151
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Vinner GK, Vladisavljević GT, Clokie MRJ, Malik DJ. Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release. PLoS One 2017; 12:e0186239. [PMID: 29023522 PMCID: PMC5638336 DOI: 10.1371/journal.pone.0186239] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/27/2017] [Indexed: 12/14/2022] Open
Abstract
The prevalence of pathogenic bacteria acquiring multidrug antibiotic resistance is a global health threat to mankind. This has motivated a renewed interest in developing alternatives to conventional antibiotics including bacteriophages (viruses) as therapeutic agents. The bacterium Clostridium difficile causes colon infection and is particularly difficult to treat with existing antibiotics; phage therapy may offer a viable alternative. The punitive environment within the gastrointestinal tract can inactivate orally delivered phages. C. difficile specific bacteriophage, myovirus CDKM9 was encapsulated in a pH responsive polymer (Eudragit® S100 with and without alginate) using a flow focussing glass microcapillary device. Highly monodispersed core-shell microparticles containing phages trapped within the particle core were produced by in situ polymer curing using 4-aminobenzoic acid dissolved in the oil phase. The size of the generated microparticles could be precisely controlled in the range 80 μm to 160 μm through design of the microfluidic device geometry and by varying flow rates of the dispersed and continuous phase. In contrast to free 'naked' phages, those encapsulated within the microparticles could withstand a 3 h exposure to simulated gastric fluid at pH 2 and then underwent a subsequent pH triggered burst release at pH 7. The significance of our research is in demonstrating that C. difficile specific phage can be formulated and encapsulated in highly uniform pH responsive microparticles using a microfluidic system. The microparticles were shown to afford significant protection to the encapsulated phage upon prolonged exposure to an acid solution mimicking the human stomach environment. Phage encapsulation and subsequent release kinetics revealed that the microparticles prepared using Eudragit® S100 formulations possess pH responsive characteristics with phage release triggered in an intestinal pH range suitable for therapeutic purposes. The results reported here provide proof-of-concept data supporting the suitability of our approach for colon targeted delivery of phages for therapeutic purposes.
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Affiliation(s)
- Gurinder K. Vinner
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | | | - Martha R. J. Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Danish J. Malik
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
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152
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Lin DM, Koskella B, Lin HC. Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World J Gastrointest Pharmacol Ther 2017; 8:162-173. [PMID: 28828194 PMCID: PMC5547374 DOI: 10.4292/wjgpt.v8.i3.162] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
The practice of phage therapy, which uses bacterial viruses (phages) to treat bacterial infections, has been around for almost a century. The universal decline in the effectiveness of antibiotics has generated renewed interest in revisiting this practice. Conventionally, phage therapy relies on the use of naturally-occurring phages to infect and lyse bacteria at the site of infection. Biotechnological advances have further expanded the repertoire of potential phage therapeutics to include novel strategies using bioengineered phages and purified phage lytic proteins. Current research on the use of phages and their lytic proteins against multidrug-resistant bacterial infections, suggests phage therapy has the potential to be used as either an alternative or a supplement to antibiotic treatments. Antibacterial therapies, whether phage- or antibiotic-based, each have relative advantages and disadvantages; accordingly, many considerations must be taken into account when designing novel therapeutic approaches for preventing and treating bacterial infection. Although much about phages and human health is still being discovered, the time to take phage therapy serious again seems to be rapidly approaching.
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153
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Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol 2017; 15:397-408. [DOI: 10.1038/nrmicro.2017.30] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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154
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Motley J, Stamps BW, Mitchell CA, Thompson AT, Cross J, You J, Powell DR, Stevenson BS, Cichewicz RH. Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes. JOURNAL OF NATURAL PRODUCTS 2017; 80:598-608. [PMID: 28335605 PMCID: PMC5368682 DOI: 10.1021/acs.jnatprod.6b00772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Indexed: 05/09/2023]
Abstract
Few secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria. To illustrate this process, this report focuses on samples obtained from the ear of a roadkill opossum (Dideiphis virginiana) as the source of two bacterial isolates (Pseudomonas sp. and Serratia sp.) that produced several new and known cyclic lipodepsipeptides (viscosin and serrawettins, respectively). These natural products inhibited biofilm formation by the human pathogenic yeast Candida albicans at concentrations well below those required to inhibit yeast viability. Phylogenetic analysis of 16S rRNA gene sequence libraries revealed the presence of diverse microbial communities associated with different sites throughout the opossum carcass. A putative biosynthetic pathway responsible for the production of the new serrawettin analogues was identified by sequencing the genome of the Serratia sp. isolate. This study provides a functional roadmap to carrying out the systematic investigation of the genomic, microbiological, and chemical parameters related to the production of natural products made by bacteria associated with non-anthropoidal mammalian microbiomes. Discoveries emerging from these studies are anticipated to provide a working framework for efforts aimed at augmenting microbiomes to deliver beneficial natural products to a host.
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Affiliation(s)
- Jeremy
L. Motley
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Blake W. Stamps
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019-0390, United States
| | - Carter A. Mitchell
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Alec T. Thompson
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Jayson Cross
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Jianlan You
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Douglas R. Powell
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Bradley S. Stevenson
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019-0390, United States
| | - Robert H. Cichewicz
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
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155
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Zelasko S, Gorski A, Dabrowska K. Delivering phage therapy per os: benefits and barriers. Expert Rev Anti Infect Ther 2016; 15:167-179. [DOI: 10.1080/14787210.2017.1265447] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Susan Zelasko
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Andrzej Gorski
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Krystyna Dabrowska
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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156
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Rashid SJ, Barylski J, Hargreaves KR, Millard AA, Vinner GK, Clokie MRJ. Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. Viruses 2016; 8:v8110310. [PMID: 27854339 PMCID: PMC5127024 DOI: 10.3390/v8110310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq. Two myoviruses, CDKM15 and CDKM9, were selected for detailed sequence analysis on the basis of their broad and potentially useful host range. CDKM9 infects 25/80 strains from 12/20 C. difficile ribotypes, and CDKM15 infects 20/80 strains from 9/20 ribotypes. Both phages can infect the clinically relevant ribotypes R027 and R001. Phylogenetic analysis based on whole genome sequencing revealed that the phages are genetically distinct from each other but closely related to other long-tailed myoviruses. A comparative genomic analysis revealed key differences in the genes predicted to encode for proteins involved in bacterial infection. Notably, CDKM15 carries a clustered regularly interspaced short palindromic repeat (CRISPR) array with spacers that are homologous to sequences in the CDKM9 genome and of phages from diverse localities. The findings presented suggest a possible shared evolutionary past for these phages and provides evidence of their widespread dispersal.
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Affiliation(s)
- Srwa J Rashid
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan 61-712, Poland.
| | | | - Andrew A Millard
- Microbiology & Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - Gurinder K Vinner
- Department of Chemical Engineering, Loughborough University, Loughborough, LE11 3TU, UK.
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
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157
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Nale JY, Chutia M, Carr P, Hickenbotham PT, Clokie MRJ. 'Get in Early'; Biofilm and Wax Moth (Galleria mellonella) Models Reveal New Insights into the Therapeutic Potential of Clostridium difficile Bacteriophages. Front Microbiol 2016; 7:1383. [PMID: 27630633 PMCID: PMC5005339 DOI: 10.3389/fmicb.2016.01383] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/22/2016] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile infection (CDI) is a global health threat associated with high rates of morbidity and mortality. Conventional antibiotic CDI therapy can result in treatment failure and recurrent infection. C. difficile produces biofilms which contribute to its virulence and impair antimicrobial activity. Some bacteriophages (phages) can penetrate biofilms and thus could be developed to either replace or supplement antibiotics. Here, we determined the impact of a previously optimized 4-phage cocktail on C. difficile ribotype 014/020 biofilms, and additionally as adjunct to vancomycin treatment in Galleria mellonella larva CDI model. The phages were applied before or after biofilm establishment in vitro, and the impact was analyzed according to turbidity, viability counts and topography as observed using scanning electron and confocal microscopy. The infectivity profiles and efficacies of orally administered phages and/or vancomycin were ascertained by monitoring colonization levels and larval survival rates. Phages prevented biofilm formation, and penetrated established biofilms. A single phage application reduced colonization causing extended longevity in the remedial treatment and prevented disease in the prophylaxis group. Multiple phage doses significantly improved the larval remedial regimen, and this treatment is comparable to vancomycin and the combined treatments. Taken together, our data suggest that the phages significantly reduce C. difficile biofilms, and prevent colonization in the G. mellonella model when used alone or in combination with vancomycin. The phages appear to be highly promising therapeutics in the targeted eradication of CDI and the use of these models has revealed that prophylactic use could be a propitious therapeutic option.
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Affiliation(s)
- Janet Y Nale
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
| | - Mahananda Chutia
- Pathology and Microbiology Division, Central Muga Eri Research and Training Institute Assam, India
| | - Philippa Carr
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
| | - Peter T Hickenbotham
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
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158
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Abstract
Fecal transplants are increasingly utilized for treatment of recurrent infections (i.e., Clostridium difficile) in the human gut and as a general research tool for gain-of-function experiments (i.e., gavage of fecal pellets) in animal models. Changes observed in the recipient's biology are routinely attributed to bacterial cells in the donor feces (~1011 per gram of human wet stool). Here, we examine the literature and summarize findings on the composition of fecal matter in order to raise cautiously the profile of its multipart nature. In addition to viable bacteria, which may make up a small fraction of total fecal matter, other components in unprocessed human feces include colonocytes (~107 per gram of wet stool), archaea (~108 per gram of wet stool), viruses (~108 per gram of wet stool), fungi (~106 per gram of wet stool), protists, and metabolites. Thus, while speculative at this point and contingent on the transplant procedure and study system, nonbacterial matter could contribute to changes in the recipient's biology. There is a cautious need for continued reductionism to separate out the effects and interactions of each component. Fecal transfers are increasingly common in animal models and humans. This essay notes that bacteria may not be the only player in donor feces that can affect the recipient's biology.
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Affiliation(s)
- Diana P. Bojanova
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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159
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Clinical News. Br J Hosp Med (Lond) 2016. [DOI: 10.12968/hmed.2016.77.7.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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160
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Kirk JA, Banerji O, Fagan RP. Characteristics of the Clostridium difficile cell envelope and its importance in therapeutics. Microb Biotechnol 2016; 10:76-90. [PMID: 27311697 PMCID: PMC5270738 DOI: 10.1111/1751-7915.12372] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 01/08/2023] Open
Abstract
Clostridium difficile infection (CDI) is a challenging threat to human health. Infections occur after disruption of the normal microbiota, most commonly through the use of antibiotics. Current treatment for CDI largely relies on the broad‐spectrum antibiotics vancomycin and metronidazole that further disrupt the microbiota resulting in frequent recurrence, highlighting the need for C. difficile‐specific antimicrobials. The cell surface of C. difficile represents a promising target for the development of new drugs. C. difficile possesses a highly deacetylated peptidoglycan cell wall containing unique secondary cell wall polymers. Bound to the cell wall is an essential S‐layer, formed of SlpA and decorated with an additional 28 related proteins. In addition to the S‐layer, many other cell surface proteins have been identified, including several with roles in host colonization. This review aims to summarize our current understanding of these different C. difficile cell surface components and their viability as therapeutic targets.
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Affiliation(s)
- Joseph A Kirk
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Oishik Banerji
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert P Fagan
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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161
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Broecker F, Klumpp J, Moelling K. Long-term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection. Ann N Y Acad Sci 2016; 1372:29-41. [PMID: 27286042 DOI: 10.1111/nyas.13100] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
Fecal microbiota transplantation (FMT) is an emerging therapeutic option for Clostridium difficile infections that are refractory to conventional treatment. FMT introduces fecal microbes into the patient's intestine that prevent the recurrence of C. difficile, leading to rapid expansion of bacteria characteristic of healthy microbiota. However, the long-term effects of FMT remain largely unknown. The C. difficile patient described in this paper revealed protracted microbiota adaptation processes from 6 to 42 months post-FMT. Ultimately, bacterial communities were donor similar, suggesting sustainable stool engraftment. Since little is known about the consequences of transmitted viruses during C. difficile infection, we also interrogated virome changes. Our approach allowed identification of about 10 phage types per sample that represented larger viral communities, and phages were found to be equally abundant in the cured patient and donor. The healthy microbiota appears to be characterized by low phage abundance. Although viruses were likely transferred, the patient established a virome distinct from the donor. Surprisingly, the patient had sequences of algal giant viruses (chloroviruses) that have not previously been reported for the human gut. Chloroviruses have not been associated with intestinal disease, but their presence in the oropharynx may influence cognitive abilities. The findings suggest that the virome is an important indicator of health or disease. A better understanding of the role of viruses in the gut ecosystem may uncover novel microbiota-modulating therapeutic strategies.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical Microbiology, University of Zürich, Zürich, Switzerland.,Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jochen Klumpp
- Institute of Food, Nutrition, and Health, ETH Zürich, Zürich, Switzerland
| | - Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical Microbiology, University of Zürich, Zürich, Switzerland
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