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Nikulin N, Nikulina A, Zimin A, Aminov R. Phages for treatment of Escherichia coli infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:171-206. [PMID: 37739555 DOI: 10.1016/bs.pmbts.2023.03.011] [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
Diseases due to infections by pathogenic Escherichia coli strains are on the rise and with the growing antimicrobial resistance among bacterial pathogens, including this group. Thus, alternative therapeutic options are actively investigated. Among these alternatives is phage therapy. In the case of E. coli, the combination of the well understood biology of this species and its bacteriophages represents a good guiding example for the establishment of phage therapy principles against this and other pathogenic bacteria. In this chapter, the procedures toward the development of phage therapy against pathogenic E. coli with the use of T-even group of phages are discussed. These steps involve the isolation, purification, characterisation and large-scale production of these phages, with formulation of phage cocktails for in vitro and in vivo studies. The main emphasis is made on phage therapy of enteropathogenic E. coli O157:H, which is one of the prominent human pathogens but persists as a commensal bacterium in many food animals. The implementation of phage therapy against E. coli O157:H within the One Health framework in carrier animals and for treatment of meat, vegetables, fruits and other agricultural produce thus would allow controlling and interrupting the transmission routes of this pathogen to the human food chain and preventing human disease. Examples of successful control and elimination of E. coli O157:H are given, while the problems encountered in phage treatment of this pathogen are also discussed.
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Affiliation(s)
- Nikita Nikulin
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Alexandra Nikulina
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Andrei Zimin
- Laboratory of Molecular Microbiology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, Pushchino, Russia
| | - Rustam Aminov
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom.
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Sagar SS, Rani S, Pushpa Sadanandan S. Combined Effect of Isolated Bacteriophage and Neem Extract on Isolated Multiple Drug-Resistant Pathogenic Escherichia coli E1 From Well Water. ENVIRONMENTAL HEALTH INSIGHTS 2023; 17:11786302231166818. [PMID: 37223331 PMCID: PMC10201146 DOI: 10.1177/11786302231166818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 05/25/2023]
Abstract
Multiple drug-resistant Escherichia coli (E. coli) is a serious cause of concern, and they can be observed in hospital settings, natural environment, and animals. Dissemination of multiple drug-resistant (MDR) E. coli can pose a high risk to public health. Moreover, they are hard to control with commercial antibiotics, since they have acquired resistance against most of them. Therefore, to control multiple drug-resistant bacteria, alternative strategies have been adopted such as phage therapy, herbal remedies, nanoparticles etc. In the current study, the combined application of neem leaf extract and bacteriophage is used to control an isolated multiple drug-resistant E. coli E1. We have applied 0.1 mg/ml concentration of neem extract in combination with an isolated phage vB_EcoM_C2 of 1011 titer and found that the combinatorial treatment approach significantly controls the growth of E. coli E1 as compared to a single non-combinatorial treatment. In this study, every E. coli cell is targeted by 2 antimicrobials (phage and neem extract) at the same time, which is more effective as compared to the sole treatment. Implementation of the neem extract with phage opens a new alternative approach to the chemotherapeutics for the control of multiple drug-resistant bacterial pathogens. This approach may be effective, economical, and eco-friendly to combat MDR.
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Affiliation(s)
- Sadhana Singh Sagar
- Sadhana Singh Sagar, Ecology and
Environment Research Group, Center for Water Resources Development and
management, Kunnamangalam, Kozhikode 673571, Kerala.
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3
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Brüssow H. The human microbiome project at ten years - some critical comments and reflections on "our third genome", the human virome. MICROBIOME RESEARCH REPORTS 2023; 2:7. [PMID: 38045612 PMCID: PMC10688805 DOI: 10.20517/mrr.2022.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 12/05/2023]
Abstract
The Human Microbiome Project (HMP) has raised great expectations claiming the far-reaching influence of the microbiome on human health and disease ranging from obesity and malnutrition to effects going well beyond the gut. So far, with the notable exception of fecal microbiota transplantation in Clostridioides difficile infection, practical application of microbiome intervention has only achieved modest clinical effects. It is argued here that we need criteria for the link between microbiome and disease modelled on the links between pathogens and infectious disease in Koch's postulates. The most important question is whether the microbiome change is a cause of the given disease or a consequence of a pathology leading to disease where the microbiome change is only a parallel event without a causal connection to the disease - in philosophical parlance, an epiphenomenon. Also discussed here is whether human virome research is a necessary complement to the microbiome project with a high potential for practical applications.
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Affiliation(s)
- Harald Brüssow
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven B-3001, Belgium
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Tomat D, Gonzalez A, Aquili V, Casabonne C, Quiberoni A. Physicochemical characterization of ten newly isolated phages against the foodborne pathogen
Shigella flexneri. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Tomat
- Área de Bacteriología, Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Agustina Gonzalez
- Área de Bacteriología, Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Virginia Aquili
- Área de Bacteriología, Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Cecilia Casabonne
- Área de Bacteriología, Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Andrea Quiberoni
- Instituto de Lactología Industrial (UNL ‐ CONICET), Facultad de Ingeniería Química Santa Fe Argentina
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The Beauty of Bacteriophage T4 Research: Lindsay W. Black and the T4 Head Assembly. Viruses 2022; 14:v14040700. [PMID: 35458430 PMCID: PMC9026906 DOI: 10.3390/v14040700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Viruses are biochemically complex structures and mainly consist of folded proteins that contain nucleic acids. Bacteriophage T4 is one of most prominent examples, having a tail structure that contracts during the infection process. Intracellular phage multiplication leads to separate self-directed assembly reactions of proheads, tails and tail fibers. The proheads are packaged with concatemeric DNA produced by tandem replication reactions of the parental DNA molecule. Once DNA packaging is completed, the head is joined with the tail and six long fibers are attached. The mature particles are then released from the cell via lysis, another tightly regulated process. These processes have been studied in molecular detail leading to a fascinating view of the protein-folding dynamics that direct the structural interplay of assembled complexes. Lindsay W. Black dedicated his career to identifying and defining the molecular events required to form the T4 virion. He leaves us with rich insights into the astonishingly precise molecular clockwork that co-ordinates all of the players in T4 assembly, both viral and cellular. Here, we summarize Lindsay’s key research contributions that are certain to stimulate our future science for many years to come.
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Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s: Genomic and Biological Characterization. Appl Environ Microbiol 2021; 87:e0112421. [PMID: 34406832 DOI: 10.1128/aem.01124-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tailed bacteriophages constitute the bulk of the intestinal viromes of vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are dominated mostly by temperate phages, while in horse feces virulent phages are more prevalent. To our knowledge, all the previously reported isolates of horse fecal coliphages are virulent. Temperate coliphage Hf4s was isolated from horse feces, from the indigenous equine Escherichia coli 4s strain. It is a podovirus related to the Lederbergvirus genus (including the well-characterized Salmonella bacteriophage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by the same bacteriophage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. IMPORTANCE The relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of animals are not always clear and may vary between species or even between individuals. The horse intestinal virome is dominated by virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. These findings raise questions on the significance of bacteriophage-bacteriophage interactions within the ecology of microbial viruses in mammal intestinal ecosystems.
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Urban-Chmiel R, Balicki I, Świąder K, Nowaczek A, Pyzik E, Stępień-Pyśniak D, Marek A, Puchalski A, Wernicki A, Poleszak E, Dec M. The in vitro efficacy of eye drops containing a bacteriophage solution specific for Staphylococcus spp. isolated from dogs with bacterial conjunctivitis. Ir Vet J 2020; 73:21. [PMID: 33319700 PMCID: PMC7643432 DOI: 10.1186/s13620-020-00175-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The purpose of the study was to evaluate the in vitro antibacterial effect of experimental eye drops with bacteriophages in elimination of Staphylococcus spp. isolated from dogs with bacterial conjunctivitis.. The bacterial material was collected from dogs with independent clinical signs of bacterial conjunctivitis. Staphylococcus spp. were identified by phenotypic and genotypic methods (MALDI-TOF MS mass spectrometry). Antibiotic resistance was determined by the disc-diffusion method. Phage activity (Plaque forming units, PFU) was determined on double-layer agar plates. Phages with lytic titres > 108 PFU were used to prepare eye drops. The stability of the antibacterial titre was evaluated for preparations stored in sealed bottles as well as after opening and reclosing. RESULTS The tests confirmed the occurrence of Staphylococcus spp. strains as etiological agents of bacterial conjunctivitis in dogs. A high percentage of strains were resistant to more than three antibiotics. The experimental phage eye drops used in the study exhibited 100% efficacy in vitro against the tested Staphylococcus isolates. Particularly noteworthy is the long duration of activity and constant antibacterial lytic titre of ≥108 PFU/mL of two eye drop solutions, nos. 7 and 12, after the bottle had been opened (21 days) and after hermetically sealed packaging (28 days) at 4-8 °C. CONCLUSIONS The results represent the first stage of research and require continuation in vivo. If positive effects are obtained in animals, the results can be used in applied research in humans and animals.
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Affiliation(s)
- Renata Urban-Chmiel
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ireneusz Balicki
- Department and Clinic of Animal Surgery, Faculty of Veterinary Medicine, Lublin, Poland
| | - Katarzyna Świąder
- Department of Applied Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Anna Nowaczek
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ewelina Pyzik
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Agnieszka Marek
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Andrzej Puchalski
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Andrzej Wernicki
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ewa Poleszak
- Department of Applied Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Marta Dec
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland.
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Cepko LCS, Garling EE, Dinsdale MJ, Scott WP, Bandy L, Nice T, Faber-Hammond J, Mellies JL. Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis. J Med Microbiol 2020; 69:309-323. [PMID: 32011231 PMCID: PMC7431101 DOI: 10.1099/jmm.0.001162] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction. Bacteriophage therapy can be developed to target emerging diarrhoeal pathogens, but doing so in the absence of microbiome disruption, which occurs with antibiotic treatment, has not been established.Aim. Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative Escherichia coli (EAEC) while leaving the human microbiome intact.Methodology. Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, PDX, was classified by electron microscopy and genome sequencing. A mouse model of infection determined whether the phage was therapeutic against EAEC. 16S metagenomic analysis of anaerobic cultures determined whether a normal human microbiome was altered by treatment.Results. Escherichia virus PDX, a member of the strictly lytic family Myoviridae, killed a case-associated EAEC isolate from a child in rural Tennessee in a dose-dependent manner, and killed EAEC isolates from Columbian children. A single dose of PDX (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. PDX also killed EAEC when cultured anaerobically in the presence of human faecal bacteria. While the addition of EAEC reduced the β-diversity of the human microbiota, that of the cultures with either faeces alone, faeces with EAEC and PDX, or with just PDX phage was not different statistically.Conclusion. PDX killed EAEC isolate EN1E-0007 in vivo and in vitro, while not altering the diversity of normal human microbiota in anaerobic culture, and thus could be part of an effective therapy for children in developing countries and those suffering from EAEC-mediated traveller's diarrhoea without causing dysbiosis.
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Affiliation(s)
- Leah C S Cepko
- 320 Longwood Avenue, Enders Building, Department of Infectious Disease, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eliotte E Garling
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Madeline J Dinsdale
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - William P Scott
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Loralee Bandy
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Tim Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Joshua Faber-Hammond
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Jay L Mellies
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
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Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, Stokholm J, Krogfelt KA, Schjørring S, Bisgaard H, Nielsen DS, Moineau S, Petit MA. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat Commun 2020; 11:378. [PMID: 31953385 PMCID: PMC6969025 DOI: 10.1038/s41467-019-14042-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics. The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.
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Affiliation(s)
- Aurélie Mathieu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Moïra Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Denise Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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Sabino J, Hirten RP, Colombel JF. Review article: bacteriophages in gastroenterology-from biology to clinical applications. Aliment Pharmacol Ther 2020; 51:53-63. [PMID: 31696976 DOI: 10.1111/apt.15557] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/25/2019] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The gut microbiota plays an important role in the pathogenesis of several gastrointestinal diseases. Its composition and function are shaped by host-microbiota and intra-microbiota interactions. Bacteriophages (phages) are viruses that target bacteria and have the potential to modulate bacterial communities. AIMS To summarise phage biology and the clinical applications of phages in gastroenterology METHODS: PubMed was searched to identify relevant studies. RESULTS Phages induce bacterial cell lysis, integration of viral DNA into the bacteria and/or coexistence in a stable equilibrium. Bacteria and phages have co-evolved and their dynamic interactions are yet to be fully understood. The increasing need to modulate microbial communities (e.g., gut microbiota, multidrug-resistant bacteria) has been a strong stimulus for research in phages as an antibacterial therapy. In gastroenterology, phage therapy has been mainly studied in infectious diseases such as cholera. However, it is currently being explored in several other circumstances such as treating Clostridioides difficile colitis, targeting adherent-invasive Escherichia coli in Crohn's disease or eradicating Fusobacterium nucleatum in colorectal cancer. Overall, phage therapy has a favourable and acceptable safety profile. Presently, trials with phage therapy are ongoing in Crohn's disease. CONCLUSIONS Phage therapy is a promising therapeutic tool against pathogenic bacteria in the fields of infectious diseases and gastroenterology. Randomised, placebo-controlled trials with phage therapy for gastroenterological diseases are ongoing.
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Affiliation(s)
- João Sabino
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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11
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Soundararajan M, von Bünau R, Oelschlaeger TA. K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917. Front Microbiol 2019; 10:2783. [PMID: 31849915 PMCID: PMC6895014 DOI: 10.3389/fmicb.2019.02783] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic Escherichia coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor® and has been successfully used in the treatment of gastrointestinal disorders. Gut bacteriophages are dominant players in maintaining the microbial homeostasis in the gut, however, their interaction with incoming probiotic bacteria remains to be at conception. The presence of bacteriophages in the gut makes it inevitable for any probiotic bacteria to be phage resistant, in order to survive and successfully colonize the gut. This study addresses the phage resistance of EcN, specifically against lytic T4 phage infection. From various experiments we could show that (i) EcN is resistant toward T4 phage infection, (ii) EcN's K5 polysaccharide capsule plays a crucial role in T4 phage resistance and (iii) EcN's lipopolysaccharide (LPS) inactivates T4 phages and notably, treatment with the antibiotic polymyxin B which neutralizes the LPS destroyed the phage inactivation ability of isolated LPS from EcN. Combination of these identified properties in EcN was not found in other tested commensal E. coli strains. Our results further indicated that N-acetylglucosamine at the distal end of O6 antigen in EcN's LPS could be the interacting partner with T4 phages. From our findings, we have reported for the first time, the role of EcN's K5 capsule and LPS in its defense against T4 phages. In addition, by inactivating the T4 phages, EcN also protects E. coli K-12 strains from phage infection in tri-culture experiments. Our research highlights phage resistance as an additional safety feature of EcN, a clinically successful probiotic E. coli strain.
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Affiliation(s)
- Manonmani Soundararajan
- Institute for Molecular Infection Biology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | | | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, Julius Maximilian University of Würzburg, Würzburg, Germany
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12
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Bumunang EW, McAllister TA, Stanford K, Anany H, Niu YD, Ateba CN. Characterization of Non-O157 STEC Infecting Bacteriophages Isolated from Cattle Faeces in North-West South Africa. Microorganisms 2019; 7:E615. [PMID: 31779135 PMCID: PMC6956337 DOI: 10.3390/microorganisms7120615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023] Open
Abstract
Non-O157 Shiga toxin-producing Escherichia coli (STEC) E. coli are emerging pathotypes that are frequently associated with diseases in humans around the world. The consequences of these serogroups for public health is a concern given the lack of effective prevention and treatment measures. In this study, ten bacteriophages (phages; SA20RB, SA79RD, SA126VB, SA30RD, SA32RD, SA35RD, SA21RB, SA80RD, SA12KD and SA91KD) isolated from cattle faeces collected in the North-West of South Africa were characterized. Activity of these phages against non-O157 STEC isolates served as hosts for these phages. All of the phages except SA80RD displayed lytic against non-O157 E. coli isolates. Of 22 non-O157 E. coli isolates, 14 were sensitive to 9 of the 10 phages tested. Phage SA35RD was able to lyse 13 isolates representing a diverse group of non-O157 E. coli serotypes including a novel O-antigen Shiga toxigenic (wzx-Onovel5:H19) strain. However, non-O157 E. coli serotypes O76:H34, O99:H9, O129:H23 and O136:H30 were insensitive to all phages. Based on transmission electron microscopy, the non-O157 STEC phages were placed into Myoviridae (n = 5) and Siphoviridae (n = 5). Genome of the phage ranged from 44 to 184.3 kb. All but three phages (SA91KD, SA80RD and SA126VB) were insensitive to EcoRI-HF and HindIII nucleases. This is the first study illustrating that cattle from North-West South Africa harbour phages with lytic potentials that could potentially be exploited for biocontrol against a diverse group of non-O157 STEC isolated from the same region.
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Affiliation(s)
- Emmanuel W. Bumunang
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Mafikeng Campus, Private Bag X2046, Mmabatho 2735, South Africa;
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada;
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada;
| | - Hany Anany
- Agriculture and Agri-Food Canada, Guelph Research and Development Centre, Guelph, ON N1G 5C9, Canada;
| | - Yan D. Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Collins N. Ateba
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Mafikeng Campus, Private Bag X2046, Mmabatho 2735, South Africa;
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13
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Pacífico C, Hilbert M, Sofka D, Dinhopl N, Pap IJ, Aspöck C, Carriço JA, Hilbert F. Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples. Front Microbiol 2019; 10:2484. [PMID: 31736918 PMCID: PMC6834657 DOI: 10.3389/fmicb.2019.02484] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes.
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Affiliation(s)
- Cátia Pacífico
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Miriam Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Dmitrij Sofka
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Nora Dinhopl
- Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Ildiko-Julia Pap
- Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - Christoph Aspöck
- Karl Landsteiner University of Health Sciences, Krems, Austria.,Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - João André Carriço
- Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | - Friederike Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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14
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Kaczorowska J, Casey E, Neve H, Franz CM, Noben JP, Lugli GA, Ventura M, van Sinderen D, Mahony J. A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection. Viruses 2019; 11:E899. [PMID: 31561510 PMCID: PMC6832132 DOI: 10.3390/v11100899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/14/2019] [Accepted: 09/24/2019] [Indexed: 12/15/2022] Open
Abstract
Shigella ssp. and enterotoxigenic Escherichia coli are the most common etiological agents of diarrheal diseases in malnourished children under five years of age in developing countries. The ever-growing issue of antibiotic resistance and the potential negative impact of antibiotic use on infant commensal microbiota are significant challenges to current therapeutic approaches. Bacteriophages (or phages) represent an alternative treatment that can be used to treat specific bacterial infections. In the present study, we screened water samples from both environmental and industrial sources for phages capable of infecting E. coli laboratory strains within our collection. Nineteen phages were isolatedand tested for their ability to infect strains within the ECOR collection and E. coli O157:H7 Δstx. Furthermore, since coliphages have been reported to cross-infect certain Shigella spp., we also evaluated the ability of the nineteen phages to infect a representative Shigella sonnei strain from our collection. Based on having distinct (although overlapping in some cases) host ranges, ten phage isolates were selected for genome sequence and morphological characterization. Together, these ten selected phages were shown to infect most of the ECOR library, with 61 of the 72 strains infected by at least one phage from our collection. Genome analysis of the ten phages allowed classification into five previously described genetic subgroups plus one previously underrepresented subgroup.
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Affiliation(s)
- Joanna Kaczorowska
- School of Microbiology and APC Microbiome Ireland, University College Cork, Western Road, T12 YT20 Cork, Ireland; (J.K.); (E.C.)
| | - Eoghan Casey
- School of Microbiology and APC Microbiome Ireland, University College Cork, Western Road, T12 YT20 Cork, Ireland; (J.K.); (E.C.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (H.N.)
| | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany; (H.N.)
| | - Jean-Paul Noben
- Biomedical Research Institute, Hasselt University, B-3590 Diepenbeek, Belgium;
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Dept. Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
| | - Marco Ventura
- Laboratory of Probiogenomics, Dept. Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Western Road, T12 YT20 Cork, Ireland; (J.K.); (E.C.)
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Western Road, T12 YT20 Cork, Ireland; (J.K.); (E.C.)
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15
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Explorative Study on Isolation and Characterization of a Microviridae G4 Bacteriophage, EMCL318, against Multi-Drug-resistant Escherichia coli 15-318. Antibiotics (Basel) 2018; 7:antibiotics7040092. [PMID: 30373114 PMCID: PMC6316680 DOI: 10.3390/antibiotics7040092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/21/2018] [Accepted: 10/24/2018] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages screened and isolated from sewage water samples exhibited antibacterial activities against multi-drug-resistant Escherichia coli strains. Five different water samples from Canadian habitats such as Kamloops Wastewater Treatment Center, Domtar, the Pacific Ocean, Bisaro Anima Cave, and alkali ponds, were used in this study. Four Enterobacteriaceae strains including one non-resistant and three clinical multi-drug Escherichia coli strains (E. coli 15-102, E. coli 15-124, and E. coli 15-318) were selected as target bacteria to screen for the bacteriophages from these collected water samples. Seeded agar assay technique was implemented for the screening. It was found that only sewage water sample exhibited a significant number of plaques count with the E. coli 15-318 (1.82 × 102 plaques/plate) cells in comparison to E. coli non-resistant strain K12 (8 plaques/plate). The phage did not produce plaques in the E. coli 15-124 and E. coli 15-102 strains. The bacteriophage, designated EMCL318, was isolated, purified, characterized, and identified to belong to the G4 species of the Family Microviridae, GenBank accession number MG563770. This is an explorative study conducted in order to reveal the viruses as alternative potentials to fight against emerging and existing multi-drug-resistant infectious diseases.
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16
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Lourenço M, De Sordi L, Debarbieux L. The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity. Viruses 2018; 10:v10060327. [PMID: 29914064 PMCID: PMC6024678 DOI: 10.3390/v10060327] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Phage therapy is based on a simple concept: the use of a virus (bacteriophage) that is capable of killing specific pathogenic bacteria to treat bacterial infections. Since the pioneering work of Félix d’Herelle, bacteriophages (phages) isolated in vitro have been shown to be of therapeutic value. Over decades of study, a large number of rather complex mechanisms that are used by phages to hijack bacterial resources and to produce their progeny have been deciphered. While these mechanisms have been identified and have been studied under optimal conditions in vitro, much less is known about the requirements for successful viral infections in relevant natural conditions. This is particularly true in the context of phage therapy. Here, we highlight the parameters affecting phage replication in both in vitro and in vivo environments, focusing, in particular, on the mammalian digestive tract. We propose avenues for increasing the knowledge-guided implementation of phages as therapeutic tools.
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Affiliation(s)
- Marta Lourenço
- Department of Microbiology, Institut Pasteur, F-75015 Paris, France.
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France.
| | - Luisa De Sordi
- Department of Microbiology, Institut Pasteur, F-75015 Paris, France.
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17
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Brüssow H. Environmental microbiology: Too much food for thought? - An argument for reductionism. Environ Microbiol 2018; 20:1929-1935. [PMID: 29626370 DOI: 10.1111/1462-2920.14125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 03/31/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Harald Brüssow
- Editor of Microbial Biotechnology, KU Leuven, Laboratory of Gene Technology, Leuven, Belgium
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18
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Brown-Jaque M, Calero-Cáceres W, Espinal P, Rodríguez-Navarro J, Miró E, González-López JJ, Cornejo T, Hurtado JC, Navarro F, Muniesa M. Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates. Int J Antimicrob Agents 2017; 51:434-442. [PMID: 29180282 DOI: 10.1016/j.ijantimicag.2017.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/07/2017] [Accepted: 11/18/2017] [Indexed: 12/31/2022]
Abstract
Phage particles have emerged as elements with the potential to mobilise antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. This study aimed to determine the occurrence of ARGs in phage particles present in faecal matter and induced from strains isolated from faeces. Nine ARGs (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 faecal samples obtained from healthy individuals who had not received antibiotic treatment or travelled abroad in the 3 months prior to sample collection. On the suspicion that the detected particles originated from bacterial flora, 82 Escherichia coli and Klebsiella pneumoniae isolates possessing at least one identified ARG (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, armA, qnrA, qnrS and sul1) were isolated and their capacity to produce phage particles carrying these ARGs following induction was evaluated. Of 150 samples, 72.7% were positive for at least one ARG, with blaTEM and blaCTX-M-9 group being the most prevalent and abundant. Of the 82 isolates, 51 (62%) showed an increase in the number of copies of the respective ARG in the phage fraction following induction, with blaTEM, blaCTX-M-1 group, blaCTX-M-9 group and sul1 being the most abundant. Phages induced from the isolates were further purified and visualised using microscopy and their DNA showed ARG levels of up to 1010 gene copies/mL. This study highlights the abundance of phage particles harbouring ARGs and indicates that bacterial strains in the intestinal habitat could be source of these particles.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Judith Rodríguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Juan José González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Thais Cornejo
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan Carlos Hurtado
- ISGlobal, Barcelona Centre for International Health Research, Department of Microbiology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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19
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Phage therapy: an alternative or adjunct to antibiotics? Emerg Top Life Sci 2017; 1:105-116. [DOI: 10.1042/etls20170005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 01/21/2023]
Abstract
Phage therapy is currently discussed as an alternative or adjunct to antibiotics whose activity is increasingly compromised by the emergence of antibiotic-resistant bacterial pathogens. The idea to use lytic bacterial viruses as antimicrobial agents is nearly a century old and is common practice in Eastern Europe. However, safety concerns and lack of controlled clinical trials proving the efficacy of phage therapy have hampered its wider medical use in the West. The present review analyzes safety aspects and compares successful with unsuccessful phage therapy clinical trials to identify potential factors determining success and failure of this approach.
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20
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Green SI, Kaelber JT, Ma L, Trautner BW, Ramig RF, Maresso AW. Bacteriophages from ExPEC Reservoirs Kill Pandemic Multidrug-Resistant Strains of Clonal Group ST131 in Animal Models of Bacteremia. Sci Rep 2017; 7:46151. [PMID: 28401893 PMCID: PMC5388864 DOI: 10.1038/srep46151] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/10/2017] [Indexed: 12/24/2022] Open
Abstract
Multi-drug resistant (MDR) enteric bacteria are of increasing global concern. A clonal group, Escherichia coli sequence type (ST) 131, harbors both MDR and a deadly complement of virulence factors. Patients with an immunocompromised system are at high risk of infections with these E. coli and there is strong epidemiologic evidence that the human intestinal tract, as well as household pets, may be a reservoir. Here, we examine if phages are an effective treatment strategy against this clonal group in murine models of bacteremia that recapitulate clinical infections. Bacteriophages isolated from known E. coli reservoirs lyse a diverse array of MDR ST131 clinical isolates. Phage HP3 reduced E. coli levels and improved health scores for mice infected with two distinct ST131 strains. Efficacy was correlated to in vitro lysis ability by the infecting phage and the level of virulence of the E. coli strain. Importantly, it is also demonstrated that E. coli bacteremia initiated from translocation across the intestinal tract in an immunocompromised host is substantially reduced after phage treatment. This study demonstrates that phage, isolated from the environment and with little experimental manipulation, can be effective in combating even the most serious of infections by E. coli “superbugs”.
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Affiliation(s)
- Sabrina I Green
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason T Kaelber
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ma
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Barbara W Trautner
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA.,Michael E. Debakey Veterans Affairs Medical Center, Houston, TX, 77030, USA
| | - Robert F Ramig
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anthony W Maresso
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Międzybrodzki R, Kłak M, Jończyk-Matysiak E, Bubak B, Wójcik A, Kaszowska M, Weber-Dąbrowska B, Łobocka M, Górski A. Means to Facilitate the Overcoming of Gastric Juice Barrier by a Therapeutic Staphylococcal Bacteriophage A5/80. Front Microbiol 2017; 8:467. [PMID: 28386250 PMCID: PMC5362586 DOI: 10.3389/fmicb.2017.00467] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 03/07/2017] [Indexed: 01/12/2023] Open
Abstract
In this article we compare the efficacy of different pharmacological agents (ranitidine, and omeprazole) to support phage transit from stomach to distal portions of the gastrointestinal tract in rats. We show that a temporal modification of environment in the animal stomach may protect Twort-like therapeutic antistaphylococcal phage A5/80 (from bacteriophage collection of the Hirszfeld Institute of Immunology and Experimental Therapy PAS in Wroclaw, Poland) from the inactivation by gastric juice effectively enough to enable a significant fraction of orally administered A5/80 to pass to the intestine. Interestingly, we found that yogurt may be a relatively strong in enhancing phage transit. Given the immunomodulating activities of phages our data may suggest that phages and yogurt can act synergistically in mediating their probiotic activities and enhancing the effectiveness of oral phage therapy. We also demonstrate that orally applied phages of similar size, morphology, and sensitivity to acidic environment may differ in their translocation into the bloodstream. This was evident in mice in which a therapeutic staphylococcal phage A5/80 reached the blood upon oral administration combined with antacid agent whilst T4 phage was not detected even when applied in 103 times higher dose. Our findings also suggest that phage penetration from digestive tract to the blood may be species-specific.
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Affiliation(s)
- Ryszard Międzybrodzki
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
| | - Marlena Kłak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Research and Development Center, Regional Specialized HospitalWrocław, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Barbara Bubak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Anna Wójcik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Marta Kaszowska
- Laboratory of Microbial Immunochemistry and Vaccines, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Małgorzata Łobocka
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences - SGGWWarsaw, Poland; Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
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22
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Sarker SA, Berger B, Deng Y, Kieser S, Foata F, Moine D, Descombes P, Sultana S, Huq S, Bardhan PK, Vuillet V, Praplan F, Brüssow H. Oral application of
E
scherichia coli
bacteriophage: safety tests in healthy and diarrheal children from
B
angladesh. Environ Microbiol 2016; 19:237-250. [DOI: 10.1111/1462-2920.13574] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Shafiqul Alam Sarker
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b)Clinical Sciences Division, 68 Shaheed Tajuddin Ahmed SharaniMohakhali Dhaka1212 Bangladesh
| | - Bernard Berger
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Ying Deng
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Silas Kieser
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Francis Foata
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Deborah Moine
- Nestlé Institute of Health Sciences, EPFL Innovation Park Functional Genomics Group, CH‐1015 Lausanne, Switzerland
| | - Patrick Descombes
- Nestlé Institute of Health Sciences, EPFL Innovation Park Functional Genomics Group, CH‐1015 Lausanne, Switzerland
| | - Shamima Sultana
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b)Clinical Sciences Division, 68 Shaheed Tajuddin Ahmed SharaniMohakhali Dhaka1212 Bangladesh
| | - Sayeeda Huq
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b)Clinical Sciences Division, 68 Shaheed Tajuddin Ahmed SharaniMohakhali Dhaka1212 Bangladesh
| | - Pradip Kumar Bardhan
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b)Clinical Sciences Division, 68 Shaheed Tajuddin Ahmed SharaniMohakhali Dhaka1212 Bangladesh
| | - Valérie Vuillet
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Fabienne Praplan
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
| | - Harald Brüssow
- Nutrition Health Research, Nestlé Research Centre, Nestec LtdVers‐chez‐les‐BlancLausanne26 CH‐1000 Switzerland
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23
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Sarker SA, Brüssow H. From bench to bed and back again: phage therapy of childhood Escherichia coli diarrhea. Ann N Y Acad Sci 2016; 1372:42-52. [PMID: 27197768 DOI: 10.1111/nyas.13087] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 12/11/2022]
Abstract
Over the last 20 years, the Nestlé Research Center in Switzerland and the International Center for Diarrhoeal Diseases Research in Bangladesh have explored the efficacy of alternative biological agents for the treatment of diarrheal diseases. This paper reviews the work of this collaborative effort, particularly on Escherichia coli phage therapy (PT), and discusses the development of the project, starting with the isolation of T4-like coliphages from the stool of diarrhea patients, their pilot plant amplification and purification, and the constitution and testing of a cocktail of T4-like phages in mice. A series of phase I clinical trials has demonstrated the safety of PT. Oral phage given without protection survived gastric passage and was recovered in the feces. Oral T4 phage cocktail was then tested in parallel to a commercial phage product in a phase II randomized, placebo-controlled single-center trial in Bangladeshi children hospitalized with acute E. coli diarrhea. It was found that oral phage did not perform better than the current standard of care by oral rehydration/zinc treatment. Furthermore, fecal E. coli pathogen titers were low and mixed infections were found to be frequent. Microbiota analysis showed a correlation between diarrhea and increased levels of Streptococcus, which raises fundamental questions on the causative agent of diarrhea that may explain PT clinical failure.
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Affiliation(s)
- Shafiqul A Sarker
- International Center for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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Vandenheuvel D, Lavigne R, Brüssow H. Bacteriophage Therapy: Advances in Formulation Strategies and Human Clinical Trials. Annu Rev Virol 2016; 2:599-618. [PMID: 26958930 DOI: 10.1146/annurev-virology-100114-054915] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently, a number of phage therapy phase I and II safety trials have been concluded, showing no notable safety concerns associated with the use of phage. Though hurdles for efficient treatment remain, these trials hold promise for future phase III clinical trials. Interestingly, most phage formulations used in these clinical trials are straightforward phage suspensions, and not much research has focused on the processing of phage cocktails in specific pharmaceutical dosage forms. Additional research on formulation strategies and the stability of phage-based drugs will be of key importance, especially with phage therapy advancing toward phase III clinical trials.
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Affiliation(s)
- Dieter Vandenheuvel
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ,
| | - Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ,
| | - Harald Brüssow
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland;
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Sarker SA, Sultana S, Reuteler G, Moine D, Descombes P, Charton F, Bourdin G, McCallin S, Ngom-Bru C, Neville T, Akter M, Huq S, Qadri F, Talukdar K, Kassam M, Delley M, Loiseau C, Deng Y, El Aidy S, Berger B, Brüssow H. Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh. EBioMedicine 2016; 4:124-37. [PMID: 26981577 PMCID: PMC4776075 DOI: 10.1016/j.ebiom.2015.12.023] [Citation(s) in RCA: 358] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 02/08/2023] Open
Abstract
Background Antibiotic resistance is rising in important bacterial pathogens. Phage therapy (PT), the use of bacterial viruses infecting the pathogen in a species-specific way, is a potential alternative. Method T4-like coliphages or a commercial Russian coliphage product or placebo was orally given over 4 days to Bangladeshi children hospitalized with acute bacterial diarrhea. Safety of oral phage was assessed clinically and by functional tests; coliphage and Escherichia coli titers and enteropathogens were determined in stool and quantitative diarrhea parameters (stool output, stool frequency) were measured. Stool microbiota was studied by 16S rRNA gene sequencing; the genomes of four fecal Streptococcus isolates were sequenced. Findings No adverse events attributable to oral phage application were observed (primary safety outcome). Fecal coliphage was increased in treated over control children, but the titers did not show substantial intestinal phage replication (secondary microbiology outcome). 60% of the children suffered from a microbiologically proven E. coli diarrhea; the most frequent diagnosis was ETEC infections. Bacterial co-pathogens were also detected. Half of the patients contained phage-susceptible E. coli colonies in the stool. E. coli represented less than 5% of fecal bacteria. Stool ETEC titers showed only a short-lived peak and were otherwise close to the replication threshold determined for T4 phage in vitro. An interim analysis after the enrollment of 120 patients showed no amelioration in quantitative diarrhea parameter by PT over standard care (tertiary clinical outcome). Stool microbiota was characterized by an overgrowth with Streptococcus belonging to the Streptococcus gallolyticus and Streptococcus salivarius species groups, their abundance correlated with quantitative diarrhea outcome, but genome sequencing did not identify virulence genes. Interpretation Oral coliphages showed a safe gut transit in children, but failed to achieve intestinal amplification and to improve diarrhea outcome, possibly due to insufficient phage coverage and too low E. coli pathogen titers requiring higher oral phage doses. More knowledge is needed on in vivo phage–bacterium interaction and the role of E. coli in childhood diarrhea for successful PT. Funding The study was supported by a grant from Nestlé Nutrition and Nestlé Health Science. The trial was registered with Identifier NCT00937274 at ClinicalTrials.gov. Coliphages given orally to children with bacterial diarrhea appeared in the stool, but did not improve clinical outcome. In microbiologically diagnosed E. coli diarrhea, pathogen titers were close to the replication threshold of coliphages. Acute bacterial diarrhea displayed a marked dysbiosis with fecal streptococci that stabilized with recovery from diarrhea.
Antibiotic resistance of bacterial infections reached alarming levels. Phage therapy is a potential alternative antimicrobial. We demonstrated that two different oral phage preparations did not improve acute bacterial diarrhea in children from Bangladesh. We observed fecal excretion of the oral phage, but no major phage amplification in the gut. E. coli pathogen levels were low and the fecal microbiota showed a transient overgrowth with streptococci. Future phage trials should first verify the titer and association of the targeted pathogen with the disease.
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Key Words
- Bacteriophages
- Bangladesh
- Bifidobacterium
- Cfu, colony forming unit
- Children
- Diarrhea
- EAEC, enteroaggregative E. coli
- EPEC, enteropathogenic E. coli
- ETEC, enterotoxigenic E. coli
- Escherichia coli
- M, ColiProteus phage cocktail from Microgen
- ORS, oral rehydration solution
- P, placebo
- PT, phage therapy
- RCT, randomized controlled trial
- Streptococcus
- T, T4 phage cocktail from NRC
- pfu, plaque forming unit
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Shafiqul Alam Sarker
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Shamima Sultana
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Gloria Reuteler
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Deborah Moine
- Nestlé Institute of Health Science, EPFL Innovation Park, CH-1015 Lausanne, Switzerland
| | - Patrick Descombes
- Nestlé Institute of Health Science, EPFL Innovation Park, CH-1015 Lausanne, Switzerland
| | - Florence Charton
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Gilles Bourdin
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Shawna McCallin
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Catherine Ngom-Bru
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Tara Neville
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Mahmuda Akter
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Sayeeda Huq
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Firdausi Qadri
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Kaisar Talukdar
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Mohamed Kassam
- Nestlé Institute of Health Science, EPFL Innovation Park, CH-1015 Lausanne, Switzerland
| | - Michèle Delley
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Chloe Loiseau
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Ying Deng
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Sahar El Aidy
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Bernard Berger
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Harald Brüssow
- Nestlé Research Centre, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
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A proposed new bacteriophage subfamily: “Jerseyvirinae”. Arch Virol 2015; 160:1021-33. [DOI: 10.1007/s00705-015-2344-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/17/2015] [Indexed: 01/21/2023]
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Bourdin G, Navarro A, Sarker SA, Pittet AC, Qadri F, Sultana S, Cravioto A, Talukder KA, Reuteler G, Brüssow H. Coverage of diarrhoea-associated Escherichia coli isolates from different origins with two types of phage cocktails. Microb Biotechnol 2014; 7:165-76. [PMID: 24528873 PMCID: PMC3937720 DOI: 10.1111/1751-7915.12113] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022] Open
Abstract
Eighty-nine T4-like phages from our phage collection were tested against four collections of childhood diarrhoea-associated Escherichia coli isolates representing different geographical origins (Mexico versus Bangladesh), serotypes (69 O, 27 H serotypes), pathotypes (ETEC, EPEC, EIEC, EAEC, VTEC, Shigella), epidemiological settings (community and hospitalized diarrhoea) and years of isolation. With a cocktail consisting of 3 to 14 T4-like phages, we achieved 54% to 69% coverage against predominantly EPEC isolates from Mexico, 30% to 53% against mostly ETEC isolates from a prospective survey in Bangladesh, 24% to 61% against a mixture of pathotypes isolated from hospitalized children in Bangladesh, and 60% coverage against Shigella isolates. In comparison a commercial Russian phage cocktail containing a complex mixture of many different genera of coliphages showed 19%, 33%, 50% and 90% coverage, respectively, against the four above-mentioned collections. Few O serotype-specific phages and no broad-host range phages were detected in our T4-like phage collection. Interference phenomena between the phage isolates were observed when constituting larger phage cocktails. Since the coverage of a given T4-like phage cocktail differed with geographical area and epidemiological setting, a phage composition adapted to a local situation is needed for phage therapy approaches against E. coli pathogens.
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Affiliation(s)
- Gilles Bourdin
- Nutrition and Health Department, Nestlé Research Center, Lausanne, Switzerland
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Jin J, Li ZJ, Wang SW, Wang SM, Chen SJ, Huang DH, Zhang G, Li YH, Wang XT, Wang J, Zhao GQ. Genome organisation of the Acinetobacter lytic phage ZZ1 and comparison with other T4-like Acinetobacter phages. BMC Genomics 2014; 15:793. [PMID: 25218338 PMCID: PMC4177764 DOI: 10.1186/1471-2164-15-793] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 09/10/2014] [Indexed: 01/18/2023] Open
Abstract
Background Phage ZZ1, which efficiently infects pathogenic Acinetobacter baumannii strains, is the fifth completely sequenced T4-like Acinetobacter phage to date. To gain a better understanding of the genetic characteristics of ZZ1, bioinformatics and comparative genomic analyses of the T4 phages were performed. Results The 166,687-bp double-stranded DNA genome of ZZ1 has the lowest GC content (34.4%) of the sequenced T4-like Acinetobacter phages. A total of 256 protein-coding genes and 8 tRNA genes were predicted. Forty-three percent of the predicted ZZ1 proteins share up to 73% amino acid identity with T4 proteins, and the homologous genes generally retained the same order and transcriptional direction. Beyond the conserved structural and DNA replication modules, T4 and ZZ1 have diverged substantially by the acquisition and deletion of large blocks of unrelated genes, especially in the first halves of their genomes. In addition, ZZ1 and the four other T4-like Acinetobacter phage genomes (Acj9, Acj61, 133, and Ac42) share a well-organised and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. Of the ZZ1 proteins, 70, 64, 61, and 56% share up to 86, 85, 81, and 83% amino acid identity with Acj9, Acj61, 133, and Ac42 proteins, respectively. ZZ1 has a different number and types of tRNAs than the other 4 Acinetobacter phages, although some of the ZZ1-encoded tRNAs share high sequence similarity with the tRNAs from these phages. Over half of ZZ1-encoded tRNAs (5 out of 8) are related to optimal codon usage for ZZ1 proteins. However, this correlation was not present in any of the other 4 Acinetobacter phages. Conclusions The comparative genomic analysis of these phages provided some new insights into the evolution and diversity of Acinetobacter phages, which might elucidate the evolutionary origin and host-specific adaptation of these phages. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-793) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Jin
- Department of Pathogen Biology and Immunology, Henan Medical College, Shuanghu Road #8, Zhengzhou 451191, P, R, China.
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De Paepe M, Leclerc M, Tinsley CR, Petit MA. Bacteriophages: an underestimated role in human and animal health? Front Cell Infect Microbiol 2014; 4:39. [PMID: 24734220 PMCID: PMC3975094 DOI: 10.3389/fcimb.2014.00039] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 01/07/2023] Open
Abstract
Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.
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Affiliation(s)
- Marianne De Paepe
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Marion Leclerc
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Colin R Tinsley
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
| | - Marie-Agnès Petit
- Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France
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Amplification and purification of T4-like escherichia coli phages for phage therapy: from laboratory to pilot scale. Appl Environ Microbiol 2013; 80:1469-76. [PMID: 24362424 DOI: 10.1128/aem.03357-13] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the amplification and purification of phage preparations with respect to titer, contamination level, stability, and technical affordability. Using various production systems (wave bags, stirred-tank reactors, and Erlenmeyer flasks), we obtained peak titers of 10(9) to 10(10) PFU/ml for T4-like coliphages. Phage lysates could be sterilized through 0.22-μm membrane filters without titer loss. Phages concentrated by differential centrifugation were not contaminated with cellular debris or bacterial proteins, as assessed by electron microscopy and mass spectrometry, respectively. Titer losses occurred by high-speed pelleting of phages but could be decreased by sedimentation through a sucrose cushion. Alternative phage concentration methods are prolonged medium-speed centrifugation, strong anion-exchange chromatography, and ultrafiltration, but the latter still allowed elevated lipopolysaccharide contamination. T4-like phages could not be pasteurized but maintained their infectivity titer in the cold chain. In the presence of 10 mM magnesium ions, phages showed no loss of titer over 1 month at 30°C.
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McLean SK, Dunn LA, Palombo EA. Phage inhibition of Escherichia coli in ultrahigh-temperature-treated and raw milk. Foodborne Pathog Dis 2013; 10:956-62. [PMID: 23909774 DOI: 10.1089/fpd.2012.1473] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli can contaminate raw milk during the milking process or via environmental contamination in milk-processing facilities. Three bacteriophages, designated EC6, EC9, and EC11, were investigated for their ability to inhibit the growth of three strains of E. coli in ultrahigh-temperature (UHT) treated and raw bovine milk. A cocktail of the three phages completely inhibited E. coli ATCC 25922 and E. coli O127:H6 in UHT milk at 25 °C and under refrigeration temperatures (5-9 °C). The phage cocktail produced similar results in raw milk; however, E. coli ATCC 25922 and O127:H6 in raw milk controls also declined to below the level of detection at both temperatures. This observation indicated that competition by the raw milk microbiota might have contributed to the decline in viable E. coli cells. A cocktail containing EC6 and EC9 completely inhibited E. coli O5:H-, an enterohemorrhagic strain, in UHT milk at both temperatures. In raw milk, the phage cocktail initially inhibited growth of E. coli O5:H- but regrowth occurred following incubation for 9 h at 25 °C and 144 h at 5-9 °C. In contrast to the other E. coli strains, O5:H- was not inhibited in the raw milk controls. This study demonstrates that bacteriophages are effective biocontrol agents against E. coli host strains in UHT and raw bovine milk at various storage temperatures.
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Affiliation(s)
- Sarah K McLean
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology , Victoria, Australia
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Brüssow H. Bacteriophage–host interaction: from splendid isolation into a messy reality. Curr Opin Microbiol 2013; 16:500-6. [DOI: 10.1016/j.mib.2013.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/16/2013] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
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Essoh C, Blouin Y, Loukou G, Cablanmian A, Lathro S, Kutter E, Thien HV, Vergnaud G, Pourcel C. The susceptibility of Pseudomonas aeruginosa strains from cystic fibrosis patients to bacteriophages. PLoS One 2013; 8:e60575. [PMID: 23637754 PMCID: PMC3634792 DOI: 10.1371/journal.pone.0060575] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/28/2013] [Indexed: 01/21/2023] Open
Abstract
Phage therapy may become a complement to antibiotics in the treatment of chronic Pseudomonas aeruginosa infection. To design efficient therapeutic cocktails, the genetic diversity of the species and the spectrum of susceptibility to bacteriophages must be investigated. Bacterial strains showing high levels of phage resistance need to be identified in order to decipher the underlying mechanisms. Here we have selected genetically diverse P. aeruginosa strains from cystic fibrosis patients and tested their susceptibility to a large collection of phages. Based on plaque morphology and restriction profiles, six different phages were purified from "pyophage", a commercial cocktail directed against five different bacterial species, including P. aeruginosa. Characterization of these phages by electron microscopy and sequencing of genome fragments showed that they belong to 4 different genera. Among 47 P. aeruginosa strains, 13 were not lysed by any of the isolated phages individually or by pyophage. We isolated two new phages that could lyse some of these strains, and their genomes were sequenced. The presence/absence of a CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and Crisper associated genes) was investigated to evaluate the role of the system in phage resistance. Altogether, the results show that some P. aeruginosa strains cannot support the growth of any of the tested phages belonging to 5 different genera, and suggest that the CRISPR-Cas system is not a major defence mechanism against these lytic phages.
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Affiliation(s)
- Christiane Essoh
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Yann Blouin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | | | | | - Serge Lathro
- Laboratoire National de Santé Publique, Abidjan, Côte d'Ivoire
| | - Elizabeth Kutter
- The Evergreen State College, Olympia, Washington, United States of America
| | - Hoang Vu Thien
- Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris (APHP), Bactériologie, Paris, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
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Abstract
Bacteriophages, or simply phages, are viruses infecting bacteria. With an estimated 1031 particles in the biosphere, phages outnumber bacteria by a factor of at least 10 and not surprisingly, they influence the evolution of most bacterial species, sometimes in unexpected ways. “Temperate” phages have the ability to integrate into the chromosome of their host upon infection, where they can reside as “quiescent” prophages until conditions favor their reactivation. Lysogenic conversion resulting from the integration of prophages encoding powerful toxins is probably the most determinant contribution of prophages to the evolution of pathogenic bacteria. We currently grasp only a small fraction of the total phage diversity. Phage biologists keep unraveling novel mechanisms developed by phages to parasitize their host. The purpose of this review is to give an overview of some of the various ways by which prophages change the lifestyle and boost virulence of some of the most dangerous bacterial pathogens.
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Affiliation(s)
- Louis-Charles Fortier
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC Canada.
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Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Ross RP. Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes 2013; 4:4-16. [PMID: 23022738 PMCID: PMC3555884 DOI: 10.4161/gmic.22371] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The human intestinal microbiota is one of the most densely populated ecosystems on Earth, containing up to 10 ( 13) bacteria/g and in some respects can be considered an organ itself given its role in human health. Bacteriophages (phages) are the most abundant replicating entities on the planet and thrive wherever their bacterial hosts exist. They undoubtedly influence the dominant microbial populations in many ecosystems including the human intestine. Within this setting, lysogeny appears to be the preferred life cycle, presumably due to nutrient limitations and lack of suitable hosts protected in biofilms, hence the predator/prey dynamic observed in many ecosystems is absent. On the other hand, free virulent phages in the gut are more common among sufferers of intestinal diseases and have been shown to increase with antibiotic usage. Many of these phages evolve from prophages of intestinal bacteria and emerge under conditions where their bacterial hosts encounter stress suggesting that prophages can significantly alter the microbial community composition. Based on these observations, we propose the "community shuffling" model which hypothesizes that prophage induction contributes to intestinal dysbiosis by altering the ratio of symbionts to pathobionts, enabling pathobiont niche reoccupation. The consequences of the increased phage load on the mammalian immune system are also addressed. While this is an area of intestinal biology which has received little attention, this review assembles evidence from the literature which supports the role of phages as one of the biological drivers behind the composition of the gut microbiota.
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Affiliation(s)
- Susan Mills
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland
| | - Fergus Shanahan
- Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Department of Medicine; University College Cork; National University of Ireland; Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland,Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Department of Microbiology; University College Cork; National University of Ireland; Cork, Ireland
| | - Aidan Coffey
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre; Moorepark; Fermoy, County Cork, Ireland,Alimentary Pharmabiotic Centre; University College Cork; National University of Ireland; Cork, Ireland,Correspondence to: R. Paul Ross,
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Al-Manasra AM, Al-Razem F. Cloning and expression of a new bacteriophage (SHPh) DNA ligase isolated from sewage. J Genet Eng Biotechnol 2012. [DOI: 10.1016/j.jgeb.2012.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Brüssow H. What is needed for phage therapy to become a reality in Western medicine? Virology 2012; 434:138-42. [DOI: 10.1016/j.virol.2012.09.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/12/2012] [Accepted: 09/18/2012] [Indexed: 01/21/2023]
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Sarker SA, McCallin S, Barretto C, Berger B, Pittet AC, Sultana S, Krause L, Huq S, Bibiloni R, Bruttin A, Reuteler G, Brüssow H. Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh. Virology 2012; 434:222-32. [PMID: 23102968 DOI: 10.1016/j.virol.2012.09.002] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
Abstract
The genomic diversity of 99 T4-like coliphages was investigated by sequencing an equimolar mixture with Illumina technology and screening them against different databases for horizontal gene transfer and undesired genes. A 9-phage cocktail was given to 15 healthy adults from Bangladesh at a dose of 3×10(9) and 3×10(7) plaque-forming units and placebo respectively. Phages were detected in 64% of the stool samples when subjects were treated with higher titer phage, compared to 30% and 28% with lower-titer phage and placebo, respectively. No Escherichia coli was present in initial stool samples, and no amplification of phage was observed. One percent of the administered oral phage was recovered from the feces. No adverse events were observed by self-report, clinical examination, or from laboratory tests for liver, kidney, and hematology function. No impact of oral phage was seen on the fecal microbiota composition with respect to bacterial 16S rRNA from stool.
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Affiliation(s)
- Shafiqul Alam Sarker
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh.
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Lau GL, Sieo CC, Tan WS, Ho YW. Characteristics of a phage effective for colibacillosis control in poultry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2657-2663. [PMID: 22505020 DOI: 10.1002/jsfa.5683] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 11/08/2011] [Accepted: 03/04/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Colibacillosis is one of the main causes of economic loss in the poultry industry worldwide. Although antibiotics have been used to control this infection, the emergence of antibiotic-resistant bacteria poses a threat to animal and human health. Phage therapy has been reported as one of the potential alternative methods to control bacterial infections. However, efficient phage therapy is highly dependent on the characteristics of the phage isolated. In the present study the characteristics of a lytic phage, ØEC1, which was found to be effective against the causative agent of colibacillosis in chickens in a previous in vivo study, are reported. RESULTS Examination by transmission electron microscopy revealed that ØEC1 is a DNA phage belonging to the Podoviridae family. ØEC1 showed an optimum multiplicity of infection of 0.1-1. The latent period of ØEC1 was 25 min, with a burst size of 200 particles per infected cell. Under the experimental conditions the maximum adsorption rate for ØEC1 was 99.9% within 8 min. ØEC1 demonstrated an optimum phage lytic activity at pH 6-9 and 25-41 °C. CONCLUSION These characteristics can serve as a guideline for selection of effective candidates for phage therapy, in this case for collibacillosis control in chickens.
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Affiliation(s)
- Gee Leng Lau
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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40
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Chibeu A, Lingohr EJ, Masson L, Manges A, Harel J, Ackermann HW, Kropinski AM, Boerlin P. Bacteriophages with the ability to degrade uropathogenic Escherichia coli biofilms. Viruses 2012; 4:471-87. [PMID: 22590682 PMCID: PMC3347319 DOI: 10.3390/v4040471] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/20/2012] [Accepted: 03/23/2012] [Indexed: 11/16/2022] Open
Abstract
Escherichia coli-associated urinary tract infections (UTIs) are among the most common bacterial infections in humans. UTIs are usually managed with antibiotic therapy, but over the years, antibiotic-resistant strains of uropathogenic E. coli (UPEC) have emerged. The formation of biofilms further complicates the treatment of these infections by making them resistant to killing by the host immune system as well as by antibiotics. This has encouraged research into therapy using bacteriophages (phages) as a supplement or substitute for antibiotics. In this study we characterized 253 UPEC in terms of their biofilm-forming capabilities, serotype, and antimicrobial resistance. Three phages were then isolated (vB_EcoP_ACG-C91, vB_EcoM_ACG-C40 and vB_EcoS_ACG-M12) which were able to lyse 80.5% of a subset (42) of the UPEC strains able to form biofilms. Correlation was established between phage sensitivity and specific serotypes of the UPEC strains. The phages' genome sequences were determined and resulted in classification of vB_EcoP_ACG-C91 as a SP6likevirus, vB_EcoM_ACG-C40 as a T4likevirus and vB_EcoS_ACG-M12 as T1likevirus. We assessed the ability of the three phages to eradicate the established biofilm of one of the UPEC strains used in the study. All phages significantly reduced the biofilm within 2-12 h of incubation.
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Affiliation(s)
- Andrew Chibeu
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada;
| | - Erika J. Lingohr
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada;
| | - Luke Masson
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, QC, H4P 2R2, Canada;
- Département de microbiologie et immunologie, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Amee Manges
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 avenue des Pins Ouest, Montréal, QC, H3A 1A2, Canada;
| | - Josée Harel
- Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP) and Centre de Recherche en infectiologie porcine (CRIP), Université de Montréal, Faculté de médecine vétérinaire, Saint-Hyacinthe, QC, J2S 7C6, Canada;
| | - Hans-W. Ackermann
- Felix d’Herelle Reference Center for Bacterial Viruses, Department of Microbiology, Immunology and Infectionlogy, Faculty of Medicine, Laval University, QC, G1K 4C6, Canada;
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada;
- Department of Molecular and Cellular Biology, University of Guelph, ON, N1G 2W1, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, ON, N1G 2W1, Canada;
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Kutter EM, Skutt-Kakaria K, Blasdel B, El-Shibiny A, Castano A, Bryan D, Kropinski AM, Villegas A, Ackermann HW, Toribio AL, Pickard D, Anany H, Callaway T, Brabban AD. Characterization of a ViI-like phage specific to Escherichia coli O157:H7. Virol J 2011; 8:430. [PMID: 21899740 PMCID: PMC3184105 DOI: 10.1186/1743-422x-8-430] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/07/2011] [Indexed: 12/16/2022] Open
Abstract
Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).
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Affiliation(s)
| | | | - Bob Blasdel
- The Evergreen State College, Olympia, WA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH
| | - Ayman El-Shibiny
- The Evergreen State College, Olympia, WA, USA
- Faculty of Environmental Agricultural Sciences, Suez Canal University, Egypt
| | - Anna Castano
- The Evergreen State College, Olympia, WA, USA
- Department of Pediatric Neurology, University of Colorado Children's Hospital, Denver, CO
| | | | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Molecular & Cellular Biology, University of Guelph, ON, Canada
| | - Andre Villegas
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Ana L Toribio
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Hany Anany
- Canadian Research Institute for Food Safety, University of Guelph, ON, Canada
- Microbiology Department, Ain Shams University, Cairo, Egypt
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Alam M, Farzana T, Ahsan CR, Yasmin M, Nessa J. Distribution of coliphages against four e. Coli virotypes in hospital originated sewage sample and a sewage treatment plant in bangladesh. Indian J Microbiol 2011; 51:188-93. [PMID: 22654163 PMCID: PMC3209889 DOI: 10.1007/s12088-011-0093-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 12/17/2009] [Indexed: 10/18/2022] Open
Abstract
The distribution of coliphages infecting different Escherichia coli virotypes (EHEC, EIEC, EPEC, ETEC) and an avirulent strain (K-12) in sewage system of a hospital and a sewage treatment plant (STP) was investigated by culture-based agar overlay methods. Coliphages were found in all the samples except stool dumping site in the sewage system of the hospital and lagoon of the STP. Bacteriophage count (pfu/ml) infecting E. coli strains showed the following ascending pattern (EHEC < EIEC < EPEC < ETEC < E coli K-12) in all the collected samples except one. Phages capable of infecting avirulent E. coli K-12 strains were present in the highest number among all the examined locations. Phages specific for E. coli K-12 presented high diversity in plaque size on the bacterial lawn. Virulent E. coli specific coliphages rarely produced plaques with diameter of 1-2 mm or over. Conventional agar overlay method was found to be not satisfactory for phage community analysis from primary stool dumping site of the hospital, probably due to the presence of high concentration of antimicrobial substances. The gradual decrease seen in the five groups of coliphage quantity with the ongoing treatment process and then the absolute absence of coliphages in the outlet of the examined treatment plant is indicative of the usefulness of the treatment processes practiced there.
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Affiliation(s)
- Muntasir Alam
- Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Tasmia Farzana
- Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | | | - Mahmuda Yasmin
- Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Jamalun Nessa
- Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
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43
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Viazis S, Akhtar M, Feirtag J, Brabban AD, Diez-Gonzalez F. Isolation and characterization of lytic bacteriophages against enterohaemorrhagic Escherichia coli. J Appl Microbiol 2011; 110:1323-31. [PMID: 21362115 DOI: 10.1111/j.1365-2672.2011.04989.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AIMS The objective of this study was to isolate, identify and characterize a collection of lytic bacteriophages capable of infecting enterohaemorrhagic Escherichia coli (EHEC) serotypes. METHODS AND RESULTS Phages were isolated from dairy and cattle feedlot manure using E. coli O157, O26 and O111 strains as hosts. Phages were enriched from faecal slurries by culture in 10× trypticase soy broth at 37°C overnight. Phage plaques were obtained by mixing the filtered culture supernatant with molten tryptone agar containing the phage E. coli host strain, pouring the inoculated agar on top of cooled TS agar and incubating the culture overnight. Phages were purified from plaques and screened against additional E. coli and EHEC strains by the efficiency of plating method (EOP). Phage CEV2, and five other phages previously isolated, were able to lyse all of the 15 O157 strains tested with EOP values consistently above 0·001. Two phages were found to be highly effective against strains of E. coli O157 through EOP tests and against O26 strains through spot tests, but not against the O serogroup 111 strains. A cocktail of eight phage that lyse E. coli O157 strains resulted in >5 log CFU ml(-1) reductions at 37°C. Multiplex-PCR revealed that none of these eight phages carried stx1, stx2, hlyA or eaeA genes. CONCLUSIONS A cocktail of bacteriophages was capable of lysing most strains of two EHEC serotypes. SIGNIFICANCE AND IMPACT OF THE STUDY This collection of phages can be combined and potentially used as an antimicrobial cocktail to inactivate E. coli strains from O serogroups 157 and 26 and reduce their incidence in the food chain.
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Affiliation(s)
- S Viazis
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN, USA
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44
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Petrov VM, Ratnayaka S, Nolan JM, Miller ES, Karam JD. Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol J 2010; 7:292. [PMID: 21029436 PMCID: PMC2993671 DOI: 10.1186/1743-422x-7-292] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 10/28/2010] [Indexed: 11/30/2022] Open
Abstract
The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.
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Affiliation(s)
- Vasiliy M Petrov
- Department of Biochemistry, Tulane University Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA, USA
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45
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Letarov A, Golomidova A, Tarasyan K. Ecological basis for rational phage therapy. Acta Naturae 2010; 2:60-72. [PMID: 22649629 PMCID: PMC3347537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Understanding the mutual interactions of bacterial and phage populations in the environment of a human or animal body is essential in any attempt to influence these complex processes, particularly for rational phage therapy. Current knowledge on the impact of naturally occurring bacteriophages on the populations of their host bacteria, and their role in the homeostasis maintenance of a macro host, is still sketchy. The existing data suggest that different mechanisms stabilize phage-bacteria coexistence in different animal species or different body sites. The defining set of parameters governing phage infection includes specific physical, chemical, and biological conditions, such as pH, nutrient densities, host prevalence, relation to mucosa and other surfaces, the presence of phage inhibiting substances, etc. Phage therapy is also an ecological process that always implies three components that form a complex pattern of interactions: populations of the pathogen, the bacteriophages used as antibacterial agents, and the macroorganism. We present a review of contemporary data on natural bacteriophages occuring in human- and animal-body associated microbial communities, and analyze ecological and physiological considerations that determine the success of phage therapy in mammals.
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Affiliation(s)
- A.V. Letarov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
| | - A.K. Golomidova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
| | - K.K. Tarasyan
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
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46
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Kim KH, Chang HW, Nam YD, Roh SW, Bae JW. Phenotypic characterization and genomic analysis of the Shigella sonnei bacteriophage SP18. J Microbiol 2010; 48:213-22. [PMID: 20437154 DOI: 10.1007/s12275-010-0055-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 04/01/2010] [Indexed: 11/29/2022]
Abstract
A novel bacteriophage that infects Shigella sonnei was isolated from the Gap River in Korea, and its phenotypic and genomic characteristics were investigated. The virus, called SP18, showed morphology characteristic of the family Myoviridae, and phylogenetic analysis of major capsid gene (gp23) sequences classified it as a T4-like phage. Based on host spectrum analysis, it is lytic to S. sonnei, but not to Shigella flexneri, Shigella boydii or members of the genera Escherichia and Salmonella. Pyrosequencing of the SP18 bacteriophage genome revealed a 170-kb length sequence. In total, 286 ORFs and 3 tRNA genes were identified, and 259 ORFs showed similarity (BLASTP e-value<0.001) to genes of other bacteriophages. The results from comparative genomic analysis indicated that the enterophage JS98, isolated from human stool, is the closest relative of SP18. Based on phylogenetic analysis of gp23 protein-coding sequences, dot plot comparison and BLASTP analysis of genomes, SP18 and JS98 appear to be closely related to T4-even phages. However, several insertions, deletions, and duplications indicate differences between SP18 and JS98. Comparison of duplicated gp24 genes and the soc gene showed that duplication events are responsible for the differentiation and evolution of T4-like bacteriophages.
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Affiliation(s)
- Kyoung-Ho Kim
- Department of Microbiology, Pukyong National University, Pusan, 608-737, Republic of Korea
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47
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Begum YA, Chakraborty S, Chowdhury A, Ghosh AN, Nair GB, Sack RB, Svennerholm AM, Qadri F. Isolation of a bacteriophage specific for CS7-expressing strains of enterotoxigenic Escherichia coli. J Med Microbiol 2010; 59:266-272. [DOI: 10.1099/jmm.0.014795-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is the most common bacterial cause of childhood diarrhoea in Bangladesh. Among the virulence factors of ETEC, toxins and colonization factors (CFs) play a major role in pathogenesis. Unlike Vibrio cholerae, the relationship between ETEC and ETEC-specific phages is poorly understood and the possible role of ETEC phages in the evolution of ETEC strains in the environment is yet to be established. This study was designed specifically to isolate phages that are specific for ETEC virulence factors. Among the 49 phages isolated from 12 different surface water samples, 13 were tested against 211 ETEC strains collected from clinical and environmental sources. One phage, designated IMM-001, showed a significant specificity towards CS7 CF as it attacked all the CS7-expressing ETEC. Electron microscopic analyses showed that the isolated phage possessed an isomeric hexagonal head and a long filamentous tail. An antibody blocking method and phage neutralization assay confirmed that CS7 pilus is required for the phage infection process, indicating the role of CS7 fimbrial protein as a potential receptor for IMM-001. In summary, this study showed the presence of a lytic phage in environmental water that is specific for the CS7 CF of ETEC.
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Affiliation(s)
- Y. A. Begum
- International Centre for Diarrhoeal Disease Research, Bangladesh, GPO Box 128, Dhaka 1000, Bangladesh
| | - S. Chakraborty
- International Centre for Diarrhoeal Disease Research, Bangladesh, GPO Box 128, Dhaka 1000, Bangladesh
| | - A. Chowdhury
- International Centre for Diarrhoeal Disease Research, Bangladesh, GPO Box 128, Dhaka 1000, Bangladesh
| | - A. N. Ghosh
- National Institute of Cholera and Enteric Diseases, Kolkata 700 010, India
| | - G. B. Nair
- National Institute of Cholera and Enteric Diseases, Kolkata 700 010, India
| | - R. B. Sack
- Department of International Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - A.-M. Svennerholm
- Department of Medical Microbiology and Immunology, The Sahlgrenska Academy at Göteborg University, Box 435, S-40530 Göteborg, Sweden
| | - F. Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh, GPO Box 128, Dhaka 1000, Bangladesh
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48
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Weiss M, Denou E, Bruttin A, Serra-Moreno R, Dillmann ML, Brüssow H. In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli. Virology 2009; 393:16-23. [PMID: 19699505 DOI: 10.1016/j.virol.2009.07.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 05/13/2009] [Accepted: 07/19/2009] [Indexed: 10/20/2022]
Abstract
The gut transit of T4 phages was studied in axenic mice mono-colonized with the non-pathogenic Escherichia coli strain K-12. Thirty minutes, 1 and 2 h after phage feeding, T4 phage had reached the jejunum, ileum and cecum, respectively. Phage was found in the lumen and was also associated with the mucosa. One day later no phage was detected in the feces. Compared to germ-free control animals, oral T4 phage led to a 300-fold higher fecal phage titer in mice mono-colonized with E. coli strain WG-5. The in vivo T4 phage replication was transient and reached peak fecal titers about 8 h after oral phage application followed by a rapid titer decrease over two days. Similar data were obtained in mice colonized with E. coli strain Nissle. In contrast, orally applied T7 phage experienced a massive and sustained in vivo replication in mice mono-colonized with E. coli strain WG-5 irrespective whether phage or E. coli host was applied first. T7 phage replication occurred mainly in the large intestine. High titers of T7 phage and high E. coli cell counts coexisted in the feces. The observation of only 20% T7 phage-resistant fecal E. coli colonies suggests a refuge model where phage-sensitive E. coli cells are physically or physiologically protected from phage infection in the gut. The difference between T7 and T4 with respect to gut replication might partly reflect their distinct in vitro capacity to replicate on slowly growing cells.
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Affiliation(s)
- Marietta Weiss
- Nestlé Research Center, Nestec Ltd P.O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
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49
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T4 phages against Escherichia coli diarrhea: Potential and problems. Virology 2009; 388:21-30. [DOI: 10.1016/j.virol.2009.03.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 12/15/2008] [Accepted: 03/01/2009] [Indexed: 12/25/2022]
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50
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Letarov A, Kulikov E. The bacteriophages in human- and animal body-associated microbial communities. J Appl Microbiol 2009; 107:1-13. [PMID: 19239553 DOI: 10.1111/j.1365-2672.2009.04143.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Felix d'Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro-organism, nevertheless remains quite fragmentary. Analysis of data in various human- and animal body-associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage-bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self-regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. 'killing the winner'). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro-organism. Alternatively, for many systems links between phages and community characteristics have not been established.
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Affiliation(s)
- A Letarov
- Winogradsky Institute of Microbiology RAS, Moscow, Russia.
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