Collapse
Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
| | - Louis-Marie Bobay
- Institut Pasteur, Microbial Evolutionary Genomics Unit, Department of Genomes and Genetics, Paris, France
- CNRS, UMR3525, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Emilie Saussereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, B-3001, Belgium
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- * E-mail:
| |
Collapse
|
15
|
Lindberg HM, McKean KA, Wang IN. Phage fitness may help predict phage therapy efficacy. BACTERIOPHAGE 2014; 4:e964081. [PMID: 26713221 PMCID: PMC4589996 DOI: 10.4161/21597073.2014.964081] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/14/2014] [Accepted: 09/05/2014] [Indexed: 12/12/2022]
Abstract
We isolated 6 phages from 2 environmental water sources and assessed their ability to treat Pseudomonas aeruginosa infection of Drosophila melanogaster. We found all 6 phages were able to significantly increase mean survival time (MST) of infected D. melanogaster. Although phage traits, such as adsorption rate, burst size, and lysis time, varied significantly among these phages, none of the traits correlated significantly with MST. Phage growth rate determined in vitro, however, was found to be significantly correlated with MST. Overall, our study shows that infected D. melanogaster can be used as a model system to test the therapeutic efficacy of phages. In addition, a more comprehensive characteristic, like the in vitro growth rate, seems to be a better indicator in predicting therapeutic success than constituent traits like the adsorption rate, burst size, or lysis time.
Collapse
|
16
|
Maura D, Debarbieux L. On the interactions between virulent bacteriophages and bacteria in the gut. BACTERIOPHAGE 2014; 2:229-233. [PMID: 23739386 PMCID: PMC3594211 DOI: 10.4161/bact.23557] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We recently described the targeting of O104:H4 Escherichia coli in mouse gut by several virulent bacteriophages, highlighting several issues relating to virus-host interactions, which we discuss further in this addendum to the original publication.
Collapse
Affiliation(s)
- Damien Maura
- Department of Surgery; Harvard Medical School and Massachusetts General Hospital; Boston, MA USA ; Department of Microbiology and Immunobiology; Harvard Medical School; Boston, MA USA ; Shriners Hospitals for Children Boston; Boston, MA USA
| | | |
Collapse
|
17
|
Abstract
Bacteria Pseudomonas aeruginosa, being opportunistic pathogens, are the major cause of nosocomial infections and, in some cases, the primary cause of death. They are virtually untreatable with currently known antibiotics. Phage therapy is considered as one of the possible approaches to the treatment of P. aeruginosa infections. Difficulties in the implementation of phage therapy in medical practice are related, for example, to the insufficient number and diversity of virulent phages that are active against P. aeruginosa. Results of interaction of therapeutic phages with bacteria in different conditions and environments are studied insufficiently. A little is known about possible interactions of therapeutic phages with resident prophages and plasmids in clinical strains in the foci of infections. This chapter highlights the different approaches to solving these problems and possible ways to expand the diversity of therapeutic P. aeruginosa phages and organizational arrangements (as banks of phages) to ensure long-term use of phages in the treatment of P. aeruginosa infections.
Collapse
Affiliation(s)
- Victor N Krylov
- Mechnikov Research Institute for Vaccines & Sera, Russian Academy of Medical Sciences, Moscow, Russia.
| |
Collapse
|
18
|
Genome Analysis of Pseudomonas aeruginosa Bacteriophage KPP23, Belonging to the Family Siphoviridae. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00233-14. [PMID: 24855291 PMCID: PMC4031330 DOI: 10.1128/genomea.00233-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteriophage (phage) therapy is expected to become an alternative therapy for Pseudomonas aeruginosa infections. P. aeruginosa phage KPP23 is a newly isolated phage belonging to the family Siphoviridae and may be a therapeutic phage candidate. We report its complete genome, which comprises 62,774 bp of double-stranded DNA containing 95 open reading frames.
Collapse
|
19
|
Miyata R, Yamaguchi K, Uchiyama J, Shigehisa R, Takemura-Uchiyama I, Kato SI, Ujihara T, Sakaguchi Y, Daibata M, Matsuzaki S. Characterization of a novel Pseudomonas aeruginosa bacteriophage, KPP25, of the family Podoviridae. Virus Res 2014; 189:43-6. [PMID: 24801109 DOI: 10.1016/j.virusres.2014.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
Pseudomonas aeruginosa phages belonging to the family Podoviridae are one of the well-characterized phage groups. In this study, a novel P. aeruginosa phage, KPP25, was isolated and characterized. Phage KPP25's morphology was indicative of the family Podoviridae; however, analyses of the whole genome and the virion proteins suggested that it did not belong to any of the known podophage genera. Based on these analyses, phage KPP25 appears to be a novel podophage infecting P. aeruginosa.
Collapse
Affiliation(s)
- Reina Miyata
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan
| | - Kotoe Yamaguchi
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan
| | - Jumpei Uchiyama
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan.
| | - Ryu Shigehisa
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan
| | - Iyo Takemura-Uchiyama
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan
| | - Shin-ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi, Japan
| | | | - Yoshihiko Sakaguchi
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection, Faculty of Medicine, Kochi University, Kochi, Japan; Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi University, Kochi, Japan
| |
Collapse
|
20
|
Abstract
The rise of antibiotic-resistant bacterial strains, causing intractable infections, has resulted in an increased interest in phage therapy. Phage therapy preceded antibiotic treatment against bacterial infections and involves the use of bacteriophages, bacterial viruses, to fight bacteria. Virulent phages are abundant and have proven to be very effective in vitro, where they in most cases lyse any bacteria within the hour. Clinical trials on animals and humans show promising results but also that the treatments are not completely effective. This is partly due to the studies being carried out with few phages, and with limited experimental groups, but also the fact that phage therapy has limitations in vivo. Phages are large compared with small antibiotic molecules, and each phage can only infect one or a few bacterial strains. A very large number of different phages are needed to treat infections as these are caused by genetically different strains of bacteria. Phages are effective only if enough of them can reach the bacteria and increase in number in situ. Taken together, this entails high demands on resources for the construction of phage libraries and the testing of individual phages. The effectiveness and host range must be characterized, and immunological risks must be assessed for every single phage.
Collapse
Affiliation(s)
- Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
21
|
Efficiency of bacteriophage therapy against Cronobacter sakazakii in Galleria mellonella (greater wax moth) larvae. Arch Virol 2014; 159:2253-61. [DOI: 10.1007/s00705-014-2055-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 03/12/2014] [Indexed: 11/26/2022]
|
22
|
Debarbieux L, Saussereau E, Maura D. [Phagotherapy: a nightmare for bacteria, a dream for physicians?]. Biol Aujourdhui 2013; 207:181-90. [PMID: 24330971 DOI: 10.1051/jbio/2013017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Indexed: 01/21/2023]
Abstract
Bacteriophages were discovered in the early 20th century and rapidly used to treat bacterial infections in humans. As the first specific antibacterial agents, they were used worldwide until antibiotics ramped up. Thereafter, rapidly forgotten, they became the favorite toolbox for researchers that used them to elucidate some of the most fundamental aspects of the cellular life at the molecular level. Today, facing the threat of antibiotic resistant bacteria, bacteriophages are being reconsidered for their use in medicine. During the past century, knowledge on bacteriophages has improved considerably, nevertheless phage therapy is still in its infancy. Taking two examples of recently published experimental phage therapy results, this article summarizes the hopes but also the challenges that surround the future development of human phage therapy.
Collapse
Affiliation(s)
- Laurent Debarbieux
- Institut Pasteur, Département de Microbiologie, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Emilie Saussereau
- Institut Pasteur, Département de Microbiologie, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Damien Maura
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, 02114 Massachusetts, USA - Department of Microbiology and Immunobiology, Harvard Medical School, Boston, 02114 Massachusetts, USA - Shriners Hospitals for Children-Boston, Boston, 02114 Massachusetts, USA
| |
Collapse
|
23
|
Predicting in vivo efficacy of therapeutic bacteriophages used to treat pulmonary infections. Antimicrob Agents Chemother 2013; 57:5961-8. [PMID: 24041900 DOI: 10.1128/aac.01596-13] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The potential of bacteriophage therapy to treat infections caused by antibiotic-resistant bacteria has now been well established using various animal models. While numerous newly isolated bacteriophages have been claimed to be potential therapeutic candidates on the basis of in vitro observations, the parameters used to guide their choice among billions of available bacteriophages are still not clearly defined. We made use of a mouse lung infection model and a bioluminescent strain of Pseudomonas aeruginosa to compare the activities in vitro and in vivo of a set of nine different bacteriophages (PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5, CHA_P1, LBL3, LUZ19, and PhiKZ). For seven bacteriophages, a good correlation was found between in vitro and in vivo activity. While the remaining two bacteriophages were active in vitro, they were not sufficiently active in vivo under similar conditions to rescue infected animals. Based on the bioluminescence recorded at 2 and 8 h postinfection, we also define for the first time a reliable index to predict treatment efficacy. Our results showed that the bacteriophages isolated directly on the targeted host were the most efficient in vivo, supporting a personalized approach favoring an optimal treatment.
Collapse
|
24
|
Rea MC, Alemayehu D, Ross RP, Hill C. Gut solutions to a gut problem: bacteriocins, probiotics and bacteriophage for control of Clostridium difficile infection. J Med Microbiol 2013; 62:1369-1378. [PMID: 23699066 DOI: 10.1099/jmm.0.058933-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major cause of morbidity and mortality among hospitalized patients and imposes a considerable financial burden on health service providers in both Europe and the USA. The incidence of CDI has dramatically increased in recent years, partly due to the emergence of a number of hypervirulent strains. The most commonly documented risk factors associated with CDIs are antibiotic usage leading to alterations of the gut microbiota, age >65 years and long-term hospital stay. Since standard therapies for antibiotic-associated diarrhoea and CDI have limited efficacy, there is now an urgent need for alternative therapeutics. In this review, we outline the current state of play with regard to the potential of gut-derived bacteriocins, probiotics and phage to act as antimicrobial agents against CDI in the human gut.
Collapse
Affiliation(s)
- Mary C Rea
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Debebe Alemayehu
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - R Paul Ross
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Colin Hill
- Department of Microbiology, University College, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College, Cork, Ireland
| |
Collapse
|
25
|
Roux D, Ricard JD. Nouveautés et perspectives thérapeutiques des pneumonies acquises sous ventilation mécanique à Pseudomonas aeruginosa. MEDECINE INTENSIVE REANIMATION 2013. [DOI: 10.1007/s13546-013-0679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Zucca M, Scutera S, Savoia D. Novel avenues forClostridium difficileinfection drug discovery. Expert Opin Drug Discov 2013; 8:459-77. [DOI: 10.1517/17460441.2013.770466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mario Zucca
- University of Torino, at S. Luigi Gonzaga Hospital, Department of Clinical and Biological Sciences, Regione Gonzole 10, Orbassano (To) 10043, Italy ;
| | - Sara Scutera
- University of Torino, Department of Public Health and Paediatric Sciences, V. Santena 9, Torino 10126, Italy
| | - Dianella Savoia
- University of Torino, at S. Luigi Gonzaga Hospital, Department of Clinical and Biological Sciences, Regione Gonzole 10, Orbassano (To) 10043, Italy ;
| |
Collapse
|