1
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Parmar K, Fackler JR, Rivas Z, Mandrekar J, Greenwood-Quaintance KE, Patel R. A comparison of phage susceptibility testing with two liquid high-throughput methods. Front Microbiol 2024; 15:1386245. [PMID: 39171268 PMCID: PMC11335653 DOI: 10.3389/fmicb.2024.1386245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
Phage therapy is a promising antibacterial strategy, especially given that drug-resistant bacterial infections are escalating worldwide. Because phages are not active against all strains of a given species, phages being considered for therapeutic use would ideally be tested against bacterial isolates from individual patients prior to administration. Standardized, clinically validated phage susceptibility testing (PST) methods are needed for assessing in vitro phage activity. This study compared two high-throughput liquid-based PST assays. The first, using the Biolog Omnilog™, assessed changes in microbial respiration leading to color changes based on a tetrazolium dye. The second, Agilent BioTek Cytation 7, assessed changes in optical density. Both used 96-well microtiter plate formats. A total of 55 diverse phages with activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, or Enterococcus faecalis were studied against their respective susceptible bacterial hosts and non-susceptible controls, with susceptibility defined based on plaque assay. PST was performed by both assays in replicates, with results compared in terms of hold times (time through which bacterial growth is inhibited by phage compared to controls). Coefficients of variance and interclass correlation coefficients were used to assess inter- and intra-assay reproducibility. Based on a ≤50% coefficient of variance cutpoint, 87% of Biolog and 84% of Agilent assays were considered valid for susceptible bacteria, with 100% considered valid for non-susceptible bacteria by both systems. Using a 8 h hold time cutpoint, 100% of the results matched between the two assays. The interclass correlation coefficient showed 26% excellent agreement, 35% good agreement, and 17% moderate agreement between the two assays for susceptible isolates and 100% excellent agreement for non-susceptible isolates. Overall, the assays compared provided good/fair statistical reproducibility for the assessment of phage susceptibility.
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Affiliation(s)
- Krupa Parmar
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Joseph R. Fackler
- Adaptive Phage Therapeutics, Inc. (APT), Gaithersburg, MD, United States
| | - Zuriel Rivas
- Adaptive Phage Therapeutics, Inc. (APT), Gaithersburg, MD, United States
| | - Jay Mandrekar
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, United States
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2
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Bayat F, Hilal A, Thirugnanasampanthar M, Tremblay D, Filipe CDM, Moineau S, Didar TF, Hosseinidoust Z. High throughput platform technology for rapid target identification in personalized phage therapy. Nat Commun 2024; 15:5626. [PMID: 38992046 PMCID: PMC11239838 DOI: 10.1038/s41467-024-49710-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
As bacteriophages continue to gain regulatory approval for personalized human therapy against antibiotic-resistant infections, there is a need for transformative technologies for rapid target identification through multiple, large, decentralized therapeutic phages biobanks. Here, we design a high throughput phage screening platform comprised of a portable library of individual shelf-stable, ready-to-use phages, in all-inclusive solid tablets. Each tablet encapsulates one phage along with luciferin and luciferase enzyme stabilized in a sugar matrix comprised of pullulan and trehalose capable of directly detecting phage-mediated adenosine triphosphate (ATP) release through ATP bioluminescence reaction upon bacterial cell burst. The tablet composition also enhances desiccation tolerance of all components, which should allow easier and cheaper international transportation of phages and as a result, increased accessibility to therapeutic phages. We demonstrate high throughput screening by identifying target phages for select multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Staphylococcus aureus with targets identified within 30-120 min.
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Affiliation(s)
- Fereshteh Bayat
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Arwa Hilal
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | | | - Denise Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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3
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Aslam S, Roach D, Nikolich MP, Biswas B, Schooley RT, Lilly-Bishop KA, Rice GK, Cer RZ, Hamilton T, Henry M, Luong T, Salabarria AC, Sisk-Hackworth L, Filippov AA, Lebreton F, Hall L, Nir-Paz R, Onallah H, Livni G, Shostak E, Wieder-Finesod A, Yahav D, Yerushalmy O, Alkalay-Oren S, Braunstein R, Khalifa L, Rimon A, Gelman D, Hazan R. Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases. Antimicrob Agents Chemother 2024; 68:e0172823. [PMID: 38470133 PMCID: PMC10989018 DOI: 10.1128/aac.01728-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular Pseudomonas aeruginosa LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14-51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in P. aeruginosa endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.
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Affiliation(s)
- Saima Aslam
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Dwayne Roach
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Mikeljon P. Nikolich
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Biswajit Biswas
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Robert T. Schooley
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | | | - Gregory K. Rice
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- Leidos, Inc, Reston, Virginia, USA
| | - Regina Z. Cer
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Theron Hamilton
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Matthew Henry
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- The Geneva Foundation, Tacoma, Washington, USA
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | | | - Andrey A. Filippov
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lindsey Hall
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hadil Onallah
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gilat Livni
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Eran Shostak
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Anat Wieder-Finesod
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Dafna Yahav
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Braunstein
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leron Khalifa
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Gelman
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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4
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Needham P, Page RC, Yehl K. Phage-layer interferometry: a companion diagnostic for phage therapy and a bacterial testing platform. Sci Rep 2024; 14:6026. [PMID: 38472239 PMCID: PMC10933294 DOI: 10.1038/s41598-024-55776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
The continuing and rapid emergence of antibiotic resistance (AMR) calls for innovations in antimicrobial therapies. A promising, 're-emerging' approach is the application of bacteriophage viruses to selectively infect and kill pathogenic bacteria, referred to as phage therapy. In practice, phage therapy is personalized and requires companion diagnostics to identify efficacious phages, which are then formulated into a therapeutic cocktail. The predominant means for phage screening involves optical-based assays, but these methods cannot be carried out in complex media, such as colored solutions, inhomogeneous mixtures, or high-viscosity samples, which are often conditions encountered in vivo. Moreover, these assays cannot distinguish phage binding and lysis parameters, which are important for standardizing phage cocktail formulation. To address these challenges, we developed Phage-layer Interferometry (PLI) as a companion diagnostic. Herein, PLI is assessed as a quantitative phage screening method and prototyped as a bacterial detection platform. Importantly, PLI is amenable to automation and is functional in complex, opaque media, such as baby formula. Due to these newfound capabilities, we foresee immediate and broad impact of PLI for combating AMR and protecting against foodborne illnesses.
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Affiliation(s)
- Patrick Needham
- Department of Chemistry and Biochemistry, Miami University, Oxford, 45056, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, 45056, USA
| | - Kevin Yehl
- Department of Chemistry and Biochemistry, Miami University, Oxford, 45056, USA.
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5
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Desmecht S, Latka A, Ceyssens PJ, Garcia-Pino A, Gillis A, Lavigne R, Lima-Mendez G, Matthijnssens J, Vázquez R, Venneman J, Wagemans J, Briers Y, Thiry D. Meeting Report of the Second Symposium of the Belgian Society for Viruses of Microbes and Launch of the Phage Valley. Viruses 2024; 16:299. [PMID: 38400074 PMCID: PMC10891784 DOI: 10.3390/v16020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
The second symposium of the Belgian Society for Viruses of Microbes (BSVoM) took place on 8 September 2023 at the University of Liège with 141 participants from 10 countries. The meeting program covered three thematic sessions opened by international keynote speakers: two sessions were devoted to "Fundamental research in phage ecology and biology" and the third one to the "Present and future applications of phages". During this one day symposium, four invited keynote lectures, nine selected talks and eight student pitches were given along with thirty presented posters. The president of the Belgian Society for Viruses of Microbes, Prof. Yves Briers, took advantage of this symposium to launch the Phage Valley concept that will put the spotlight on the exceptionally high density of researchers investigating viruses of microbes as well as the successful triple helix approach between academia, industry and government in Belgium.
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Affiliation(s)
- Salomé Desmecht
- Veterinary Bacteriology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liège (ULiège), 4000 Liège, Belgium;
| | - Agnieszka Latka
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, University of Ghent (UGent), 9000 Gent, Belgium; (A.L.); (R.V.)
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, 51-148 Wroclaw, Poland
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculty of Sciences, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), 1348 Louvain-la-Neuve, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, 3001 Leuven, Belgium; (R.L.); (J.W.)
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, Belgium;
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium;
| | - Roberto Vázquez
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, University of Ghent (UGent), 9000 Gent, Belgium; (A.L.); (R.V.)
| | - Jolien Venneman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, 3001 Leuven, Belgium; (R.L.); (J.W.)
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, University of Ghent (UGent), 9000 Gent, Belgium; (A.L.); (R.V.)
| | - Damien Thiry
- Veterinary Bacteriology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liège (ULiège), 4000 Liège, Belgium;
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6
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Gencay YE, Jasinskytė D, Robert C, Semsey S, Martínez V, Petersen AØ, Brunner K, de Santiago Torio A, Salazar A, Turcu IC, Eriksen MK, Koval L, Takos A, Pascal R, Schou TS, Bayer L, Bryde T, Johansen KC, Bak EG, Smrekar F, Doyle TB, Satlin MJ, Gram A, Carvalho J, Jessen L, Hallström B, Hink J, Damholt B, Troy A, Grove M, Clube J, Grøndahl C, Haaber JK, van der Helm E, Zdravkovic M, Sommer MOA. Engineered phage with antibacterial CRISPR-Cas selectively reduce E. coli burden in mice. Nat Biotechnol 2024; 42:265-274. [PMID: 37142704 PMCID: PMC10869271 DOI: 10.1038/s41587-023-01759-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Antibiotic treatments have detrimental effects on the microbiome and lead to antibiotic resistance. To develop a phage therapy against a diverse range of clinically relevant Escherichia coli, we screened a library of 162 wild-type (WT) phages, identifying eight phages with broad coverage of E. coli, complementary binding to bacterial surface receptors, and the capability to stably carry inserted cargo. Selected phages were engineered with tail fibers and CRISPR-Cas machinery to specifically target E. coli. We show that engineered phages target bacteria in biofilms, reduce the emergence of phage-tolerant E. coli and out-compete their ancestral WT phages in coculture experiments. A combination of the four most complementary bacteriophages, called SNIPR001, is well tolerated in both mouse models and minipigs and reduces E. coli load in the mouse gut better than its constituent components separately. SNIPR001 is in clinical development to selectively kill E. coli, which may cause fatal infections in hematological cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Lev Koval
- SNIPR BIOME ApS, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Morten Otto Alexander Sommer
- SNIPR BIOME ApS, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, DTU Biosustain, Kongens Lyngby, Denmark.
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7
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Qiu J, Nie W, Ding H, Dai J, Wei Y, Li D, Zhang Y, Xie J, Tian X, Wu N, Qiu T. PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy. Brief Bioinform 2024; 25:bbae010. [PMID: 38344864 PMCID: PMC10859729 DOI: 10.1093/bib/bbae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/16/2023] [Accepted: 01/05/2024] [Indexed: 02/15/2024] Open
Abstract
Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship of phages across strain mutants. This has hindered the development of phage therapeutics based on the prediction of phage-bacteria relationships. In this paper, we present, PB-LKS, to predict the phage-bacteria interaction based on local K-mer strategy with higher performance and wider applicability. The utility of PB-LKS is rigorously validated through (i) large-scale historical screening, (ii) case study at the class level and (iii) in vitro simulation of bacterial antiphage resistance at the strain mutant level. The PB-LKS approach could outperform the current state-of-the-art methods and illustrate potential clinical utility in pre-optimized phage therapy design.
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Affiliation(s)
- Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Wanchun Nie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hao Ding
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Jia Dai
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yiwen Wei
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yuxi Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Junting Xie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xinxin Tian
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
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8
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Merabishvili M, Pirnay JP, De Vos D. Guidelines to Compose an Ideal Bacteriophage Cocktail. Methods Mol Biol 2024; 2734:49-66. [PMID: 38066362 DOI: 10.1007/978-1-0716-3523-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Properly designed bacteriophage therapeutics are the cornerstone for a successful outcome of bacteriophage therapy. Here we present an overview of the different strategies and steps that can be taken to develop a bacteriophage cocktail that complies with relevant quality and safety requirements. It is based on empirical bacteriophage therapy knowledge from over a century of experience, more recently performed studies, and emerging technologies. We emphasize the selection of adequate bacteriophages and describe a modified Appelmans' method to improve the overall performance of therapeutic bacteriophages individually and collectively in the cocktail. We present two versions of the method, which differ from each other by the employed techniques to evaluate phage activity and synergy: photometric assessment of bacterial growth versus measurement of bacterial respiration via the Omnilog® system.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium.
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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9
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Parmar K, Komarow L, Ellison DW, Filippov AA, Nikolich MP, Fackler JR, Lee M, Nair A, Agrawal P, Tamma PD, Souli M, Evans SR, Greenwood-Quaintance KE, Cunningham SA, Patel R. Interlaboratory comparison of Pseudomonas aeruginosa phage susceptibility testing. J Clin Microbiol 2023; 61:e0061423. [PMID: 37962552 PMCID: PMC10729752 DOI: 10.1128/jcm.00614-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023] Open
Abstract
Standardized approaches to phage susceptibility testing (PST) are essential to inform selection of phages for study in patients with bacterial infections. There is no reference standard for assessing bacterial susceptibility to phage. We compared agreement between PST performed at three centers: two centers using a liquid assay standardized between the sites with the third, a plaque assay. Four Pseudomonas aeruginosa phages: PaWRA01ø11 (EPa11), PaWRA01ø39 (EPa39), PaWRA02ø83 (EPa83), PaWRA02ø87 (EPa87), and a cocktail of all four phages were tested against 145 P. aeruginosa isolates. Comparisons were made within measurements at the two sites performing the liquid assay and between these two sites. Agreement was assessed based on coverage probability (CP8), total deviation index, concordance correlation coefficient (CCC), measurement accuracy, and precision. For the liquid assay, there was satisfactory agreement among triplicate measurements made on different days at site 1, and high agreement based on accuracy and precision between duplicate measurements made on the same run at site 2. There was fair accuracy between measurements of the two sites performing the liquid assay, with CCCs below 0.6 for all phages tested. When compared to the plaque assay (performed once at site 3), there was less agreement between results of the liquid and plaque assays than between the two sites performing the liquid assay. Similar findings to the larger group were noted in the subset of 46 P. aeruginosa isolates from cystic fibrosis. Results of this study suggest that reproducibility of PST methods needs further development.
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Affiliation(s)
- Krupa Parmar
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lauren Komarow
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Damon W. Ellison
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mikeljon P. Nikolich
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Martin Lee
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Anjna Nair
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Priyesh Agrawal
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Pranita D. Tamma
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maria Souli
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Scott R. Evans
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., USA
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - for the Antibacterial Resistance Leadership Group
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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10
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Bosco K, Lynch S, Sandaradura I, Khatami A. Therapeutic Phage Monitoring: A Review. Clin Infect Dis 2023; 77:S384-S394. [PMID: 37932121 DOI: 10.1093/cid/ciad497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
With the global rise in antimicrobial resistance, there has been a renewed interest in the application of therapeutic phages to treat bacterial infections. Therapeutic phage monitoring (TPM) is proposed as an essential element of phage therapy (PT) protocols to generate data and fill knowledge gaps regarding the in vivo efficacy of therapeutic phages, patients' immune responses to PT, and the wider ecological effects of PT. By monitoring phage concentrations in blood and tissues, together with immune responses and possible ecological changes during PT, TPM may enable the optimization of dosing and the implementation of precision medicine approaches. Furthermore, TPM can validate diagnostic surrogates of efficacy, direct research efforts, and establish quality assurance indicators for therapeutic phage products. Thus, TPM holds great potential for enhancing our understanding of the multidirectional phage-bacteria-host interactions and advancing "best practice" PT, ultimately improving patient care.
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Affiliation(s)
- Kiran Bosco
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Lynch
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Indy Sandaradura
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ameneh Khatami
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
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11
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Yerushalmy O, Braunstein R, Alkalay-Oren S, Rimon A, Coppenhagn-Glazer S, Onallah H, Nir-Paz R, Hazan R. Towards Standardization of Phage Susceptibility Testing: The Israeli Phage Therapy Center "Clinical Phage Microbiology"-A Pipeline Proposal. Clin Infect Dis 2023; 77:S337-S351. [PMID: 37932122 DOI: 10.1093/cid/ciad514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Using phages as salvage therapy for nonhealing infections is gaining recognition as a viable solution for patients with such infections. The escalating issue of antibiotic resistance further emphasizes the significance of using phages in treating bacterial infections, encompassing compassionate-use scenarios and clinical trials. Given the high specificity of phages, selecting the suitable phage(s) targeting the causative bacteria becomes critical for achieving treatment success. However, in contrast to conventional antibiotics, where susceptibility-testing procedures were well established for phage therapy, there is a lack of standard frameworks for matching phages from a panel to target bacterial strains and assessing their interactions with antibiotics or other agents. This review discusses and compares published methods for clinical phage microbiology, also known as phage susceptibility testing, and proposes guidelines for establishing a standard pipeline based on our findings over the past 5 years of phage therapy at the Israeli Phage Therapy Center.
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Affiliation(s)
- Ortal Yerushalmy
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Braunstein
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
- The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Rimon
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shunit Coppenhagn-Glazer
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadil Onallah
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ran Nir-Paz
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ronen Hazan
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
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12
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Onallah H, Hazan R, Nir-Paz R, Brownstein MJ, Fackler JR, Horne B, Hopkins R, Basu S, Yerushalmy O, Alkalay-Oren S, Braunstein R, Rimon A, Gelman D, Khalifa L, Adler K, Abdalrhman M, Gelman S, Katvan E, Coppenhagen-Glazer S, Moses A, Oster Y, Dekel M, Ben-Ami R, Khoury A, Kedar DJ, Meijer SE, Ashkenazi I, Bishouty N, Yahav D, Shostak E, Livni G, Paul M, Gross M, Ormianer M, Aslam S, Ritter M, Urish KL, La Hoz RM, Khatami A, Britton PN, Lin RCY, Iredell JR, Petrovic-Fabijan A, Lynch S, Tamma PD, Yamshchikov A, Lesho E, Morales M, Werzen A, Saharia K. Refractory Pseudomonas aeruginosa infections treated with phage PASA16: A compassionate use case series. MED 2023; 4:600-611.e4. [PMID: 37562400 DOI: 10.1016/j.medj.2023.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND A growing number of compassionate phage therapy cases were reported in the last decade, with a limited number of clinical trials conducted and few unsuccessful clinical trials reported. There is only a little evidence on the role of phages in refractory infections. Our objective here was to present the largest compassionate-use single-organism/phage case series in 16 patients with non-resolving Pseudomonas aeruginosa infections. METHODS We summarized clinical phage microbiology susceptibility data, administration protocol, clinical data, and outcomes of all cases treated with PASA16 phage. In all intravenous phage administrations, PASA16 phage was manufactured and provided pro bono by Adaptive Phage Therapeutics. PASA16 was administered intravenously, locally to infection site, or by topical use to 16 patients, with data available for 15 patients, mainly with osteoarticular and foreign-device-associated infections. FINDINGS A few minor side effects were noted, including elevated liver function enzymes and a transient reduction in white blood cell count. Good clinical outcome was documented in 13 out of 15 patients (86.6%). Two clinical failures were reported. The minimum therapy duration was 8 days with a once- to twice-daily regimen. CONCLUSIONS PASA16 with antibiotics was found to be relatively successful in patients for whom traditional treatment approaches have failed previously. Such pre-phase-1 cohorts can outline potential clinical protocols and facilitate the design of future trials. FUNDING The study was funded in part by The Israeli Science Foundation IPMP (ISF_1349/20), Rosetrees Trust (A2232), United States-Israel Binational Science Foundation (2017123), and the Milgrom Family Support Program.
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Affiliation(s)
- Hadil Onallah
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel
| | - Ronen Hazan
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ran Nir-Paz
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel.
| | | | | | - Bri'Anna Horne
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Robert Hopkins
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Subhendu Basu
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Ortal Yerushalmy
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sivan Alkalay-Oren
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ron Braunstein
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amit Rimon
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Daniel Gelman
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Leron Khalifa
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Karen Adler
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mohanad Abdalrhman
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel
| | - Shira Gelman
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Eyal Katvan
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar Ilan University, Ramat-Gan 52900, Israel; Peres Academic Center, Rehovot 7610202, Israel
| | - Shunit Coppenhagen-Glazer
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem 9112102, Israel; Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Allon Moses
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel
| | - Yonatan Oster
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel
| | - Michal Dekel
- Infectious Diseases Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Ronen Ben-Ami
- Infectious Diseases Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Amal Khoury
- Infectious Diseases Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Daniel J Kedar
- Department of Plastic and Reconstructive Surgery, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Suzy E Meijer
- Department of Plastic and Reconstructive Surgery, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Itay Ashkenazi
- Division of Orthopedic Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Nancy Bishouty
- Pharmacy Department, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Dafna Yahav
- Infectious Disease Unit, Rabin Medical Center, Petah Tikva 49100, Israel
| | - Eran Shostak
- Pediatric Cardiac Intensive Care Unit, Schneider Children's Medical Center, Petah Tikva 4920235, Israel
| | - Gilat Livni
- Pediatric Infectious Diseases Unit, Schneider Children's Medical Center, Petah Tikva 4920235, Israel
| | - Mical Paul
- Rambam Health Care Campus and Faculty of Medicine, The Technion - Israel Institute of Technology, Haifa 3109601, Israel
| | - Menachem Gross
- Department of Otolaryngology-Head and Neck Surgery, Hadassah-Hebrew University Medical Center, Jerusalem 9112000, Israel
| | - Matityahou Ormianer
- Department of Otolaryngology-Head and Neck Surgery, Hadassah-Hebrew University Medical Center, Jerusalem 9112000, Israel
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92093, USA; Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michele Ritter
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kenneth L Urish
- Bone and Joint Center, Magee Hospital, Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Ricardo M La Hoz
- Division of Infectious Disease and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ameneh Khatami
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ruby C Y Lin
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Jonathan R Iredell
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Aleksandra Petrovic-Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Stephanie Lynch
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Pranita D Tamma
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexandra Yamshchikov
- Infectious Diseases Unit, Rochester Regional Health, Rochester, NY 14617, USA; Infectious Diseases Unit, University of Rochester Medical Center, Rochester, NY 14617, USA
| | - Emil Lesho
- Infectious Diseases Unit, Rochester Regional Health, Rochester, NY 14617, USA
| | - Megan Morales
- Division of Infectious Diseases, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Alissa Werzen
- Division of Infectious Diseases, Jefferson Medicine, Philadelphia, PA 19107, USA
| | - Kapil Saharia
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
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13
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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14
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Jones JD, Trippett C, Suleman M, Clokie MRJ, Clark JR. The Future of Clinical Phage Therapy in the United Kingdom. Viruses 2023; 15:721. [PMID: 36992430 PMCID: PMC10053292 DOI: 10.3390/v15030721] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Bacteriophage (phage) therapy is a promising alternative antimicrobial strategy with the potential to transform the way bacterial infections are treated. In the United Kingdom, phages are classed as a biological medicine. Although no phages are licensed for UK use, they may be used as unlicensed medicinal products where licensed alternatives cannot meet a patient's clinical needs. In the last 2 years, 12 patients in the UK have received phage therapy, and there is burgeoning clinical interest. Currently, clinical phage provision in the UK is ad hoc and relies upon networking with international sources of phages. The provision of phage therapy in the UK will not progress beyond an increasing number of ad hoc cases until an onshore sustainable and scalable source of well-characterised phages manufactured in accordance with Good Manufacturing Practice (GMP) is established. Here, we present an exciting new collaboration between UK Phage Therapy, the Centre for Phage Research at University of Leicester, CPI, and Fixed Phage. These partners, and others as we develop, will establish sustainable, scalable, and equitable phage therapy provision in the UK. We set out a vision for how phage therapy will be integrated into the NHS and healthcare more broadly, including the complementarity between licensed (cocktail) and unlicensed (personalised) phage preparations. Key elements of phage therapy infrastructure in the UK will be GMP phage manufacturing, a national phage library, and a national clinical phage centre. Together, this infrastructure will support NHS microbiology departments to develop and oversee phage therapy provision across the UK. As it will take time to deliver this, we also describe considerations for clinicians seeking to use unlicensed phage therapy in the interim. In summary, this review sets out a roadmap for the delivery of clinical phage therapy to the UK, the benefits of which we hope will reverberate for patients for decades to come.
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Affiliation(s)
| | - Clare Trippett
- CPI, 1 Union Square, Central Park, Darlington DL1 1GL, UK
| | - Mehrunisha Suleman
- The Ethox Centre, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, UK
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Jason R. Clark
- Fixed Phage, West of Scotland Science Park, Block 2, Kelvin Campus, 2317 Maryhill Road, Glasgow G20 0SP, UK
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15
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Suh GA, Patel R. Clinical phage microbiology: a narrative summary. Clin Microbiol Infect 2023:S1198-743X(23)00059-9. [PMID: 36805835 DOI: 10.1016/j.cmi.2023.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Although phage therapy has been in existence for a century, a recent resurgence in interest has occurred because of the continued emergence of antimicrobial resistance and the rising use of indwelling medical devices, resulting in biofilm-associated infections, for which conventional antibiotics are of limited use. Despite this, the clinical successes have been inconsistent because of multiple reasons, including (1) the narrow host range of phages, (2) challenges with concentrating phages at the site of infection, (3) development of resistance of bacteria to phages and (4) immune neutralization. Microbiologic assays have the potential to help guide the course of clinical therapy and improve outcomes. Methods developed decades ago remain the mainstay of phage diagnostics and recently, newer diagnostics are closing the gap needed to further advance clinical phage therapy. OBJECTIVES To review the current state of clinical phage microbiology and identify gaps. SOURCES A PubMed search was performed using the terms "phage microbiology", "phage susceptibility test", "phage host range", "phage biofilm", and "phage therapeutic monitoring". CONTENT Phage susceptibility testing, biofilm assays, phage-antibiotic combination testing, therapeutic drug monitoring, and immune monitoring assays are the current foundation for clinical phage diagnostics. Standardization of these assays and better understanding as to if and how they should be used in terms of clinical management of patients receiving phage therapy is needed. IMPLICATIONS A substantial gap between in vitro studies and in vivo outcomes indicates that further work is needed in phage pharmacokinetics to accurately assay phage particles at the site of infection; recapitulate in vivo biofilm; capture the complex interactions between phages and antibiotics, phages and their target bacteria, among phages in a cocktail, and with the superhost immune system.
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Affiliation(s)
- Gina A Suh
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA; Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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16
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Egido JE, Toner-Bartelds C, Costa AR, Brouns SJJ, Rooijakkers SHM, Bardoel BW, Haas PJ. Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye. Sci Rep 2023; 13:856. [PMID: 36646746 PMCID: PMC9842612 DOI: 10.1038/s41598-023-27734-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Catherine Toner-Bartelds
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bart W Bardoel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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17
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 140] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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18
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Tamma PD, Souli M, Billard M, Campbell J, Conrad D, Ellison DW, Evans B, Evans SR, Greenwood-Quaintance KE, Filippov AA, Geres HS, Hamasaki T, Komarow L, Nikolich MP, Lodise TP, Nayak SU, Norice-Tra C, Patel R, Pride D, Russell J, Van Tyne D, Chambers HF, FowlerJr VG, Schooley RT. Safety and microbiological activity of phage therapy in persons with cystic fibrosis colonized with Pseudomonas aeruginosa: study protocol for a phase 1b/2, multicenter, randomized, double-blind, placebo-controlled trial. Trials 2022; 23:1057. [PMID: 36578069 PMCID: PMC9795609 DOI: 10.1186/s13063-022-07047-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Bacteriophages (phages) are a promising anti-infective option for human disease. Major gaps remain in understanding their potential utility. METHODS This is a randomized, placebo-controlled, double-blind study of a single dose of intravenous phage in approximately 72 clinically stable adult cystic fibrosis volunteers recruited from up to 20 US sites with Pseudomonas aeruginosa airway colonization. The single dose of phage consists of a mixture of four anti-pseudomonal phages. Six sentinel participants will be sequentially enrolled with dose escalation of the phage mixture by one log10 beginning with 4 × 107 plaque-forming units in an unblinded stage 1. If no serious adverse events related to the study product are identified, the trial will proceed to a double-blinded stage 2. In stage 2a, 32 participants will be randomly assigned to one of three phage dosages or placebo in a 1:1:1:1 allocation. An interim analysis will be performed to determine the phage dosage with the most favorable safety and microbiological activity profile to inform phage dosing in stage 2b. During stage 2b, up to 32 additional volunteers will be randomized 1:1 to the phage or placebo arm. Primary outcomes include (1) the number of grade 2 or higher treatment-emergent adverse events, (2) change in log10 P. aeruginosa total colony counts in sputum, and (3) the probability of a randomly selected subject having a more favorable outcome ranking if assigned to receive phage therapy versus placebo. Exploratory outcomes include (1) sputum and serum phage pharmacokinetics, (2) the impact of phage on lung function, (3) the proportion of P. aeruginosa isolates susceptible to the phage mixture before and after study product administration, and (4) changes in quality of life. DISCUSSION This trial will investigate the activity of phages in reducing P. aeruginosa colony counts and provide insights into the safety profile of phage therapy. TRIAL REGISTRATION ClinicalTrials.gov NCT05453578. Registered on 12 July 2022.
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Affiliation(s)
- Pranita D. Tamma
- grid.21107.350000 0001 2171 9311Department of Pediatrics, Johns Hopkins University School of Medicine, 200 North Wolfe Street, Room 3149, Baltimore, MD 21287 USA
| | - Maria Souli
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | | | - Joseph Campbell
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Douglas Conrad
- grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, San Diego, CA USA
| | - Damon W. Ellison
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Beth Evans
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | - Scott R. Evans
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | | | - Andrey A. Filippov
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Holly S. Geres
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | - Toshimitsu Hamasaki
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | - Lauren Komarow
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | - Mikeljon P. Nikolich
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Thomas P. Lodise
- grid.413555.30000 0000 8718 587XDepartment of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, NY USA
| | - Seema U. Nayak
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Carmelle Norice-Tra
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Robin Patel
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA ,grid.66875.3a0000 0004 0459 167XInfectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | - David Pride
- grid.266100.30000 0001 2107 4242Departments of Medicine and Pathology, University of California San Diego, San Diego, CA USA
| | - Janie Russell
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Daria Van Tyne
- grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Henry F. Chambers
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Vance G. FowlerJr
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA ,grid.189509.c0000000100241216Department of Medicine, Duke University Medical Center, Durham, NC USA
| | - Robert T. Schooley
- grid.266100.30000 0001 2107 4242Departments of Medicine and Pathology, University of California San Diego, San Diego, CA USA
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19
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Patpatia S, Schaedig E, Dirks A, Paasonen L, Skurnik M, Kiljunen S. Rapid hydrogel-based phage susceptibility test for pathogenic bacteria. Front Cell Infect Microbiol 2022; 12:1032052. [PMID: 36569196 PMCID: PMC9771388 DOI: 10.3389/fcimb.2022.1032052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Phage therapy is one alternative to cure infections caused by antibiotic resistant bacteria. Due to the narrow host range of phages, hundreds to thousands of phages are required to cover the diversity of bacterial pathogens. In personalized phage therapy, fast selection of the phages for individual patients is essential for successful therapy. The aims of this study were to set up a rapid hydrogel-based liquid phage susceptibility assay (PST) for the selection of phages for therapeutic use and to establish a "ready-to-screen" plate concept, where phages are readily stored in hydrogel as small droplets in microtiter plate wells. We first tested four commercially available hydrogels (GrowDex, Askina, Purilon, and Intrasite) for their suitability as phage matrices in PSTs with four phages, two of which infecting Escherichia coli and two Staphylococcus aureus. Of these four hydrogels, GrowDex was the best matrix for PST, as it did not inhibit bacterial growth, released phages quickly when mixed with bacterial culture, and maintained phage viability well. We then optimized the assay for both optical density and microscopy readers using GrowDex as matrix with 23 bacterial strains representing 10 different species and 23 phages possessing different morphologies and genome sizes. When the bacterial growth was monitored by microscopy reader, the PST was executed in just 3 hours, and there was no need for overnight culturing bacterial cells prior to the assay, whereas using optical density reader, bacteria had to be pre-cultured overnight, and the assay time was five hours. Finally, we evaluated the effect of three different chemical stabilizers (trehalose, hyaluronic acid, and gelatin) in a six-month stability assay with six model phages. These phages assay behaved very differently in respect to the chemical stabilizers, and there was not a single stabilizer suitable for all phages. However, when gelatin (0.01%) or hyaluronic acid (0.2 mg/ml) was used as stabilizer, all tested phages were still considered as positives in PST after a six-month storage in 1 ml volume. In "ready-to-screen" plates, the differences in phage stabilities were even more profound, varying from two to six months for the most and least stable phages, respectively.
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Affiliation(s)
- Sheetal Patpatia
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eric Schaedig
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Dirks
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Mikael Skurnik
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Saija Kiljunen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland,*Correspondence: Saija Kiljunen,
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20
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Daubie V, Chalhoub H, Blasdel B, Dahma H, Merabishvili M, Glonti T, De Vos N, Quintens J, Pirnay JP, Hallin M, Vandenberg O. Determination of phage susceptibility as a clinical diagnostic tool: A routine perspective. Front Cell Infect Microbiol 2022; 12:1000721. [PMID: 36211951 PMCID: PMC9532704 DOI: 10.3389/fcimb.2022.1000721] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.
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Affiliation(s)
- Valéry Daubie
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Houssein Chalhoub
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bob Blasdel
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Hafid Dahma
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Nathalie De Vos
- Department of Clinical Chemistry, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Johan Quintens
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- *Correspondence: Olivier Vandenberg,
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21
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Doub JB, Urish K, Chan B. Bacteriophage therapy for periprosthetic joint infections: Current limitations and research needed to advance this therapeutic. J Orthop Res 2022; 41:1097-1104. [PMID: 36031587 DOI: 10.1002/jor.25432] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/19/2022] [Accepted: 08/22/2022] [Indexed: 02/04/2023]
Abstract
Bacteriophage therapy is a promising treatment for periprosthetic joint infections (PJIs), particularly given these agents have innate abilities to degrade the biofilm matrix and lyse bacteria within. However, many aspects of this therapy are poorly understood causing treatments to lack uniform effectiveness and reproducibility, which is in part a consequence of several inherent limitations to using bacteriophages to treat PJI. Herein, these limitations are discussed as are additional translational research that needs to be conducted to advance this therapeutic. These include determining if bacteria causing PJIs are polyclonal, consequences of bacteriophage attachment receptor phenotypic variations and ramifications of bacteriophage activity when bacteria interact with in vivo macromolecules. Only with the realization of the current limitations and subsequent knowledge gained from translational research will the potential of bacteriophages to reduce the morbidity and mortality in PJI be fully elucidated.
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Affiliation(s)
- James B Doub
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ken Urish
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Benjamin Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Yale Center for Phage Biology & Therapy, Yale University, New Haven, Connecticut, USA
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22
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Doss JH, Barekzi N, Gauthier DT. Improving high-throughput techniques for bacteriophage discovery in multi-well plates. METHODS IN MICROBIOLOGY 2022; 200:106542. [PMID: 35882287 DOI: 10.1016/j.mimet.2022.106542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/21/2022] [Accepted: 07/16/2022] [Indexed: 10/16/2022]
Abstract
Bacteriophages (also called phages) are viruses of bacteria that have numerous applications in medicine, agriculture, ecology, and molecular biology. With the increasing interest in phages for their many uses, it is now especially important to make phage discovery more efficient and economical. Using the host Mycobacterium smegmatis mc2155, which is a model organism for phage discovery research and is closely related to important pathogens of humans and other animals, we investigated three procedures that are an integral part of phage discovery: enrichment of environmental samples, phage isolation and detection (which can also be used for host range determination), and phage purification. Enrichment in 6-well plates was successful with most environmental samples, and enrichment in 24- and 96-well plates was successful with some environmental samples, demonstrating that larger sample volumes are preferred when possible, but smaller sample volumes may be acceptable if the starting concentration of phages is sufficiently high. Measuring absorbance in multi-well plates was at least as sensitive as the traditional plaque assay for the detection of phages. We also demonstrated a technique for the purification of single phage types from mixed cultures in liquid medium. Multi-well techniques can be used as alternatives or complementary approaches to traditional methods of phage discovery and characterization depending on the needs of the researcher in terms of time, available resources, host species, phage-bacteria matches, and specific goals. In the future, these techniques could be applied to the discovery of phages of aquatic mycobacteria and other hosts for which few phages have currently been isolated.
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Affiliation(s)
- Janis H Doss
- The Association of Public Health Laboratories, Silver Spring, MD, USA.
| | - Nazir Barekzi
- Department of Biology, Norfolk State University, Norfolk, VA, USA.
| | - David T Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA.
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23
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Cunningham SA, Mandrekar JN, Suh G, Patel R. Preliminary Reproducibility Evaluation of a Phage Susceptibility Testing Method Using a Collection of Escherichia coli and Staphylococcus aureus Phages. J Appl Lab Med 2022; 7:1468-1475. [DOI: 10.1093/jalm/jfac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Background
Increasing antimicrobial resistance combined with a lagging pipeline of novel antimicrobial compounds have resulted in a resurgence of interest in phage therapy. To select optimal phage or phage combinations for patients for whom phage therapy is considered, assessment of activity of a panel of phages against the patients’ bacterial isolate(s) should ideally be performed. Classical phage susceptibility testing methods (i.e., agar overlay) may be laborious, with expertise outside of normal training and competency of medical laboratory science staff needed.
Content
Adaptive Phage Therapeutics™ leveraged a commercially available phenotyping system (Biolog OmniLog®) to generate the PhageBank Susceptibility Test™, which uses a custom data analysis pipeline (PhageSelect™) to measure the delay in reaching log-phase metabolic activity (“hold time”) when a given isolate is challenged with a specific phage. The goal of this study was to preliminarily assess reproducibility of this approach by testing 2 bacterial species at 2 sites, APT and an academic site. Nineteen Escherichia coli phages were tested against 18 bacterial isolates, and 21 Staphylococcus aureus phages, against 11 bacterial isolates. Result comparisons were statistically excellent for E. coli (κ = 0.7990) and good/fair for S. aureus (κ = 0.6360).
Summary
The described method provides good/fair to excellent statistical reproducibility for assessment of phage susceptibility of 2 commonly encountered bacterial species.
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Affiliation(s)
- Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
| | - Jayawant N Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic , Rochester, MN , USA
| | - Gina Suh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic , Rochester, MN , USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic , Rochester, MN , USA
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24
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Antibiotic susceptibility testing of Staphylococcus aureus using the Biolog OmniLog® system, a metabolic phenotyping assay. Diagn Microbiol Infect Dis 2022; 104:115759. [DOI: 10.1016/j.diagmicrobio.2022.115759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022]
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25
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Ultrafast and Multiplexed Bacteriophage Susceptibility Testing by Surface Plasmon Resonance and Phase Imaging of Immobilized Phage Microarrays. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In the context of bacteriophage (phage) therapy, there is an urgent need for a method permitting multiplexed, parallel phage susceptibility testing (PST) prior to the formulation of personalized phage cocktails for administration to patients suffering from antimicrobial-resistant bacterial infections. Methods based on surface plasmon resonance imaging (SPRi) and phase imaging were demonstrated as candidates for very rapid (<2 h) PST in the broth phase. Biosensing layers composed of arrays of phages 44AHJD, P68, and gh-1 were covalently immobilized on the surface of an SPRi prism and exposed to liquid culture of either Pseudomonas putida or methicillin-resistant Staphylococcus aureus (i.e., either the phages’ host or non-host bacteria). Monitoring of reflectivity reveals susceptibility of the challenge bacteria to the immobilized phage strains. Investigation of phase imaging of lytic replication of gh-1 demonstrates PST at the single-cell scale, without requiring phage immobilization. SPRi sensorgrams show that on-target regions increase in reflectivity more slowly, stabilizing later and to a lower level compared to off-target regions. Phage susceptibility can be revealed in as little as 30 min in both the SPRi and phase imaging methods.
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26
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Mutalik VK, Arkin AP. A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)-viruses targeting bacteria-offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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Affiliation(s)
- Vivek K. Mutalik
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adam P. Arkin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
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27
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Successful Use of Salvage Bacteriophage Therapy for a Recalcitrant MRSA Knee and Hip Prosthetic Joint Infection. Pharmaceuticals (Basel) 2022; 15:ph15020177. [PMID: 35215290 PMCID: PMC8877365 DOI: 10.3390/ph15020177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/13/2022] Open
Abstract
Prosthetic joint infections are a serious complication of joint replacement surgery due to the significant morbidity and financial burden that is associated with conventional treatments. When patients fail the gold standard two-stage revision surgery, very limited, well-defined standardized approaches are available. Herein, we discuss the case of a sixty-four-year-old woman who had a recalcitrant MRSA prosthetic joint infection of her knee and hip that failed repeated conventional surgical and medical treatments. Only after receiving intraoperative and intravenous bacteriophage therapy was the patient able to achieve cure of her prosthetic joint infections, as demonstrated by the lack of clinical recurrence and sterility of intraoperative cultures while off antibiotics. This case reinforces that bacteriophage therapy holds promise in the treatment of prosthetic joint infections and more specifically in complicated cases who have failed conventional surgical and medical interventions.
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28
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Critically ill patient with multidrug-resistant Acinetobacter baumannii respiratory infection successfully treated with intravenous and nebulized bacteriophage therapy. Antimicrob Agents Chemother 2021; 66:e0082421. [PMID: 34662188 DOI: 10.1128/aac.00824-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hospitalized patients are at risk of developing serious multi-drug resistant bacterial infections. This risk is heightened in patients who are on mechanical ventilation, are immunocompromised, and/or have chronic comorbidities. We report the case of a 52-year-old critically ill patient with a multidrug resistant Acinetobacter baumannii (MDR-A) respiratory infection who was successfully treated with antibiotics and intravenous and nebulized bacteriophage therapy.
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29
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Gelman D, Yerushalmy O, Alkalay-Oren S, Rakov C, Ben-Porat S, Khalifa L, Adler K, Abdalrhman M, Coppenhagen-Glazer S, Aslam S, Schooley RT, Nir-Paz R, Hazan R. Clinical Phage Microbiology: a suggested framework and recommendations for the in-vitro matching steps of phage therapy. THE LANCET MICROBE 2021; 2:e555-e563. [DOI: 10.1016/s2666-5247(21)00127-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
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30
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A Case of In Situ Phage Therapy against Staphylococcus aureus in a Bone Allograft Polymicrobial Biofilm Infection: Outcomes and Phage-Antibiotic Interactions. Viruses 2021; 13:v13101898. [PMID: 34696328 PMCID: PMC8539586 DOI: 10.3390/v13101898] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 01/10/2023] Open
Abstract
Phage therapy (PT) shows promising potential in managing biofilm infections, which include refractory orthopedic infections. We report the case of a 13-year-old girl who developed chronic polymicrobial biofilm infection of a pelvic bone allograft after Ewing's sarcoma resection surgery. Chronic infection by Clostridium hathewayi, Proteus mirabilis and Finegoldia magna was worsened by methicillin-susceptible Staphylococcus aureus exhibiting an inducible Macrolides-Lincosamides-Streptogramin B resistance phenotype (iMLSB). After failure of conventional conservative treatment, combination of in situ anti-S. aureus PT with surgical debridement and intravenous antibiotic therapy led to marked clinical and microbiological improvement, yet failed to prevent a recurrence of infection on the midterm. This eventually led to surgical graft replacement. Multiple factors can explain this midterm failure, among which incomplete coverage of the polymicrobial infection by PT. Indeed, no phage therapy against C. hathewayi, P. mirabilis or F. magna could be administered. Phage-antibiotic interactions were investigated using OmniLog® technology. Our results suggest that phage-antibiotic interactions should not be considered "unconditionally synergistic", and should be assessed on a case-by-case basis. Specific pharmacodynamics of phages and antibiotics might explain these differences. More than two years after final graft replacement, the patient remains cured of her sarcoma and no further infections occurred.
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Loganathan A, Manohar P, Eniyan K, VinodKumar CS, Leptihn S, Nachimuthu R. Phage therapy as a revolutionary medicine against Gram-positive bacterial infections. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:49. [PMID: 34485539 PMCID: PMC8401357 DOI: 10.1186/s43088-021-00141-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/17/2021] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Antibiotic resistance among pathogenic bacteria has created a global emergency, prompting the hunt for an alternative cure. Bacteriophages were discovered over a century ago and have proven to be a successful replacement during antibiotic treatment failure. This review discusses on the scientific investigation of phage therapy for Gram-positive pathogens and general outlook of phage therapy clinical trials and commercialization. MAIN BODY OF THE ABSTRACT This review aimed to highlight the phage therapy in Gram-positive bacteria and the need for phage therapy in the future. Phage therapy to treat Gram-positive bacterial infections is in use for a very long time. However, limited review on the phage efficacy in Gram-positive bacteria exists. The natural efficiency and potency of bacteriophages against bacterial strains have been advantageous amidst the other non-antibiotic agents. The use of phages to treat oral biofilm, skin infection, and recurrent infections caused by Gram-positive bacteria has emerged as a predominant research area in recent years. In addition, the upsurge in research in the area of phage therapy for spore-forming Gram-positive bacteria has added a wealth of information to phage therapy. SHORT CONCLUSION We conclude that the need of phage as an alternative treatment is obvious in future. However, phage therapy can be used as reserve treatment. This review focuses on the potential use of phage therapy in treating Gram-positive bacterial infections, as well as their therapeutic aspects. Furthermore, we discussed the difficulties in commercializing phage drugs and their problems as a breakthrough medicine.
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Affiliation(s)
- Archana Loganathan
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu India
| | - Prasanth Manohar
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, School of Medicine, Haining, 314400 Zhejiang People’s Republic of China
- School of Medicine, The Second Affiliated Hospital Zhejiang University (SAHZU), Hangzhou, Zhejiang People’s Republic of China
| | - Kandasamy Eniyan
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu India
| | - C. S. VinodKumar
- Department of Microbiology, S.S. Institute of Medical Sciences and Research Centre, Davanagere, India
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, School of Medicine, Haining, 314400 Zhejiang People’s Republic of China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Medicine, Biomedical Sciences, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, 1 George Square, Edinburgh, EH8 9JZ UK
| | - Ramesh Nachimuthu
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu India
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Tamma PD, Suh GA. Phage Are All the Rage: Bacteriophage in Clinical Practice. J Pediatric Infect Dis Soc 2021; 10:749-753. [PMID: 33755148 DOI: 10.1093/jpids/piab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 01/17/2023]
Affiliation(s)
- Pranita D Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Gina A Suh
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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Successful Intratracheal Treatment of Phage and Antibiotic Combination Therapy of a Multi-Drug Resistant Pseudomonas aeruginosa Murine Model. Antibiotics (Basel) 2021; 10:antibiotics10080946. [PMID: 34438996 PMCID: PMC8388862 DOI: 10.3390/antibiotics10080946] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/21/2023] Open
Abstract
Background: Pseudomonas aeruginosa (PsA) is a common etiology of bacteria-mediated lower respiratory tract infections, including pneumonia, hospital acquired pneumonia (HAP), and ventilator-associated pneumonia (VAP). Given the paucity of novel antibiotics in our foreseeable pipeline, developing novel non-antibiotic antimicrobial therapies saliently targeting drug resistant PsA isolates remains a priority. Lytic bacteriophages (or phages) have come under scrutiny as a potential antimicrobial for refractory bacterial infections. We evaluated intratracheally and intraperitoneally (IP) administered phage therapy (with/without meropenem) in an acute immunocompromised mouse model of multi-drug resistant (MDR) PsA pulmonary infection. The MDR P. aeruginosa respiratory disease model used in these studies was developed to investigate novel therapies that might have efficacy as either monotherapies or as combination therapy with meropenem. Methods: We utilized eight-week-old, 18 g BALB/cJ female mice and an MDR strain of PsA (UNC-D). Mice were immunosuppressed with cyclophosphamide. We employed a three-phage cocktail targeting PsA (PaAH2ΦP (103), PaBAP5Φ2 (130), and PaΦ (134)), confirmed to exhibit in vitro suppression of the infecting isolate out to 45 h. Suppression was confirmed with phages acting in isolation and in combination with meropenem. Results: IP administration of phage did not protect mice from death. A one-time delivery of phage directly to the lungs via a single intubation-mediated, intratracheal (IMIT) instillation protected mice from lethal infection. Protection was observed despite delaying therapy out to 6 h. Finally, we observed that, by slowing the progression of infection by treatment with a sub-efficacious dose of meropenem, we could protect the mice from lethal infection via IP phage administration coupled to meropenem, observing partial additive effects of phage–antibiotic combination therapy. Conclusions: A personalized phage cocktail administered via IMIT exhibits high therapeutic efficacy, despite delayed treatment of 6 h in a lethal MDR PsA pneumonia model. IP phage alone did not forestall mortality, but exhibited efficacy when combined with meropenem and IMIT-administered phage. These additive effects of combined IP phage and meropenem confirm that phage may indeed reach the lung bed via the systemic circulation and protect mice if the infection is not too acute. Therefore, adjunctive phage therapy with concerted attention to identifying optimal phage targeting of the infecting isolate in vitro may exhibit transformative potential for combating the specter of MDR bacterial infections. Phage should serve as an integral component of a four-pronged approach coupled with antibiotics, source control, and immune optimization.
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Ramirez-Sanchez C, Gonzales F, Buckley M, Biswas B, Henry M, Deschenes MV, Horne B, Fackler J, Brownstein MJ, Schooley RT, Aslam S. Successful Treatment of Staphylococcus aureus Prosthetic Joint Infection with Bacteriophage Therapy. Viruses 2021; 13:1182. [PMID: 34205687 PMCID: PMC8233819 DOI: 10.3390/v13061182] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Successful joint replacement is a life-enhancing procedure with significant growth in the past decade. Prosthetic joint infection occurs rarely; it is a biofilm-based infection that is poorly responsive to antibiotic alone. Recent interest in bacteriophage therapy has made it possible to treat some biofilm-based infections, as well as those caused by multidrug-resistant pathogens, successfully when conventional antibiotic therapy has failed. Here, we describe the case of a 61-year-old woman who was successfully treated after a second cycle of bacteriophage therapy administered at the time of a two-stage exchange procedure for a persistent methicillin-sensitive Staphylococcus aureus (MSSA) prosthetic knee-joint infection. We highlight the safety and efficacy of both intravenous and intra-articular infusions of bacteriophage therapy, a successful outcome with a single lytic phage, and the development of serum neutralization with prolonged treatment.
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Affiliation(s)
- Claudia Ramirez-Sanchez
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093, USA; (C.R.-S.); (R.T.S.)
| | - Francis Gonzales
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA; (F.G.); (M.B.)
| | - Maureen Buckley
- Department of Surgery, University of California San Diego, La Jolla, CA 92093, USA; (F.G.); (M.B.)
| | - Biswajit Biswas
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA; (B.B.); (M.H.); (M.V.D.)
| | - Matthew Henry
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA; (B.B.); (M.H.); (M.V.D.)
- The Geneva Foundation, Tacoma, WA 98402, USA
| | - Michael V. Deschenes
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA; (B.B.); (M.H.); (M.V.D.)
- Leidos, Reston, VA 20190, USA
| | - Bri’Anna Horne
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA; (B.H.); (J.F.); (M.J.B.)
| | - Joseph Fackler
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA; (B.H.); (J.F.); (M.J.B.)
| | | | - Robert T. Schooley
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093, USA; (C.R.-S.); (R.T.S.)
- Center for Innovative Phage Therapy and Applications, University of California San Diego, La Jolla, CA 92093, USA
| | - Saima Aslam
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92093, USA; (C.R.-S.); (R.T.S.)
- Center for Innovative Phage Therapy and Applications, University of California San Diego, La Jolla, CA 92093, USA
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Aghaee BL, Mirzaei MK, Alikhani MY, Mojtahedi A. Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa. BMC Microbiol 2021; 21:132. [PMID: 33931013 PMCID: PMC8088035 DOI: 10.1186/s12866-021-02197-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 04/15/2021] [Indexed: 01/21/2023] Open
Abstract
Background P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard to cure. One possible alternative to antibiotics is to use phages. However, the isolation of phages suitable for phage therapy— be lytic, be efficient, and have a broad host range —against some target bacteria has proven difficult. To identify the best places to look for these phages against P. aeruginosa we screened hospital sewages, soils, and rivers in two cities. Results We isolated eighteen different phages, determined their host range, infection property, and plaque morphology. We found that the sewage and sewage-contaminated environments are the most reliable sources for the isolation of Pseudomonas phages. In addition, phages isolated from hospital sewage showed the highest efficiency in lysing the bacteria used for host range determination. In contrast, phages from the river had larger plaque size and lysed bacteria with higher levels of antibiotic resistance. Conclusions Our findings provided additional support for the importance of sewage as the source of phage isolation. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02197-z.
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Affiliation(s)
- Bahareh Lashtoo Aghaee
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran. .,Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran. .,Brucellosis research center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Ali Mojtahedi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
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Zelcbuch L, Yitzhaki E, Nissan O, Gidron E, Buchshtab N, Kario E, Kredo-Russo S, Zak NB, Bassan M. Luminescent Phage-Based Detection of Klebsiella pneumoniae: From Engineering to Diagnostics. Pharmaceuticals (Basel) 2021; 14:347. [PMID: 33918942 PMCID: PMC8069110 DOI: 10.3390/ph14040347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages ("phages") infect and multiply within specific bacterial strains, causing lysis of their target. Due to the specific nature of these interactions, phages allow a high-precision approach for therapy which can also be exploited for the detection of phage-sensitive pathogens associated with chronic diseases due to gut microbiome imbalance. As rapid phage-mediated detection assays becoming standard-of-care diagnostic tools, they will advance the more widespread application of phage therapy in a precision approach. Using a conventional method and a new cloning approach to develop luminescent phages, we engineered two phages that specifically detect a disease-associated microbial strain. We performed phage sensitivity assays in liquid culture and in fecal matrices and tested the stability of spiked fecal samples stored under different conditions. Different reporter gene structures and genome insertion sites were required to successfully develop the two nluc-reporter phages. The reporter phages detected spiked bacteria in five fecal samples with high specificity. Fecal samples stored under different conditions for up to 30 days did not display major losses in reporter-phage-based detection. Luminescent phage-based diagnostics can provide a rapid co-diagnostic tool to guide the growing field of phage therapy, particularly for a precision-based approach to chronic diseases treatment.
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Affiliation(s)
- Lior Zelcbuch
- Research Department, BiomX Ltd., Ness Ziona 7414002, Israel; (E.Y.); (O.N.); (E.G.); (N.B.); (E.K.); (S.K.-R.); (N.B.Z.); (M.B.)
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Malik DJ. Approaches for manufacture, formulation, targeted delivery and controlled release of phage-based therapeutics. Curr Opin Biotechnol 2021; 68:262-271. [PMID: 33744823 DOI: 10.1016/j.copbio.2021.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 11/17/2022]
Abstract
A future successful bacteriophage industry requires development of robust scalable manufacturing platforms for upstream production of high phage titres and their downstream purification and concentration whilst achieving processing yields en route. Development of a broadly applicable process flow sheet employing well-characterised unit operations with knowledge of their critical process parameters is beginning to emerge. A quality-by-design approach is advocated for the development of cost-effective phage production platforms. The use of on-line and at-line process analytical tools for process monitoring, control and quality assurance are discussed. Phage biophysical characterisation tools allowing rational development of liquid formulations and dry powder forms are presented. Recent innovations in phage encapsulation methods highlight the potential innovation opportunities in this research space that could have significant impact on the future prospects of this industry.
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Affiliation(s)
- Danish J Malik
- Chemical Engineering Department, Loughborough University, Loughborough LE11 3TU, United Kingdom.
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Pires DP, Costa AR, Pinto G, Meneses L, Azeredo J. Current challenges and future opportunities of phage therapy. FEMS Microbiol Rev 2021; 44:684-700. [PMID: 32472938 DOI: 10.1093/femsre/fuaa017] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance is a major public health challenge worldwide, whose implications for global health might be devastating if novel antibacterial strategies are not quickly developed. As natural predators of bacteria, (bacterio)phages may play an essential role in escaping such a dreadful future. The rising problem of antibiotic resistance has revived the interest in phage therapy and important developments have been achieved over the last years. But where do we stand today and what can we expect from phage therapy in the future? This is the question we set to answer in this review. Here, we scour the outcomes of human phage therapy clinical trials and case reports, and address the major barriers that stand in the way of using phages in clinical settings. We particularly address the potential of phage resistance to hinder phage therapy and discuss future avenues to explore the full capacity of phage therapy.
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Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luciana Meneses
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Abstract
Severe infections caused by multidrug-resistant Klebsiella pneumoniae sequence type 258 (ST258) highlight the need for new therapeutics with activity against this pathogen. Bacteriophage (phage) therapy is an alternative treatment approach for multidrug-resistant bacterial infections that has shown efficacy in experimental animal models and promise in clinical case reports. In this study, we assessed microbiologic, histopathologic, and survival outcomes following systemic administration of phage in ST258-infected mice. We found that prompt treatment with two phages, either individually or in combination, rescued mice with K. pneumoniae ST258 bacteremia. Among the three treatment groups, mice that received combination phage therapy demonstrated the greatest increase in survival and the lowest frequency of phage resistance among bacteria recovered from mouse blood and tissue. Our findings support the utility of phage therapy as an approach for refractory ST258 infections and underscore the potential of this treatment modality to be enhanced through strategic phage selection.
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Moses S, Vagima Y, Tidhar A, Aftalion M, Mamroud E, Rotem S, Steinberger-Levy I. Characterization of Yersinia pestis Phage Lytic Activity in Human Whole Blood for the Selection of Efficient Therapeutic Phages. Viruses 2021; 13:v13010089. [PMID: 33440682 PMCID: PMC7827537 DOI: 10.3390/v13010089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 12/19/2022] Open
Abstract
The global increase in multidrug-resistant (MDR) pathogenic bacteria has led to growing interest in bacteriophage ("phage") therapy. Therapeutic phages are usually selected based on their ability to infect and lyse target bacteria, using in vitro assays. In these assays, phage infection is determined using target bacteria grown in standard commercial rich media, while evaluation of the actual therapeutic activity requires the presence of human blood. In the present work, we characterized the ability of two different Yersinia pestis lytic phages (ϕA1122 and PST) to infect and kill a luminescent Y. pestis EV76 strain suspended in Brain Heart Infusion (BHI)-rich medium or in human whole blood, simulating the host environment. We found that the ability of the phages to infect and lyse blood-suspended Y. pestis was not correlated with their ability to infect and lyse BHI-suspended bacteria. While the two different phages exhibited efficient infective capacity in a BHI-suspended culture, only the PST phage showed efficient lysis ability against blood-suspended bacteria. Therefore, we recommend that for personalized phage therapy, selection of phage(s) for efficient treatment of patients suffering from MDR bacterial infections should include prior testing of the candidate phage(s) for their lysis ability in the presence of human blood.
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Sozhamannan S, Hofmann ER. The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. Viruses 2020; 12:v12121393. [PMID: 33291831 PMCID: PMC7762055 DOI: 10.3390/v12121393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Accurate pathogen detection and diagnosis is paramount in clinical success of treating patients. There are two general paradigms in pathogen detection: molecular and immuno-based, and phage-based detection is a third emerging paradigm due to its sensitivity and selectivity. Molecular detection methods look for genetic material specific for a given pathogen in a sample usually by polymerase chain reaction (PCR). Immuno-methods look at the pathogen components (antigens) by antibodies raised against that pathogen specific antigens. There are different variations and products based on these two paradigms with advantages and disadvantages. The third paradigm at least for bacterial pathogen detection entails bacteriophages specific for a given bacterium. Sensitivity and specificity are the two key parameters in any pathogen detection system. By their very nature, bacteriophages afford the best sensitivity for bacterial detection. Bacteria and bacteriophages form the predator-prey pair in the evolutionary arms race and has coevolved over time to acquire the exquisite specificity of the pair, in some instances at the strain level. This specificity has been exploited for diagnostic purposes of various pathogens of concern in clinical and other settings. Many recent reviews focus on phage-based detection and sensor technologies. In this review, we focus on a very special group of pathogens that are of concern in biodefense because of their potential misuse in bioterrorism and their extremely virulent nature and as such fall under the Centers for Disease and Prevention (CDC) Category A pathogen list. We describe the currently available phage methods that are based on the usual modalities of detection from culture, to molecular and immuno- and fluorescent methods. We further highlight the gaps and the needs for more modern technologies and sensors drawing from technologies existing for detection and surveillance of other pathogens of clinical relevance.
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Affiliation(s)
- Shanmuga Sozhamannan
- National Security Science & Technology, Management Advisory Services, Logistics Management Institute, 7940 Jones Branch Drive, Tysons, VA 22102, USA;
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense (CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), 110 Thomas Johnson Drive, Suite 250, Frederick, MD 21702, USA
| | - Edward R. Hofmann
- EXCET, Inc., 6225 Brandon Ave #360, Springfield, VA 22150, USA
- US Army Combat Capabilities Development Command, Chemical Biological Center, 8908 Guard St, E3831, Edgewood, MD 21010, USA
- Correspondence:
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de Jonge PA, Smit Sibinga DJC, Boright OA, Costa AR, Nobrega FL, Brouns SJJ, Dutilh BE. Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions. J Virol 2020; 94:e01559-20. [PMID: 32938760 PMCID: PMC7654272 DOI: 10.1128/jvi.01559-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023] Open
Abstract
The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Dieuwke J C Smit Sibinga
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Oliver A Boright
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
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Olsen NS, Hendriksen NB, Hansen LH, Kot W. A New High-Throughput Screening Method for Phages: Enabling Crude Isolation and Fast Identification of Diverse Phages with Therapeutic Potential. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:137-148. [PMID: 36147828 PMCID: PMC9041460 DOI: 10.1089/phage.2020.0016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bacteriophage therapy and application of phages for biocontrol necessitate acquisition of suitable phages. The exclusivity of phage-host relations and the risk of phage resistance instigate a need to rapidly isolate and characterize novel phages and continually build sizeable phage libraries. Current methods for phage isolation are both laborious and time consuming, suitable for the isolation of a limited number of phages. The high-throughput screening method for phages upscales and organizes enrichment of phages for fast isolation and identification of potentially hundreds of distinct phages against single hosts. This enables screening of hundreds of samples, in multiple simultaneous setups with varying parameters, increasing the likelihood of isolating multiple distinct phages specific for the given conditions. The efficiency of the method is emphasized by our screening of 200 environmental samples, resulting in the identification of an abundance of unique phage species virulent to Escherichia coli, Salmonella enterica, Enterococcus faecalis, and Pseudomonas aeruginosa.
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Affiliation(s)
- Nikoline S. Olsen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | - Lars H. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis 2020; 7:ofaa389. [PMID: 33005701 PMCID: PMC7519779 DOI: 10.1093/ofid/ofaa389] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/21/2020] [Indexed: 12/03/2022] Open
Abstract
Background Due to increasing multidrug-resistant (MDR) infections, there is an interest in assessing the use of bacteriophage therapy (BT) as an antibiotic alternative. After the first successful case of intravenous BT to treat a systemic MDR infection at our institution in 2017, the Center for Innovative Phage Applications and Therapeutics (IPATH) was created at the University of California, San Diego, in June 2018. Methods We reviewed IPATH consult requests from June 1, 2018, to April 30, 2020, and reviewed the regulatory process of initiating BT on a compassionate basis in the United States. We also reviewed outcomes of the first 10 cases at our center treated with intravenous BT (from April 1, 2017, onwards). Results Among 785 BT requests to IPATH, BT was administered to 17 of 119 patients in whom it was recommended. One-third of requests were for Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacterium abscessus. Intravenous BT was safe with a successful outcome in 7/10 antibiotic-recalcitrant infections at our center (6 were before IPATH). BT may be safely self-administered by outpatients, used for infection suppression/prophylaxis, and combined successfully with antibiotics despite antibiotic resistance, and phage resistance may be overcome with new phage(s). Failure occurred in 2 cases despite in vitro phage susceptibility. Conclusions We demonstrate the safety and feasibility of intravenous BT for a variety of infections and discuss practical considerations that will be critical for informing future clinical trials.
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Affiliation(s)
- Saima Aslam
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA.,Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth Lampley
- Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, California, USA
| | - Darcy Wooten
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA
| | - Maile Karris
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA
| | - Constance Benson
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA.,Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, California, USA
| | - Steffanie Strathdee
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA.,Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, California, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, USA.,Center for Innovative Phage Applications and Therapeutics, University of California, San Diego, La Jolla, California, USA
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Duplessis CA, Biswas B. A Review of Topical Phage Therapy for Chronically Infected Wounds and Preparations for a Randomized Adaptive Clinical Trial Evaluating Topical Phage Therapy in Chronically Infected Diabetic Foot Ulcers. Antibiotics (Basel) 2020; 9:antibiotics9070377. [PMID: 32635429 PMCID: PMC7400337 DOI: 10.3390/antibiotics9070377] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/21/2022] Open
Abstract
The advent and increasing prevalence of antimicrobial resistance commensurate with the absence of novel antibiotics on the horizon raises the specter of untreatable infections. Phages have been safely administered to thousands of patients exhibiting signals of efficacy in many experiencing infections refractory to antecedent antibiotics. Topical phage therapy may represent a convenient and efficacious treatment modality for chronic refractory infected cutaneous wounds spanning all classifications including venous stasis, burn-mediated, and diabetic ulcers. We will initially provide results from a systematic literature review of topical phage therapy used clinically in refractorily infected chronic wounds. We will then segue into a synopsis of the preparations for a forthcoming phase II a randomized placebo-controlled clinical trial assessing the therapeutic efficacy exploiting adjunctive personalized phage administration, delivered topically, intravenously (IV) and via a combination of both modalities (IV + topical) in the treatment of infected diabetic foot ulcers (perhaps the canonical paradigm representing complicated recalcitrant infected cutaneous wounds).
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Salvage Bacteriophage Therapy for a Chronic MRSA Prosthetic Joint Infection. Antibiotics (Basel) 2020; 9:antibiotics9050241. [PMID: 32397354 PMCID: PMC7277870 DOI: 10.3390/antibiotics9050241] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/02/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023] Open
Abstract
This is a case of a 72 year old male with a chronic methicillin-resistant Staphylococcus aureus prosthetic joint infection. After the third intravenous dose of bacteriophage therapy, an unusual, reversible transaminitis prompted stoppage of bacteriophage therapy. Nevertheless, treatment was successful and the patient’s severe chronic infection was eradicated.
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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Aslam S, Courtwright AM, Koval C, Lehman SM, Morales S, Langlais Furr CL, Rosas F, Brownstein MJ, Fackler JR, Sisson BM, Biswas B, Henry M, Luu T, Bivens BN, Hamilton T, Duplessis C, Logan C, Law N, Yung G, Turowski J, Anesi J, Strathdee SA, Schooley RT. Early clinical experience of bacteriophage therapy in 3 lung transplant recipients. Am J Transplant 2019; 19:2631-2639. [PMID: 31207123 PMCID: PMC6711787 DOI: 10.1111/ajt.15503] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 01/25/2023]
Abstract
Bacteriophage therapy (BT) uses bacteriophages to treat pathogenic bacteria and is an emerging strategy against multidrug-resistant (MDR) infections. Experience in solid organ transplant is limited. We describe BT in 3 lung transplant recipients (LTR) with life-threatening MDR infections caused by Pseudomonas aeruginosa (n = 2) and Burkholderia dolosa (n = 1). For each patient, lytic bacteriophages were selected against their bacterial isolates. BT was administered for variable durations under emergency Investigational New Drug applications and with patient informed consent. Safety was assessed using clinical/laboratory parameters and observed clinical improvements described, as appropriate. All patients received concurrent antibiotics. Two ventilator-dependent LTR with large airway complications and refractory MDR P. aeruginosa pneumonia received BT. Both responded clinically and were discharged from the hospital off ventilator support. A third patient had recurrent B. dolosa infection following transplant. Following BT initiation, consolidative opacities improved and ventilator weaning was begun. However, infection relapsed on BT and the patient died. No BT-related adverse events were identified in the 3 cases. BT was well tolerated and associated with clinical improvement in LTRs with MDR bacterial infection not responsive to antibiotics alone. BT may be a viable adjunct to antibiotics for patients with MDR infections.
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Affiliation(s)
- Saima Aslam
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA
| | - Andrew M. Courtwright
- Department of Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia, PA
| | - Christine Koval
- Department of Infectious Diseases, Cleveland Clinic Foundation, Cleveland, OH
| | | | | | | | | | | | | | | | - Biswajit Biswas
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Matthew Henry
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Truong Luu
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Brittany N. Bivens
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Christopher Duplessis
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD
| | - Cathy Logan
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA
| | - Nancy Law
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA
| | - Gordon Yung
- Division of Pulmonary, Critical Care & Sleep Medicine, University of California San Diego, La Jolla, CA
| | - Jason Turowski
- Department of Pulmonary Medicine, Cleveland Clinic Foundation, Cleveland, OH
| | - Judith Anesi
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia PA
| | - Steffanie A. Strathdee
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA
| | - Robert T. Schooley
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA
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Hesse S, Adhya S. Phage Therapy in the Twenty-First Century: Facing the Decline of the Antibiotic Era; Is It Finally Time for the Age of the Phage? Annu Rev Microbiol 2019; 73:155-174. [PMID: 31185183 DOI: 10.1146/annurev-micro-090817-062535] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Burgeoning problems of antimicrobial resistance dictate that new solutions be developed to combat old foes. Use of lytic bacteriophages (phages) for the treatment of drug-resistant bacterial infections is one approach that has gained significant traction in recent years. Fueled by reports of experimental phage therapy cases with very positive patient outcomes, several early-stage clinical trials of therapeutic phage products have been launched in the United States. Eventual licensure enabling widespread access to phages is the goal; however, new paths to regulatory approval and mass-market distribution, distinct from those of small-molecule antibiotics, must be forged first. This review highlights unique aspects related to the clinical use of phages, including advantages to be reaped as well as challenges to be overcome.
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Affiliation(s)
- Shayla Hesse
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
| | - Sankar Adhya
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
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