1
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Pal N, Sharma P, Kumawat M, Singh S, Verma V, Tiwari RR, Sarma DK, Nagpal R, Kumar M. Phage therapy: an alternative treatment modality for MDR bacterial infections. Infect Dis (Lond) 2024; 56:785-817. [PMID: 39017931 DOI: 10.1080/23744235.2024.2379492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
The increasing global incidence of multidrug-resistant (MDR) bacterial infections threatens public health and compromises various aspects of modern medicine. Recognising the urgency of this issue, the World Health Organisation has prioritised the development of novel antimicrobials to combat ESKAPEE pathogens. Comprising Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli, such pathogens represent a spectrum of high to critical drug resistance, accounting for a significant proportion of hospital-acquired infections worldwide. In response to the waning efficacy of antibiotics against these resilient pathogens, phage therapy (PT) has emerged as a promising therapeutic strategy. This review provides a comprehensive summary of clinical research on PT and explores the translational journey of phages from laboratory settings to clinical applications. It examines recent advancements in pre-clinical and clinical developments, highlighting the potential of phages and their proteins, alone or in combination with antibiotics. Furthermore, this review underlines the importance of establishing safe and approved routes of phage administration to patients. In conclusion, the evolving landscape of phage therapy offers a beacon of hope in the fight against MDR bacterial infections, emphasising the imperative for continued research, innovation and regulatory diligence to realise its full potential in clinical practice.
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Affiliation(s)
- Namrata Pal
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
- Department of Microbiology, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Poonam Sharma
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Samradhi Singh
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Rajnarayan R Tiwari
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition and Integrative Physiology, College of Health and Human Sciences, Florida State University, Tallahassee, FL, USA
| | - Manoj Kumar
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
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2
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Kolenda C, Jourdan J, Roussel-Gaillard T, Medina M, Laurent F. Phage susceptibility testing methods or 'phagograms': where do we stand and where should we go? J Antimicrob Chemother 2024:dkae325. [PMID: 39271114 DOI: 10.1093/jac/dkae325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024] Open
Abstract
Phage therapy is a highly promising approach to address the challenge that is presented by the global burden of antimicrobial resistance. Given the natural specificity of phages, phage susceptibility testing (PST) is a prerequisite for successful personalized therapy, allowing the selection of active phages from large and diverse collections. However, the issue of an easy-to-use and standardized technique remains. In this review, we describe the principles, advantages and drawbacks of two routinely used PST techniques: plaque and growth kinetic assays. These are labour-intensive and time-consuming methods that require automation of one or more steps, including preparation of test panels, incubation, reading and analysis of results. In addition to automation, there is an urgent need to establish a reference method to enable efficient of PST techniques selection of therapeutic phages. We discuss knowledge gaps and parameters that need to be investigated to work towards this goal.
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Affiliation(s)
- Camille Kolenda
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Julie Jourdan
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | - Mathieu Medina
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Frédéric Laurent
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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3
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Wahid B, Tiwana MS, Ali A. Revolutionising infection control: building the next generation of phage banks. Drug Resist Updat 2024:101143. [PMID: 39214817 DOI: 10.1016/j.drup.2024.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
The escalating global burden of antimicrobial resistance (AMR) represents a critical public health challenge. This rise in antibiotic resistance is concomitant with heightened antibiotic consumption, with an estimated annual usage of 100,000 to 200,000 tons. A recent systematic review, which analysed data from 204 countries, reported that AMR was responsible for 4.95 million deaths in 2019 (Murray et al., 2022). The growing threat of AMR is imposing a significant financial burden on the global economy, with the CDC reporting an additional annual cost of $20 billion in the U.S. and €9 billion in Europe. The emerging field of bacteriophage therapy offers promising potential as a game-changer in the era of AMR. However, existing literature reveals numerous research gaps and technological challenges, including insufficient information on phage pharmacology, genomics, and a lack of preclinical and clinical data. In addition to conducting further research to address existing knowledge gaps, establishing phage banks in clinical facilities could be a transformative advancement in the fight against AMR.
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Affiliation(s)
- Braira Wahid
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168 Australia.
| | - Muhammad Salman Tiwana
- School of Computer Science, Faculty of Engineering and Information Technology, University of Technology (UTS) Sydney, Australia.
| | - Akhtar Ali
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, 32306, United States.
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4
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Wortelboer K, Herrema H. Opportunities and challenges in phage therapy for cardiometabolic diseases. Trends Endocrinol Metab 2024; 35:687-696. [PMID: 38637223 DOI: 10.1016/j.tem.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
The worldwide prevalence of cardiometabolic diseases (CMD) is increasing, and emerging evidence implicates the gut microbiota in this multifactorial disease development. Bacteriophages (phages) are viruses that selectively target a bacterial host; thus, phage therapy offers a precise means of modulating the gut microbiota, limiting collateral damage on the ecosystem. Several studies demonstrate the potential of phages in human disease, including alcoholic and steatotic liver disease. In this opinion article we discuss the potential of phage therapy as a predefined medicinal product for CMD and discuss its current challenges, including the generation of effective phage combinations, product formulation, and strict manufacturing requirements.
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Affiliation(s)
- Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Diabetes, and Metabolism, Amsterdam UMC, Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Diabetes, and Metabolism, Amsterdam UMC, Amsterdam, The Netherlands.
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5
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Onallah H, Yerushalmy O, Braunstein R, Alkalay-Oren S, Rimon A, Gelman D, Coppenhagen-Glazer S, Hazan R, Nir-Paz R. Protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections. STAR Protoc 2024; 5:102949. [PMID: 38691464 PMCID: PMC11070627 DOI: 10.1016/j.xpro.2024.102949] [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: 11/22/2023] [Revised: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 05/03/2024] Open
Abstract
Phage therapy has re-emerged as a promising treatment for non-resolving infections. Given the lack of approved phage treatments, there is a need to establish a compassionate use pipeline. Here, we present a protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections. We describe steps for consultation and request implementation, evaluating and comparing different aspects of phage activity, and phage production. We then detail procedures for multidisciplinary meetings, ethics approvals, phage therapy, and follow-up. For complete details on the use and execution of this protocol, please refer to Onallah et al.1,2.
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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; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center (HHUMC), Jerusalem 9112000, Israel
| | - 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
| | - 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
| | - 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
| | - 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; Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, 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; Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, 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
| | - 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.
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Markusková B, Elnwrani S, Andrezál M, Sedláčková T, Szemes T, Slobodníková L, Kajsik M, Drahovská H. Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains. Arch Virol 2024; 169:142. [PMID: 38851653 PMCID: PMC11162368 DOI: 10.1007/s00705-024-06063-x] [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: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024]
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections, and strains that are resistant to antibiotics are a major problem in treating these infections. Phage therapy is a promising alternative approach that can be used to treat infections caused by polyresistant bacterial strains. In the present study, 16 bacteriophages isolated from sewage and surface water were investigated. Phage host specificity was tested on a collection of 77 UPEC strains. The phages infected 2-44 strains, and 80% of the strains were infected by at least one phage. The susceptible E. coli strains belonged predominantly to the B2 phylogenetic group, including strains of two clones, CC131 and CC73, that have a worldwide distribution. All of the phages belonged to class Caudoviricetes and were identified as members of the families Straboviridae, Autographiviridae, and Drexlerviridae and the genera Kagunavirus, Justusliebigvirus, and Murrayvirus. A phage cocktail composed of six phages - four members of the family Straboviridae and two members of the family Autographiviridae - was prepared, and its antibacterial activity was tested in liquid medium. Complete suppression of bacterial growth was observed after 5-22 hours of cultivation, followed by partial regrowth. At 24 hours postinfection, the cocktail suppressed bacterial growth to 43-92% of control values. Similar results were obtained when testing the activity of the phage cocktail in LB and in artificial urine medium. The results indicate that our phage cocktail has potential to inhibit bacterial growth during infection, and they will therefore be preserved in the national phage bank, serving as valuable resources for therapeutic applications.
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Affiliation(s)
- Barbora Markusková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sulafa Elnwrani
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tatiana Sedláčková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Szemes
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lívia Slobodníková
- Institute of Microbiology, Faculty of Medicine, Comenius University in Bratislava and University Hospital Bratislava, Bratislava, Slovakia
| | - Michal Kajsik
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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7
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Schwarz C, Mathieu J, Laverde Gomez J, Miller MR, Tikhonova M, Hamor C, Alvarez PJJ. Isolation and Characterization of Six Novel Fusobacterium necrophorum Phages. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:63-75. [PMID: 39119211 PMCID: PMC11304844 DOI: 10.1089/phage.2023.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Introduction Fusobacterium necrophorum, a human and animal pathogen, is the primary etiologic agent of bovine liver abscesses and a driving factor for prophylactic antibiotic use in the fed cattle industry. Considering calls to reduce agricultural antibiotic use, we isolated phages capable of killing F. necrophorum as an alternative or complementary biocontrol strategy. Methods Six novel phages (φFN37, φRTG5, φKSUM, φHugo, φPaco, and φBB) were isolated from rumen fluid or ruminal F. necrophorum isolates and subjected to host range testing on both F. necrophorum subspecies. Four F. necrophorum subspecies, necrophorum phages, were tested for cross-resistance and host growth inhibition individually and in pairs. Additionally, genomic sequencing, annotation, and analysis were performed.s. Results Four of six isolated phages were able to form lysogens, although all six contained lysogeny-related genes. φKSUM and φBB, did not form lysogens and were able to infect both subspecies. Four phages could infect F. necrophorum 8L1 (a liver abscess model challenge strain) in vitro. Genomic analysis showed that these phages belong to class Caudoviricetes with genome sizes ranging from 35 kbp to 111 kbp and GC values ranging from 26% to 36% and have extremely limited similarity to other deposited phage genomes infecting Fusobacterium or other genera. Conclusions Although all phages isolated contained sequences bearing similarities to genes implicated in lysogeny, the four selected for use in cocktails showed potential in inhibiting host growth, with several demonstrating promising attributes for biocontrol and therapeutic applications. Phage cocktails that may offer enhanced antibacterial activity were also identified, indicating the potential of some lysogenic phages to be adapted for biocontrol or therapeutic purposes when lytic phages are difficult to obtain.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | | | - Megan R. Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | | | - Clark Hamor
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
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Kenney PO, Gómez-Duarte OG. Low-volume enrichment method supports high throughput bacteriophage screening and isolation from wastewater. PLoS One 2024; 19:e0298833. [PMID: 38626205 PMCID: PMC11020952 DOI: 10.1371/journal.pone.0298833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/30/2024] [Indexed: 04/18/2024] Open
Abstract
Bacteriophage therapy is a rapidly growing field of study. Narrow host ranges, bacterial resistance, and limited antibiotic availability make lytic phages a feasible therapeutic potential. Phage discovery, a critical step in developing phage therapy, is a pathway to accessible treatment. This has always been a laborious, time-consuming and resource-intensive process. In this paper, we describe a 96-well plate low-volume bacteriophage enrichment method with concentrated environmental sources to rapidly discover and isolate phages targeting multiple organisms simultaneously. Samples from natural water sources, wastewater influent, and activated sludge were tested in large volume enrichment cultures and low-volume 96-well plate format. Each plate has the capacity to run as many as 48 different combinations with multiple bacterial hosts. The time to identify the presence of phage in a sample was 5 to 10 hours in the low-volume format versus a minimum of 2 days in the traditional enrichment method. The labor and expense involved also favor the 96-well plate format. There was some loss of discovered phages using this technique, primarily targeting bacterial species less prevalent in the environment. This is an easily modifiable method that is amenable to automation and a variety of potential phage sources.
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Affiliation(s)
- Patrick O. Kenney
- Division of Pediatric Infectious Disease, Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY, United States of America
| | - Oscar G. Gómez-Duarte
- Division of Pediatric Infectious Disease, Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY) at Buffalo, Buffalo, NY, United States of America
- Levine Children’s Hospital, Atrium Health/Wake Forest University, Charlotte, NC, United States of America
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9
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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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10
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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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11
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Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, Whitehead N, Soothill J, Michell S, Temperton B. The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK. Microorganisms 2024; 12:253. [PMID: 38399657 PMCID: PMC10893117 DOI: 10.3390/microorganisms12020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
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Affiliation(s)
- Julie Fletcher
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Robyn Manley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christian Fitch
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christina Bugert
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Michelle Michelsen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Shayma Alathari
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Nicola Senior
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Alice Mills
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - Natalie Whitehead
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - James Soothill
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - Stephen Michell
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Ben Temperton
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
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12
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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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13
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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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14
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McCallin S, Drulis-Kawa Z, Ferry T, Pirnay JP, Nir-Paz R. Phages and phage-borne enzymes as new antibacterial agents. Clin Microbiol Infect 2023:S1198-743X(23)00528-1. [PMID: 37866680 DOI: 10.1016/j.cmi.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND Persistent and resistant infections caused by bacteria are increasing in numbers and pose a treatment challenge to the medical community and public health. However, solutions with new agents that will enable effective treatment are lacking or delayed by complex development and authorizations. Bacteriophages are known as a possible solution for invasive infections for decades but were seldom used in the Western world. OBJECTIVES To provide an overview of the current status and emerging use of bacteriophage therapy and phage-based products, as well as touch on the socioeconomic and regulatory issues surrounding their development. SOURCES Peer-reviewed articles and authors' first-hand experience. CONTENT Although phage therapy is making a comeback since its early discovery, there are many hurdles to its current use. The lack of appropriate standardized bacterial susceptibility testing; lack of a simple business model and authorization for the need of many phages to treat a single species infection; and the lack of knowledge on predictable outcome measures are just a few examples. In this review, we explore the possible routes for phage use, either based on local specialty centres or by industry; the current status of phage therapy, which is mainly based on single-centre or single-bacterial cohorts, and emerging clinical trials; local country-level frameworks for phage utilization even without full authorization; and the use of phage-derived products as alternatives to antibiotics. We also explore what may be the current indications based on the possible availability of phages. IMPLICATIONS Although phages are emerging as a potential treatment for non-resolving and life-threatening infections, the models for their use and production still need to be defined by the medical community, regulatory bodies, and industry. Bacteriophages may have a great potential for infection treatment but many aspects still need to be defined before their routine use in the clinic.
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Affiliation(s)
- Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Zürich, Switzerland; ESGNTA - ESCMID study group for non-traditional antibacterials, Basel, Switzerland
| | - Zuzanna Drulis-Kawa
- ESGNTA - ESCMID study group for non-traditional antibacterials, Basel, Switzerland; Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Tristan Ferry
- ESGNTA - ESCMID study group for non-traditional antibacterials, Basel, Switzerland; Centre interrégional de référence pour la prise en charge des infections ostéoarticulaires complexes, CRIOAc Lyon, Hospices Civils de Lyon, Lyon, France; Infectious Diseases, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; CIRI-Centre International de Recherche en Infectiologie, Inserm, Universite Claude Bernard Lyon, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Jean-Paul Pirnay
- ESGNTA - ESCMID study group for non-traditional antibacterials, Basel, Switzerland; Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Ran Nir-Paz
- ESGNTA - ESCMID study group for non-traditional antibacterials, Basel, Switzerland; Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; Israeli Phage Therapy Center of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel.
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15
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Jo SJ, Kwon J, Kim SG, Lee SJ. The Biotechnological Application of Bacteriophages: What to Do and Where to Go in the Middle of the Post-Antibiotic Era. Microorganisms 2023; 11:2311. [PMID: 37764155 PMCID: PMC10534921 DOI: 10.3390/microorganisms11092311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Amid the escalating challenges of antibiotic resistance, bacterial infections have emerged as a global threat. Bacteriophages (phages), viral entities capable of selectively infecting bacteria, are gaining momentum as promising alternatives to traditional antibiotics. Their distinctive attributes, including host specificity, inherent self-amplification, and potential synergy with antibiotics, render them compelling candidates. Phage engineering, a burgeoning discipline, involves the strategic modification of bacteriophages to enhance their therapeutic potential and broaden their applications. The integration of CRISPR-Cas systems facilitates precise genetic modifications, enabling phages to serve as carriers of functional genes/proteins, thereby enhancing diagnostics, drug delivery, and therapy. Phage engineering holds promise in transforming precision medicine, addressing antibiotic resistance, and advancing diverse applications. Emphasizing the profound therapeutic potential of phages, this review underscores their pivotal role in combatting bacterial diseases and highlights their significance in the post-antibiotic era.
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Affiliation(s)
- Su Jin Jo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan City 54596, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Seung-Jun Lee
- Department of Pharmaceutical Science and Engineering, Seowon University, 377-3 Musimseoro, Seowon-gu, Cheong-ju City 28674, Republic of Korea
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16
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Abedon ST. Automating Predictive Phage Therapy Pharmacology. Antibiotics (Basel) 2023; 12:1423. [PMID: 37760719 PMCID: PMC10525195 DOI: 10.3390/antibiotics12091423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses that infect as well as often kill bacteria are called bacteriophages, or phages. Because of their ability to act bactericidally, phages increasingly are being employed clinically as antibacterial agents, an infection-fighting strategy that has been in practice now for over one hundred years. As with antibacterial agents generally, the development as well as practice of this phage therapy can be aided via the application of various quantitative frameworks. Therefore, reviewed here are considerations of phage multiplicity of infection, bacterial likelihood of becoming adsorbed as a function of phage titers, bacterial susceptibility to phages also as a function of phage titers, and the use of Poisson distributions to predict phage impacts on bacteria. Considered in addition is the use of simulations that can take into account both phage and bacterial replication. These various approaches can be automated, i.e., by employing a number of online-available apps provided by the author, the use of which this review emphasizes. In short, the practice of phage therapy can be aided by various mathematical approaches whose implementation can be eased via online automation.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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17
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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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18
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Kalpana S, Lin WY, Wang YC, Fu Y, Wang HY. Alternate Antimicrobial Therapies and Their Companion Tests. Diagnostics (Basel) 2023; 13:2490. [PMID: 37568853 PMCID: PMC10417861 DOI: 10.3390/diagnostics13152490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Wan-Ying Lin
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA;
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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19
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Meneses L, Brandão AC, Coenye T, Braga AC, Pires DP, Azeredo J. A systematic review of the use of bacteriophages for in vitro biofilm control. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04638-1. [PMID: 37407800 DOI: 10.1007/s10096-023-04638-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Bacteriophages (phages) are very promising biological agents for the prevention and control of bacterial biofilms. However, little is known about the parameters that can influence the efficacy of phages on biofilms. This systematic review provides a summary and analysis of the published data about the use of phages to control pre-formed biofilms in vitro, suggesting recommendations for future experiments in this area. A total of 68 articles, containing data on 605 experiments addressing the efficacy of phages to control biofilms in vitro were included, after a search conducted in Web of Science, Embase, and Medline (PubMed). The data collected from each experiment included information about biofilm growth conditions, phage characteristics, treatment conditions and biofilm reduction. In most cases, biofilms were formed in the surface of microtiter plates (82.5%); the median time for biofilm formation was 24 h, as is the median treatment duration. Quantification of biofilm biomass (52.6%), viable cells (25.5%) and metabolic activity (17.9%) were the most common biofilm assessment methods. Correlation analysis revealed that some phage parameters can influence the treatment outcome: higher phage concentrations were strongly associated with improved biofilm control, leading to higher levels of biofilm reduction, and phages with higher burst sizes and shorter latent periods seem to be the best candidates to control biofilms in vitro. However, the great variability of the methodologies used prompts the need for the development of standardized in vitro methodologies to characterize phage/biofilm interactions and to assess the efficacy of phages to control biofilms.
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Affiliation(s)
- Luciana Meneses
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Ana Catarina Brandão
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- ESCMID Study Group for Biofilms (ESGB), Basel, Switzerland
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- ESCMID Study Group for Biofilms (ESGB), Basel, Switzerland
| | | | - Diana Priscila Pires
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- ESCMID Study Group for Biofilms (ESGB), Basel, Switzerland.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- ESCMID Study Group for Biofilms (ESGB), Basel, Switzerland.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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20
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Song F, Sheng J, Tan J, Xie H, Wang X, Guo W. Characterization of an Enterococcus faecalis bacteriophage SFQ1 as a potential therapeutic agent. Front Microbiol 2023; 14:1210319. [PMID: 37426023 PMCID: PMC10324664 DOI: 10.3389/fmicb.2023.1210319] [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: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus faecalis is a well-established resident of the human gastrointestinal tract and is also a major cause of human infections. Unfortunately, therapeutic options for E. faecalis infections remain limited, particularly with the emergence of vancomycin-resistant strains in hospital settings. Consequently, there has been a renewed interest in phage therapy as an alternative to antibiotics. In this study, we have isolated a bacteriophage, vB_EfaS-SFQ1, from hospital sewage, which effectively infects E. faecalis strain EFS01. Phage SFQ1 is a siphovirus and exhibits a relatively broad host range. Furthermore, it has a short latent period of approximately 10 min and a large burst size of about 110 PFU/cell at a multiplicity of infection (MOI) of 0.01, and it could effectively disrupt the biofilms formed by E. faecalis. Thus, this study provides a detailed characterization of E. faecalis phage SFQ1, which has great potential for treating E. faecalis infections.
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Affiliation(s)
- Fuqiang Song
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Jun Sheng
- Department of Orthopaedics, The General Hospital of Western Theater Command, Chengdu, China
| | - Jishan Tan
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Huajie Xie
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaoyu Wang
- Department of Clinical Pharmacy, The General Hospital of Western Theater Command, Chengdu, China
| | - Wenqiong Guo
- School of Nursing, Chengdu Medical College, Chengdu, China
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21
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Maas E, Penders J, Venema K. Investigating the survival and activity of a bacteriophage in the complex colon environment with the use of a dynamic model of the colon (TIM-2). Microb Pathog 2023; 178:106061. [PMID: 36906154 DOI: 10.1016/j.micpath.2023.106061] [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: 02/01/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
The rise of antibiotic resistance poses a global problem. To avoid this, alternative therapeutic options should be explored, e.g. lytic bacteriophage therapy. Well-designed and described research on effectivity of oral bacteriophage therapy is lacking, therefore the aim of this study was to determine whether the in vitro model of the colon (TIM-2) could be used to investigate the survival and efficacy of therapeutic bacteriophages. For this, an antibiotic-resistant (CmR) E. coli DH5α(pGK11) was used in combination with a corresponding bacteriophage. For the survival study, the TIM-2 model was inoculated with the microbiota of healthy individuals and a standard feeding (SIEM) was fed over the course of the 72 h experiment. To test the bacteriophage, different interventions were carried out. Survival of bacteriophages and bacteria was followed by plating of the lumen samples at different time points 0, 2, 4, 8, 24, 48, and 72 h. In addition, the stability of the bacterial community was determined with the use of 16S rRNA sequencing. Results showed that the phage titers could be decreased by activity from the commensal microbiota. Levels of the phage host (here E.coli) were decreased in the interventions with the phage shot. Multiple shots did not seem to be more effective than a single shot. At the same time, the bacterial community was not disturbed and remained stable throughout the experiment, which is in stark contrast to treatment with antibiotics. Mechanistic studies such as this one are required to optimize efficacy of phage therapy.
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Affiliation(s)
- Evy Maas
- Centre for Healthy Eating & Food Innovation, Maastricht University - Campus Venlo, Villafloraweg 1, 5928 SZ, Venlo, the Netherlands; Euregional Microbiome Center, P. Debyelaan 25, 6229 HX, Maastricht, the Netherlands
| | - John Penders
- Euregional Microbiome Center, P. Debyelaan 25, 6229 HX, Maastricht, the Netherlands; Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Maastricht University, P. Debyelaan 25, 6229 HX, Maastricht, the Netherlands
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation, Maastricht University - Campus Venlo, Villafloraweg 1, 5928 SZ, Venlo, the Netherlands; Euregional Microbiome Center, P. Debyelaan 25, 6229 HX, Maastricht, the Netherlands.
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22
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Onallah H, Hazan R, Nir-Paz R. Compassionate Use of Bacteriophages for Failed Persistent Infections During the First 5 Years of the Israeli Phage Therapy Center. Open Forum Infect Dis 2023; 10:ofad221. [PMID: 37234511 PMCID: PMC10205549 DOI: 10.1093/ofid/ofad221] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
The use of bacteriophages (phages) is reemerging as a potential treatment option for antibiotic-resistant or nonresolving bacterial infections. Phages are bacteria-specific viruses that may serve as a personalized therapeutic option with minimal collateral damage to the patient or the microbiome. In 2018 we established the Israeli Phage Therapy Center (IPTC) as a shared initiative of the Hadassah Medical Center and the Hebrew University of Jerusalem, aiming to conduct all of the steps required for phage-based solutions, from phage isolation and characterization to treatments, for nonresolving bacterial infections. So far, a total of 159 requests for phage therapy arrived to the IPTC; 145 of them were from Israel and the rest from other countries. This number of registered requests is growing annually. Multidrug-resistant bacteria accounted for 38% of all phage requests. Respiratory and bone infections were the most prevalent among clinical indications and accounted for 51% of the requests. To date, 20 phage therapy courses were given to 18 patients by the IPTC. In 77.7% (n = 14) of the cases, a favorable clinical outcome of infection remission or recovery was seen. Clearly, establishing an Israeli phage center has led to an increased demand for compassionate use of phages with favorable outcomes for many previously failed infections. As clinical trials are still lacking, publishing patient data from cohort studies is pertinent to establish clinical indications, protocols, and success and failure rates. Last, workflow processes and bottlenecks should be shared to enable faster availability and authorization of phages for clinical use.
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Affiliation(s)
- Hadil Onallah
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Israeli Phage Therapy Center of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
| | - Ronen Hazan
- Correspondence: Ran Nir-Paz, MD, Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel (); Ronen Hazan, PhD, Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel ()
| | - Ran Nir-Paz
- Correspondence: Ran Nir-Paz, MD, Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel (); Ronen Hazan, PhD, Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel ()
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23
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Arivarasan VK. Unlocking the potential of phages: Innovative approaches to harnessing bacteriophages as diagnostic tools for human diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:133-149. [PMID: 37770168 DOI: 10.1016/bs.pmbts.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phages, viruses that infect bacteria, have been explored as promising tools for the detection of human disease. By leveraging the specificity of phages for their bacterial hosts, phage-based diagnostic tools can rapidly and accurately detect bacterial infections in clinical samples. In recent years, advances in genetic engineering and biotechnology have enabled the development of more sophisticated phage-based diagnostic tools, including those that express reporter genes or enzymes, or target specific virulence factors or antibiotic resistance genes. However, despite these advancements, there are still challenges and limitations to the use of phage-based diagnostic tools, including concerns over phage safety and efficacy. This review aims to provide a comprehensive overview of the current state of phage-based diagnostic tools, including their advantages, limitations, and potential for future development. By addressing these issues, we hope to contribute to the ongoing efforts to develop safe and effective phage-based diagnostic tools for the detection of human disease.
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Affiliation(s)
- Vishnu Kirthi Arivarasan
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India.
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24
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Popovic M. The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. MICROBIAL RISK ANALYSIS 2023; 23:100249. [PMID: 36777924 PMCID: PMC9898946 DOI: 10.1016/j.mran.2023.100249] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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25
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Administration of Bacteriophages via Nebulization during Mechanical Ventilation: In Vitro Study and Lung Deposition in Macaques. Viruses 2023; 15:v15030602. [PMID: 36992312 PMCID: PMC10051375 DOI: 10.3390/v15030602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Bacteriophages have been identified as a potential treatment option to treat lung infection in the context of antibiotic resistance. We performed a preclinical study to predict the efficacy of delivery of bacteriophages against Pseudomonas aeruginosa (PA) when administered via nebulization during mechanical ventilation (MV). We selected a mix of four anti-PA phages containing two Podoviridae and two Myoviridae, with a coverage of 87.8% (36/41) on an international PA reference panel. When administered via nebulization, a loss of 0.30–0.65 log of infective phage titers was measured. No difference between jet, ultrasonic and mesh nebulizers was observed in terms of loss of phage viability, but a higher output was measured with the mesh nebulizer. Interestingly, Myoviridae are significantly more sensitive to nebulization than Podoviridae since their long tail is much more prone to damage. Phage nebulization has been measured as compatible with humidified ventilation. Based on in vitro measurement, the lung deposition prediction of viable phage particles ranges from 6% to 26% of the phages loaded in the nebulizer. Further, 8% to 15% of lung deposition was measured by scintigraphy in three macaques. A phage dose of 1 × 109 PFU/mL nebulized by the mesh nebulizer during MV predicts an efficient dose in the lung against PA, comparable with the dose chosen to define the susceptibility of the strain.
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26
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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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27
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Nang SC, Lin YW, Petrovic Fabijan A, Chang RYK, Rao GG, Iredell J, Chan HK, Li J. Pharmacokinetics/pharmacodynamics of phage therapy: a major hurdle to clinical translation. Clin Microbiol Infect 2023:S1198-743X(23)00046-0. [PMID: 36736661 DOI: 10.1016/j.cmi.2023.01.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND The increasing emergence of antimicrobial resistance worldwide has led to renewed interest in phage therapy. Unlike antibiotics, the lack of pharmacokinetics/pharmacodynamics (PK/PD) information represents a major challenge for phage therapy. As therapeutic phages are biological entities with the ability to self-replicate in the presence of susceptible bacteria, their PK/PD is far more complicated than that of antibiotics. OBJECTIVES This narrative review examines the current literature on phage pharmacology and highlights major pharmacological challenges for phage therapy. SOURCES Included articles were identified by searching PubMed and Google Scholar till June 2022. The search terms were 'bacteriophage', 'antimicrobial', 'pharmacokinetics' and 'pharmacodynamics'. Additional relevant references were obtained from articles retrieved from the primary search. CONTENT In this review, phage PK is first discussed, focusing on absorption, distribution, metabolism, and elimination. Key factors affecting phage antimicrobial activities are reviewed, including multiplicity of infection, passive and active phage therapy, and the involvement of the human immune system. Importantly, we emphasize the impact of phage self-replication on the PK/PD and the fundamental phage characteristics that are required for PK/PD modelling and clinical translation. IMPLICATIONS Recent progress in phage pharmacology has shown that we are in a far better position now to treat infections with phage therapy than a century ago. However, phage therapy is still in its infancy when compared to antibiotics due to the scarce pharmacological knowledge (e.g. PK/PD). Optimization of phage PK/PD is key for translation of phage therapy in patients.
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Affiliation(s)
- Sue C Nang
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Aleksandra Petrovic Fabijan
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Rachel Y K Chang
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia; AcuraBio Pty Ltd, Darra, Queensland, Australia
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, North Carolina, USA
| | - Jonathan Iredell
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia.
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28
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Srisangthong I, Sangseedum C, Chaichanit N, Surachat K, Suanyuk N, Mittraparp-arthorn P. Characterization and Genome Analysis of Vibrio campbellii Lytic Bacteriophage OPA17. Microbiol Spectr 2023; 11:e0162322. [PMID: 36719217 PMCID: PMC10101143 DOI: 10.1128/spectrum.01623-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Vibrio campbellii is a marine bacterium that is associated with luminous vibriosis, especially in the hatchery and nursery stages of penaeid shrimp cultivation worldwide, which has led to low survival rates of shrimp during aquaculture. Phage therapy has been reported as an alternative biocontrol agent which can reduce or replace the use of antibiotics and other chemicals. This study characterized a lytic V. campbellii bacteriophage, OPA17, originally isolated from bloody clams and investigated its biocontrol efficacy against V. campbellii infection in a model system, Artemia franciscana. Phage OPA17 lysed 83.89% of V. campbellii strains tested (n = 118) with clear plaque morphology. Some strains of Vibrio parahaemolyticus and Vibrio vulnificus were also infected by phage OPA17. Transmission electron microscopy and genetic features indicated that OPA17 belongs to the Siphoviridae family. The latent period and burst size of OPA17 were approximately 50 min and 123 PFU/cell, respectively. Moreover, it survived in artificial seawater throughout the 2-month study period and effectively destroyed Vibrio campbellii biofilms after 4 h of incubation. The addition of OPA17 significantly increased the survival of A. franciscana nauplii infected with V. campbellii. The genome sequence of OPA17 showed that it does not carry genes unsuitable for phage therapy. The phylogenetic tree analysis showed that OPA17 was closely related to the V. vulnificus lytic phage SSP002 (98.90% similarity), which was previously reported as a potential biocontrol agent. Accordingly, the results of this study provide valuable information regarding the potential biocontrol application of phage OPA17 against V. campbellii. IMPORTANCE V. campbellii is an emerging luminous pathogen associated with vibriosis, especially in marine shrimp hatcheries. Several strategies, including pond management and use of natural antimicrobials and probiotics, have been studied for control of this organism. Phage therapy is considered one of the effective biocontrol strategies against bacterial infections in aquaculture. However, there has been limited study of V. campbellii bacteriophages. In this study, V. campbellii-specific bacteriophage OPA17 was isolated, characterized, and investigated for its biocontrol efficacy against V. campbellii infection in an Artemia nauplii model. Phage OPA17 belongs to the Siphoviridae family and shares significant genome similarity to phage SSP002, a potential biocontrol agent against V. vulnificus infection in a murine model. However, the host range of OPA17 was broader than that of SSP002. Overall, we discuss the potential of OPA17 for phage therapy application in shrimp hatcheries.
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Affiliation(s)
- Intraporn Srisangthong
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chadtida Sangseedum
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Netnapa Chaichanit
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Naraid Suanyuk
- Aquatic Science and Innovative Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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29
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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] [MESH Headings] [Grants] [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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30
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Interruption of Capsular Polysaccharide Biosynthesis Gene wbaZ by Insertion Sequence IS 903B Mediates Resistance to a Lytic Phage against ST11 K64 Carbapenem-Resistant Klebsiella pneumoniae. mSphere 2022; 7:e0051822. [PMID: 36377881 PMCID: PMC9769513 DOI: 10.1128/msphere.00518-22] [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] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major challenge for clinical management worldwide with limited antimicrobial options. Phages are considered an alternative option. Here, we isolated and identified a phage able to lyse ST11-K64 CRKP, the major type in China. This phage has a narrow host range, only lysing ST11-K64 CRKP, and inhibits the growth of host strains for 3 h forming large clear plaques (3.0 to 6.0 mm in diameter) with a surrounding halo. This phage exhibited excellent stability in different temperatures and pH and did not contain any virulence, lysogenic, antimicrobial resistance genes nor tRNA, meeting the criteria for phage therapy. Genomic analysis revealed that it represents a novel species of the Przondovirus genus according to ICTV standards. However, phage-resistant bacterial mutants emerged after 4-h exposure. Compared to the parental strain, phage-resistant mutants showed nonmucoid appearance and exhibited significantly reduced virulence for Galleria mellonella larva. Three randomly selected phage-resistant mutants were genome sequenced. Interruption of capsular polysaccharide biosynthesis-associated gene wcaJ or wbaZ by IS903B alone or an IS903-formed composite transposon was identified. Interruption of wcaJ is a known phage resistant mechanism, while that of wbaZ is not. By complementing the intact wbaZ, the phage susceptibility was restored, confirming the role of wbaZ interruption in phage resistance. This highlights that alteration in the capsular polysaccharide biosynthesis gene cluster, which could be due to transposable elements, is a major mechanism for resistance to Przondovirus phages in CRKP. Noncapsule-targeting phages may be combined for improving phage therapy against CRKP. IMPORTANCE Phage therapy is an alternative approach against multidrug resistant microorganisms such as carbapenem-resistant Klebsiella pneumoniae (CRKP), which represents a major challenge for treatment due to very limited options of antimicrobial agents. For optimizing phage therapy, more new lytic phages are needed. Here, we isolated and characterized a phage of a novel species able to rapidly lyse a major type of CRKP without carrying any virulence, lysogenic, antimicrobial resistance genes. This phage is therefore suitable for clinical treatment. However, phage-resistant mutants of CRKP strains were observed after exposure. We found a new mechanism, i.e., interruption of a capsular polysaccharide biosynthesis gene wbaZ by an insertion sequence-formed composite transposon. Our study demonstrates the capsular polysaccharide biosynthesis gene cluster as a major source of resistance to certain lytic phages in CRKP. This requires more studies to counter phage resistance. Our studies also highlight the critical role of insertion sequences in phage resistance.
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31
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Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022). Vaccines (Basel) 2022; 10:vaccines10122112. [PMID: 36560522 PMCID: PMC9784531 DOI: 10.3390/vaccines10122112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.
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32
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Application and challenge of bacteriophage in the food protection. Int J Food Microbiol 2022; 380:109872. [PMID: 35981493 DOI: 10.1016/j.ijfoodmicro.2022.109872] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
Abstract
In recent years, foodborne diseases caused by pathogens have been increasing. Therefore, it is essential to control the growth and transmission of pathogens. Bacteriophages (phages) have the potential to play an important role in the biological prevention, control, and treatment of these foodborne diseases due to their favorable advantages. Phages not only effectively inhibit pathogenic bacteria and prolong the shelf life of food, but also possess the advantages of specificity and an absence of chemical residues. Currently, there are many cases of phage applications in agriculture, animal disease prevention and control, food safety, and the treatment of drug-resistant disease. In this review, we summarize the recent research progress on phages against foodborne pathogenic bacteria, including Escherichia coli, Salmonella, Campylobacter, Listeria monocytogenes, Shigella, Vibrio parahaemolyticus, and Staphylococcus aureus. We also discuss the main issues and their corresponding solutions in the application of phages in the food industry. In recent years, although researchers have discovered more phages with potential applications in the food industry, most researchers use these phages based on their host spectrum, and the application environment is mostly in the laboratory. Therefore, the practical application of these phages in different aspects of the food industry may be unsatisfactory and even have some negative effects. Thus, we suggest that before using these phages, it is necessary to identify their specific receptors. Using their specific receptors as the selection basis for their application and combining phages with other phages or phages with traditional antibacterial agents may further improve their safety and application efficiency. Collectively, this review provides a theoretical reference for the basic research and application of phages in the food industry.
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33
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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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34
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Wu S, Wu B, Liu Y, Deng S, Lei L, Zhang H. Mini Review Therapeutic Strategies Targeting for Biofilm and Bone Infections. Front Microbiol 2022; 13:936285. [PMID: 35774451 PMCID: PMC9238355 DOI: 10.3389/fmicb.2022.936285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 12/21/2022] Open
Abstract
Bone infection results in a complex inflammatory response and bone destruction. A broad spectrum of bacterial species has been involved for jaw osteomyelitis, hematogenous osteomyelitis, vertebral osteomyelitis or diabetes mellitus, such as Staphylococcus aureus (S. aureus), coagulase-negative Staphylococcus species, and aerobic gram-negative bacilli. S. aureus is the major pathogenic bacterium for osteomyelitis, which results in a complex inflammatory response and bone destruction. Although various antibiotics have been applied for bone infection, the emergence of drug resistance and biofilm formation significantly decrease the effectiveness of those agents. In combination with gram-positive aerobes, gram-negative aerobes and anaerobes functionally equivalent pathogroups interact synergistically, developing as pathogenic biofilms and causing recurrent infections. The adhesion of biofilms to bone promotes bone destruction and protects bacteria from antimicrobial agent stress and host immune system infiltration. Moreover, bone is characterized by low permeability and reduced blood flow, further hindering the therapeutic effect for bone infections. To minimize systemic toxicity and enhance antibacterial effectiveness, therapeutic strategies targeting on biofilm and bone infection can serve as a promising modality. Herein, we focus on biofilm and bone infection eradication with targeting therapeutic strategies. We summarize recent targeting moieties on biofilm and bone infection with peptide-, nucleic acid-, bacteriophage-, CaP- and turnover homeostasis-based strategies. The antibacterial and antibiofilm mechanisms of those therapeutic strategies include increasing antibacterial agents’ accumulation by bone specific affinity, specific recognition of phage-bacteria, inhibition biofilm formation in transcription level. As chronic inflammation induced by infection can trigger osteoclast activation and inhibit osteoblast functioning, we additionally expand the potential applications of turnover homeostasis-based therapeutic strategies on biofilm or infection related immunity homeostasis for host-bacteria. Based on this review, we expect to provide useful insights of targeting therapeutic efficacy for biofilm and bone infection eradication.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Binjie Wu
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Shu Deng
- Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, United States
| | - Lei Lei
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Lei Lei,
| | - Hui Zhang
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
- Hui Zhang,
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35
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Rimon A, Gelman D, Yerushalmy O, Coppenhagen-Glazer S, Katvan E, Nir-Paz R, Hazan R. Phage Therapy in Israel, Past, Present, and Future. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:85-94. [PMID: 36157284 PMCID: PMC9436258 DOI: 10.1089/phage.2022.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The fascinating scientific history of phage therapy has been documented in numerous publications. In this study, however, we focus on an angle of the story that hitherto has remained relatively neglected, namely, phage therapy treatments, and the protagonists that conducted these in Mandatory-Palestine and subsequently the state of Israel, as part of a global trend. We complete the story by describing efforts in the new era of phage therapy in present-day Israel.
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Affiliation(s)
- Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Military Medicine, Faculty of Medicine, The 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
- Department of Military Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Katvan
- Bar Ilan University, Ramat Gan, Israel
- Peres Academic Center, Rehovot, Israel
| | - Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Diseases, Jerusalem, and the Faculty of Medicine, The 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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36
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Koskella B, Hernandez CA, Wheatley RM. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annu Rev Virol 2022; 9:57-78. [PMID: 35584889 DOI: 10.1146/annurev-virology-091919-075914] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA;
| | - Catherine A Hernandez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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37
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Chen LK, Chang JC, Chu HT, Chen YT, Jiang HL, Wang LS, Teh SH, Yang HH, Chen DS, Li YZ, Chang CC, Sankhla D, Tseng CC. Preoptimized phage cocktail for use in aerosols against nosocomial transmission of carbapenem-resistant Acinetobacter baumannii: A 3-year prospective intervention study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 236:113476. [PMID: 35367880 DOI: 10.1016/j.ecoenv.2022.113476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Using bacteriophages (phages) as environmental sanitizers has been recognized as a potential alternative method to remove bacterial contamination in vitro; however, very few studies are available on the application of phages for infection control in hospitals. Here, we performed a 3-year prospective intervention study using aerosolized phage cocktails as biocontrol agents against carbapenem-resistant Acinetobacter baumannii (CRAB) infection in the hospital. When a CRAB-infected patient was identified in an intensive care unit (ICU), their surrounding environment was chosen for phage aerosol decontamination. Before decontamination, 501 clinical specimens from the patients were subjected to antibiotic resistance analysis and phage typing. The optimal phage cocktails were a combination of different phage families or were constructed by next-evolutionary phage typing with the highest score for the host lysis zone to prevent the development of environmental CRAB phage resistance. The phage infection percentage of the antibiotic-resistant A. baumannii strains was 97.1%, whereas the infection percentage in the antibiotic-susceptible strains was 79.3%. During the phage decontamination periods from 2017 to 2019, the percentage of carbapenem-resistant A. baumannii in test ICUs decreased significantly from 65.3% to 55%. The rate of new acquisitions of CRAB infection over the three years was 4.4 per 1000 patient-days, which was significantly lower than that in the control wards (8.9 per 1000 patient-days) where phage decontamination had never been performed. In conclusion, our results support the potential of phage cocktails to decrease CRAB infection rates, and the aerosol generation process may make this approach more comprehensive and time-saving.
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Affiliation(s)
- Li-Kuang Chen
- Institute of Medical Sciences, Department of Laboratory Diagnostic, College of Medicine, Tzu Chi University, Hualien, Taiwan; Branch of Clinical Pathology, Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Jui-Chih Chang
- Department of Surgery, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Section 3, Zhongyang Rd., Hualien, Taiwan; Department of Surgery, School of Medicine, Tzu Chi University, No. 701, Section 3, Zhongyang Rd., Hualien, Taiwan.
| | - Hsiu-Tzu Chu
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan; Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
| | - Yi-Ting Chen
- Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
| | - Hui-Li Jiang
- Unit of Infection Control and Management, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Lih-Shinn Wang
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Soon-Hian Teh
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Hui-Hua Yang
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
| | - Dar-Sen Chen
- School of Pharmacy, China Medical University, Taiwan.
| | - Yu-Zhong Li
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Chin-Cheng Chang
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Debangana Sankhla
- Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
| | - Chun-Chieh Tseng
- Department and Graduate Institute of Public Health, Tzu Chi University, Hualien, Taiwan.
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38
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A Method to Determine the Efficacy of a Commercial Phage Preparation against Uropathogens in Urine and Artificial Urine Determined by Isothermal Microcalorimetry. Microorganisms 2022; 10:microorganisms10050845. [PMID: 35630291 PMCID: PMC9147073 DOI: 10.3390/microorganisms10050845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Urinary tract infections are commonly encountered and often treated with antibiotics. However, the inappropriate use of the latter has led to the appearance of resistant strains. In this context we investigate the use of calorimetry to rapidly determine if a phage cocktail can be used as alternative to antibiotics. Methods: We used a commercially available phage cocktail from an online pharmacy and tested it against a strain of Escherichia coli and a strain of Proteus mirabilis. We used isothermal microcalorimetry to follow the metabolic activity of the bacterial culture treated with the phage cocktail. Results: Isothermal microcalorimetry was able to follow the dynamic of the bacterial metabolic activity reduction by the phage cocktail. Both pathogens were strongly inhibited; however, some regrowth was observed for E. coli in urine. Conclusions: Isothermal microcalorimetry proved to be a valuable technique when investigating the efficacy of phage cocktails against uropathogens. We foresee that isothermal microcalorimetry could be used to obtain rapid phagograms.
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39
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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: 14] [Impact Index Per Article: 7.0] [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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40
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Würstle S, Stender J, Hammerl JA, Vogele K, Rothe K, Willy C, Bugert JJ. Practical Assessment of an Interdisciplinary Bacteriophage Delivery Pipeline for Personalized Therapy of Gram-Negative Bacterial Infections. Pharmaceuticals (Basel) 2022; 15:186. [PMID: 35215298 PMCID: PMC8879309 DOI: 10.3390/ph15020186] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/24/2022] Open
Abstract
Despite numerous advances in personalized phage therapy, smooth logistics are challenging, particularly for multidrug-resistant Gram-negative bacterial infections requiring high numbers of specific lytic phages. We conducted this study to pave the way for efficient logistics for critically ill patients by (1) closely examining and improving a current pipeline under realistic conditions, (2) offering guidelines for each step, leading to safe and high-quality phage supplies, and (3) providing a tool to evaluate the pipeline's efficiency. Due to varying stipulations for quality and safety in different countries, we focused the pipeline on all steps up to a required phage product by a cell-free extract system. The first of three study runs included patients with respiratory bacterial infections from four intensive care units, and it revealed a cumulative time of up to 23 days. Ultimately, adjustment of specific set points of the vulnerable components of the pipeline, phage isolation, and titration increased the pipeline's efficiency by 15% and decreased the maximum required time to 13 days. We present a site-independent practical approach to establish and optimize pipelines for personalized phage delivery, the co-organization of pipeline components between different institutions, non-binding guidelines for every step, and an efficiency check for phage laboratories.
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Affiliation(s)
- Silvia Würstle
- Department of Internal Medicine II, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Jana Stender
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany;
| | - Jens André Hammerl
- Unit Epidemiology, Zoonoses and Antimicrobial Resistances, Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | - Kilian Vogele
- Physics of Synthetic Biological Systems-E14, Physics-Department and ZNN, Technical University Munich, 85748 Munich, Germany;
| | - Kathrin Rothe
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
| | - Christian Willy
- Trauma & Orthopaedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Bundeswehr (Military) Academic Hospital Berlin, 10115 Berlin, Germany;
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41
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You X, Klose N, Kallies R, Harms H, Chatzinotas A, Wick LY. Mycelia-Assisted Isolation of Non-Host Bacteria Able to Co-Transport Phages. Viruses 2022; 14:195. [PMID: 35215789 PMCID: PMC8877629 DOI: 10.3390/v14020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/27/2022] Open
Abstract
Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90-95% for hydrophobic T4 and 30-95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments.
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Affiliation(s)
- Xin You
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
| | - Niclas Klose
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
| | - René Kallies
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
| | - Hauke Harms
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Talstr.33, 04103 Leipzig, Germany
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany; (X.Y.); (N.K.); (R.K.); (H.H.); (A.C.)
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Sørensen PE, Ng DYK, Duchateau L, Ingmer H, Garmyn A, Butaye P. Classification of In Vitro Phage-Host Population Growth Dynamics. Microorganisms 2021; 9:2470. [PMID: 34946072 PMCID: PMC8708399 DOI: 10.3390/microorganisms9122470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
The therapeutic use of bacteriophages (phage therapy) represents a promising alternative to antibiotics to control bacterial pathogens. However, the understanding of the phage-bacterium interactions and population dynamics seems essential for successful phage therapy implementation. Here, we investigated the effect of three factors: phage species (18 lytic E. coli-infecting phages); bacterial strain (10 APEC strains); and multiplicity of infection (MOI) (MOI 10, 1, and 0.1) on the bacterial growth dynamics. All factors had a significant effect, but the phage appeared to be the most important. The results showed seven distinct growth patterns. The first pattern corresponded to the normal bacterial growth pattern in the absence of a phage. The second pattern was complete bacterial killing. The remaining patterns were in-between, characterised by delayed growth and/or variable killing of the bacterial cells. In conclusion, this study demonstrates that the phage-host dynamics is an important factor in the capacity of a phage to eliminate bacteria. The classified patterns show that this is an essential factor to consider when developing a phage therapy. This methodology can be used to rapidly screen for novel phage candidates for phage therapy. Accordingly, the most promising candidates were phages found in Group 2, characterised by growth dynamics with high bacterial killing.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
| | - Duncan Y. K. Ng
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Luc Duchateau
- Biometrics Research Center, Ghent University, 9820 Merelbeke, Belgium;
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, 9820 Merelbeke, Belgium; (A.G.); (P.B.)
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 42123, Saint Kitts and Nevis
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Ben Porat S, Gelman D, Yerushalmy O, Alkalay-Oren S, Coppenhagen-Glazer S, Cohen-Cymberknoh M, Kerem E, Amirav I, Nir-Paz R, Hazan R. Expanding clinical phage microbiology: simulating phage inhalation for respiratory tract infections. ERJ Open Res 2021; 7:00367-2021. [PMID: 34760998 PMCID: PMC8573233 DOI: 10.1183/23120541.00367-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/05/2021] [Indexed: 11/12/2022] Open
Abstract
Phage therapy is a promising antibacterial strategy for resistant respiratory tract infections. Phage inhalation may serve this goal; however, it requires a careful assessment of their delivery by this approach. Here we present an in vitro model to evaluate phage inhalation. Eight phages, most of which target pathogens common in cystic fibrosis, were aerosolised by jet nebuliser and administered to a real-scale computed tomography-derived 3D airways model with a breathing simulator. Viable phage loads reaching the output of the nebuliser and the tracheal level of the model were determined and compared to the loaded amount. Phage inhalation resulted in a diverse range of titre reduction, primarily associated with the nebulisation process. No correlation was found between phage delivery to the phage physical or genomic dimensions. These findings highlight the need for tailored simulations of phage delivery, ideally by a patient-specific model in addition to proper phage matching, to increase the potential of phage therapy success.
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Affiliation(s)
- Shira Ben Porat
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Dept of Military Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- These authors contributed equally
| | - Daniel Gelman
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Dept of Military Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Dept of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
- These authors contributed equally
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Malena Cohen-Cymberknoh
- Pediatric Pulmonology Unit and Cystic Fibrosis Center, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eitan Kerem
- Pediatric Pulmonology Unit and Cystic Fibrosis Center, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Israel Amirav
- Pediatric Pulmonary Unit, Dana-Dwek Children's Hospital, Tel Aviv, Israel
| | - Ran Nir-Paz
- Dept of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- These authors contributed equally
| | - Ronen Hazan
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- These authors contributed equally
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Paul K, Merabishvili M, Hazan R, Christner M, Herden U, Gelman D, Khalifa L, Yerushalmy O, Coppenhagen-Glazer S, Harbauer T, Schulz-Jürgensen S, Rohde H, Fischer L, Aslam S, Rohde C, Nir-Paz R, Pirnay JP, Singer D, Muntau AC. Bacteriophage Rescue Therapy of a Vancomycin-Resistant Enterococcus faecium Infection in a One-Year-Old Child following a Third Liver Transplantation. Viruses 2021; 13:1785. [PMID: 34578366 PMCID: PMC8472888 DOI: 10.3390/v13091785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/21/2021] [Accepted: 09/01/2021] [Indexed: 12/23/2022] Open
Abstract
Phage therapy is an experimental therapeutic approach used to target multidrug-resistant bacterial infections. A lack of reliable data with regard to its efficacy and regulatory hurdles hinders a broad application. Here we report, for the first time, a case of vancomycin-resistant Enterococcus faecium abdominal infection in a one-year-old, critically ill, and three times liver transplanted girl, which was successfully treated with intravenous injections (twice per day for 20 days) of a magistral preparation containing two Enterococcus phages. This correlated with a reduction in baseline C-reactive protein (CRP), successful weaning from mechanical ventilation and without associated clinical adverse events. Prior to clinical use, phage genome was sequenced to confirm the absence of genetic determinants conferring lysogeny, virulence or antibiotic resistance, and thus their safety. Using a phage neutralization assay, no neutralizing anti-phage antibodies in the patient's serum could be detected. Vancomycin-susceptible E. faecium isolates were identified in close relation to phage therapy and, by using whole-genome sequencing, it was demonstrated that vancomycin-susceptible E. faecium emerged from vancomycin-resistant progenitors. Covering a one year follow up, we provide further evidence for the feasibility of bacteriophage therapy that can serve as a basis for urgently needed controlled clinical trials.
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Affiliation(s)
- Kevin Paul
- Department of Pediatrics, Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.H.); (S.S.-J.); (D.S.); (A.C.M.)
| | - Maya Merabishvili
- Burn Centre, Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, B-1120 Brussels, Belgium;
| | - Ronen Hazan
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 9112001, Israel; (D.G.); (L.K.); (O.Y.); (S.C.-G.)
| | - Martin Christner
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.C.); (H.R.)
| | - Uta Herden
- Department of Visceral Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (U.H.); (L.F.)
| | - Daniel Gelman
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 9112001, Israel; (D.G.); (L.K.); (O.Y.); (S.C.-G.)
| | - Leron Khalifa
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 9112001, Israel; (D.G.); (L.K.); (O.Y.); (S.C.-G.)
| | - Ortal Yerushalmy
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 9112001, Israel; (D.G.); (L.K.); (O.Y.); (S.C.-G.)
| | - Shunit Coppenhagen-Glazer
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 9112001, Israel; (D.G.); (L.K.); (O.Y.); (S.C.-G.)
| | - Theresa Harbauer
- Department of Pediatrics, Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.H.); (S.S.-J.); (D.S.); (A.C.M.)
| | - Sebastian Schulz-Jürgensen
- Department of Pediatrics, Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.H.); (S.S.-J.); (D.S.); (A.C.M.)
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.C.); (H.R.)
| | - Lutz Fischer
- Department of Visceral Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (U.H.); (L.F.)
| | - Saima Aslam
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA;
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany;
| | - Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Disease, Hadassah University Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel;
| | - Jean-Paul Pirnay
- Burn Centre, Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, B-1120 Brussels, Belgium;
| | - Dominique Singer
- Department of Pediatrics, Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.H.); (S.S.-J.); (D.S.); (A.C.M.)
| | - Ania Carolina Muntau
- Department of Pediatrics, Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.H.); (S.S.-J.); (D.S.); (A.C.M.)
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