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Costa P, Pereira C, Romalde JL, Almeida A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 2024; 599:110209. [PMID: 39186863 DOI: 10.1016/j.virol.2024.110209] [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: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.
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Affiliation(s)
- Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS - Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain.
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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2
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Rao GG, Vallé Q, Mahadevan R, Sharma R, Barr JJ, Van Tyne D. Crossing the Chasm: How to Approach Translational Pharmacokinetic-Pharmacodynamic Modeling of Phage Dosing. Clin Pharmacol Ther 2024. [PMID: 39313763 DOI: 10.1002/cpt.3426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/28/2024] [Indexed: 09/25/2024]
Abstract
Effectively treating multidrug-resistant bacterial infections remains challenging due to the limited drug development pipeline and a scarcity of novel agents effective against these highly resistant pathogens. Bacteriophages (phages) are a potential addition to the antimicrobial treatment arsenal. Though, phages are currently being tested in clinical trials for antibiotic-resistant infections, phages lack a fundamental understanding of optimal dosing in humans. Rationally designed preclinical studies using in vitro and in vivo infection models, allow us to assess clinically relevant phage +/- antibiotic exposure (pharmacokinetics), the resulting treatment impact on the infecting pathogen (pharmacodynamics) and host immune response (immunodynamics). A mechanistic modeling framework allows us to integrate this knowledge gained from preclinical studies to develop predictive models. We reviewed recently published mathematical models based on in vitro and/or in vivo data that evaluate the effects of varying bacterial or phage densities, phage characteristics (burst size, adsorption rate), phage pharmacokinetics, phage-antibiotic combinations and host immune responses. In our review, we analyzed study designs and the data used to inform the development of these mechanistic models. Insights gained from model-based simulations were reviewed as they help identify crucial phage parameters for determining effective phage dosing. These efforts contribute to bridging the gap between phage therapy research and its clinical translation.
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Affiliation(s)
- Gauri G Rao
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Quentin Vallé
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Ramya Mahadevan
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Rajnikant Sharma
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Zborowsky S, Seurat J, Balacheff Q, Ecomard S, Nguyen Ngoc Minh C, Titécat M, Evrard E, Rodriguez-Gonzalez RA, Marchi J, Weitz JS, Debarbieux L. Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575879. [PMID: 38293203 PMCID: PMC10827109 DOI: 10.1101/2024.01.16.575879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused by Pseudomonas aeruginosa relies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting the P. aeruginosa load in the lungs. Unexpectedly, upon bacteriophage treatment, pulmonary levels of P. aeruginosa were significantly lower in AM-depleted than in immunocompetent mice. To explore potential mechanisms underlying the benefit of AM-depletion in treated mice, we developed a mathematical model of phage, bacteria, and innate immune system dynamics. Simulations from the model fitted to data suggest that AM reduce bacteriophage density in the lungs. We experimentally confirmed that the in vivo decay of bacteriophage is faster in immunocompetent compared to AM-depleted animals. These findings demonstrate the involvement of feedback between bacteriophage, bacteria, and the immune system in shaping the outcomes of phage therapy in clinical settings.
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Affiliation(s)
- Sophia Zborowsky
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- These authors contributed equally
| | - Jérémy Seurat
- Institut de Biologie, Ecole Normale Supérieure, Paris 75005, France
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- These authors contributed equally
| | - Quentin Balacheff
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- CHU Felix Guyon, Service des maladies respiratoires, La Réunion, France
| | - Solène Ecomard
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- DGA, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Chau Nguyen Ngoc Minh
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Marie Titécat
- Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, Lille 59000, France
| | - Emma Evrard
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
| | - Rogelio A. Rodriguez-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta GA 30332, USA
| | - Jacopo Marchi
- Department of Biology, University of Maryland, College Park MD 20742, USA
| | - Joshua S. Weitz
- Institut de Biologie, Ecole Normale Supérieure, Paris 75005, France
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- Department of Biology, University of Maryland, College Park MD 20742, USA
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
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4
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Karami M, Goudarztalejerdi A, Mohammadzadeh A, Berizi E. In vitro evaluation of two novel Escherichia bacteriophages against multiple drug resistant avian pathogenic Escherichia coli. BMC Infect Dis 2024; 24:497. [PMID: 38755537 PMCID: PMC11100137 DOI: 10.1186/s12879-024-09402-0] [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: 12/26/2023] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND In recent years, there has been a growing interest in phage therapy as an effective therapeutic tool against colibacillosis caused by avian pathogenic Escherichia coli (APEC) which resulted from the increasing number of multidrug resistant (MDR) APEC strains. METHODS In the present study, we reported the characterization of a new lytic bacteriophage (Escherichia phage AG- MK-2022. Basu) isolated from poultry slaughterhouse wastewater. In addition, the in vitro bacteriolytic activity of the newly isolated phage (Escherichia phage AG- MK-2022. Basu) and the Escherichia phage VaT-2019a isolate PE17 (GenBank: MK353636.1) were assessed against MDR- APEC strains (n = 100) isolated from broiler chickens with clinical signs of colibacillosis. RESULTS Escherichia phage AG- MK-2022. Basu belongs to the Myoviridae family and exhibits a broad host range. Furthermore, the phage showed stability under a wide range of temperatures, pH values and different concentrations of NaCl. Genome analysis of the Escherichia phage AG- MK-2022. Basu revealed that the phage possesses no antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and any E. coli virulence associated genes. In vitro bacterial challenge tests demonstrated that two phages, the Escherichia phage VaT-2019a isolate PE17 and the Escherichia phage AG- MK-2022. Basu exhibited high bactericidal activity against APEC strains and lysed 95% of the tested APEC strains. CONCLUSIONS The current study findings indicate that both phages could be suggested as safe biocontrol agents and alternatives to antibiotics for controlling MDR-APEC strains isolated from broilers.
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Affiliation(s)
- Mobina Karami
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran
| | - Ali Goudarztalejerdi
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran.
| | - Abdolmajid Mohammadzadeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran
| | - Enayat Berizi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Bagińska N, Grygiel I, Orwat F, Harhala MA, Jędrusiak A, Gębarowska E, Letkiewicz S, Górski A, Jończyk-Matysiak E. Stability study in selected conditions and biofilm-reducing activity of phages active against drug-resistant Acinetobacter baumannii. Sci Rep 2024; 14:4285. [PMID: 38383718 PMCID: PMC10881977 DOI: 10.1038/s41598-024-54469-z] [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: 09/25/2023] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
Acinetobacter baumannii is currently a serious threat to human health, especially to people with immunodeficiency as well as patients with prolonged hospital stays and those undergoing invasive medical procedures. The ever-increasing percentage of strains characterized by multidrug resistance to widely used antibiotics and their ability to form biofilms make it difficult to fight infections with traditional antibiotic therapy. In view of the above, phage therapy seems to be extremely attractive. Therefore, phages with good storage stability are recommended for therapeutic purposes. In this work, we present the results of studies on the stability of 12 phages specific for A. baumannii under different conditions (including temperature, different pH values, commercially available disinfectants, essential oils, and surfactants) and in the urine of patients with urinary tract infections (UTIs). Based on our long-term stability studies, the most optimal storage method for the A. baumannii phage turned out to be - 70 °C. In contrast, 60 °C caused a significant decrease in phage activity after 1 h of incubation. The tested phages were the most stable at a pH from 7.0 to 9.0, with the most inactivating pH being strongly acidic. Interestingly, ethanol-based disinfectants caused a significant decrease in phage titers even after 30 s of incubation. Moreover, copper and silver nanoparticle solutions also caused a decrease in phage titers (which was statistically significant, except for the Acba_3 phage incubated in silver solution), but to a much lesser extent than disinfectants. However, bacteriophages incubated for 24 h in essential oils (cinnamon and eucalyptus) can be considered stable.
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Affiliation(s)
- Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Ilona Grygiel
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Filip Orwat
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Marek Adam Harhala
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Adam Jędrusiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Elżbieta Gębarowska
- Division of Biogeochemistry and Environmental Microbiology, Department of Plant Protection, Wroclaw University of Environmental and Life Sciences, Grunwaldzka 53, 50-357, Wrocław, Poland
| | | | - Andrzej Górski
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland.
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Wang SY, Tan X, Liu ZQ, Ma H, Liu TB, Yang YQ, Ying Y, Gao RY, Zhang DZ, Ma YF, Chen K, Lin L, Jiang ZH, Yu JL. Pharmacokinetics and safety evaluation of intravenously administered Pseudomonas phage PA_LZ7 in a mouse model. Microbiol Spectr 2024; 12:e0188223. [PMID: 38014983 PMCID: PMC10783130 DOI: 10.1128/spectrum.01882-23] [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: 09/11/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Phage therapy is gaining traction as an alternative to antibiotics due to the rise of multi-drug-resistant (MDR) bacteria. This study assessed the pharmacokinetics and safety of PA_LZ7, a phage targeting MDR Pseudomonas aeruginosa, in mice. After intravenous administration, the phage showed an exponential decay in plasma and its concentration dropped significantly within 24 h for all dosage groups. Although there was a temporary increase in certain plasma cytokines and spleen weight at higher dosages, no significant toxicity was observed. Therefore, PA_LZ7 shows potential as an effective and safe candidate for future phage therapy against MDR P. aeruginosa infections.
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Affiliation(s)
- Si-yun Wang
- Department of Neonatology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xin Tan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zi-qiang Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Ma
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Tian-bin Liu
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Yong-qing Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yong Ying
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Ru-yue Gao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Dai-zhou Zhang
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Ying-fei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kai Chen
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Lin Lin
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Zhi-huan Jiang
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Jia-lin Yu
- Department of Neonatology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Chongqing, China
- Department of Neonatology, Southern University of Science and Technology Hospital, Shenzhen, China
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7
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Mason G, Footer MJ, Rojas ER. Mechanosensation induces persistent bacterial growth during bacteriophage predation. mBio 2023; 14:e0276622. [PMID: 37909775 PMCID: PMC10746221 DOI: 10.1128/mbio.02766-22] [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: 09/30/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.
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Affiliation(s)
- Guy Mason
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Matthew J. Footer
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Enrique R. Rojas
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
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8
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Chae D. Phage-host-immune system dynamics in bacteriophage therapy: basic principles and mathematical models. Transl Clin Pharmacol 2023; 31:167-190. [PMID: 38196997 PMCID: PMC10772058 DOI: 10.12793/tcp.2023.31.e17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 01/11/2024] Open
Abstract
Phage therapy is progressively being recognized as a viable alternative to conventional antibiotic treatments, particularly in the context of multi-drug resistant bacterial challenges. However, the intricacies of the pharmacokinetics and pharmacodynamics (PKPD) pertaining to phages remain inadequately elucidated. A salient characteristic of phage PKPD is the inherent ability of phages to undergo replication. In this review, I proffer mathematical models that delineate the intricate dynamics encompassing the phage, the host organism, and the immune system. Fundamental tenets associated with proliferative and inundation thresholds are explored, and distinctions between active and passive therapies are accentuated. Furthermore, I present models that aim to illuminate the multifaceted interactions amongst diverse phage strains and bacterial subpopulations, each possessing distinct sensitivities to phages. The synergistic relationship between phages and the immune system is critically examined, demonstrating how the host's immunological function can influence the requisite phage dose for an optimal therapeutic outcome. A profound understanding of the presented modeling methodologies is paramount for researchers in the realms of clinical pharmacology and PKPD modeling interested in phage therapy. Such insights facilitate a more nuanced interpretation of dose-response relationships, enable the selection of potent phages, and aid in the optimization of phage cocktails.
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Affiliation(s)
- Dongwoo Chae
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Korea
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9
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Smith NM, Nguyen TD, Chin WH, Sanborn JT, de Souza H, Ho BM, Luong T, Roach DR. A mechanism-based pathway toward administering highly active N-phage cocktails. Front Microbiol 2023; 14:1292618. [PMID: 38045026 PMCID: PMC10690594 DOI: 10.3389/fmicb.2023.1292618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023] Open
Abstract
Bacteriophage (phage) therapy is being explored as a possible response to the antimicrobial resistance public health emergency. Administering a mixture of different phage types as a cocktail is one proposed strategy for therapeutic applications, but the optimal method for formulating phage cocktails remains a major challenge. Each phage strain has complex pharmacokinetic/pharmacodynamic (PK/PD) properties which depend on the nano-scale size, target-mediated, self-dosing nature of each phage strain, and rapid selection of resistant subpopulations. The objective of this study was to explore the pharmacodynamics (PD) of three unique and clinically relevant anti-Pseudomonas phages after simulation of dynamic dosing strategies. The Hollow Fiber Infection Model (HFIM) is an in vitro system that mimics in vivo pharmacokinetics (PK) with high fidelity, providing an opportunity to quantify phage and bacteria concentration profiles over clinical time scales with rich sampling. Exogenous monotherapy-bolus (producing max concentrations of Cmax = 7 log10 PFU/mL) regimens of phages LUZ19, PYO2, and E215 produced Pseudomonas aeruginosa nadirs of 0, 2.14, or 2.99 log10 CFU/mL after 6 h of treatment, respectively. Exogenous combination therapy bolus regimens (LUZ19 + PYO2 or LUZ19 + E215) resulted in bacterial reduction to <2 log10 CFU/mL. In contrast, monotherapy as a continuous infusion (producing a steady-state concentration of Css,avg = 2 log10PFU/mL) was less effective at reducing bacterial densities. Specifically, PYO2 failed to reduce bacterial density. Next, a mechanism-based mathematical model was developed to describe phage pharmacodynamics, phage-phage competition, and phage-dependent adaptive phage resistance. Monte Carlo simulations supported bolus dose regimens, predicting lower bacterial counts with bolus dosing as compared to prolonged phage infusions. Together, in vitro and in silico evaluation of the time course of phage pharmacodynamics will better guide optimal patterns of administration of individual phages as a cocktail.
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Affiliation(s)
- Nicholas M. Smith
- Division of Clinical and Translational Therapeutics, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, NY, United States
| | - Thomas D. Nguyen
- Division of Clinical and Translational Therapeutics, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, NY, United States
| | - Wai Hoe Chin
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Jacob T. Sanborn
- Division of Clinical and Translational Therapeutics, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, NY, United States
| | - Harriet de Souza
- Division of Clinical and Translational Therapeutics, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, NY, United States
| | - Brian M. Ho
- Division of Clinical and Translational Therapeutics, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, NY, United States
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, CA, United States
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10
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Wen H, Zhou W, Wu Y, Li Y, Zhu G, Zhang Z, Gu X, Wang C, Yang Z. Effective treatment of a broad-host-range lytic phage SapYZU15 in eliminating Staphylococcus aureus from subcutaneous infection. Microbiol Res 2023; 276:127484. [PMID: 37659336 DOI: 10.1016/j.micres.2023.127484] [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: 06/24/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/04/2023]
Abstract
Multidrug resistance (MDR) Staphylococcus aureus is frequently isolated from food products, and can cause severe clinical infection. Bacteriophage (phage) therapy is a promising biocontrol agent against MDR S. aureus in food contamination and clinical infections. In this study, the antimicrobial susceptibility of 47 S. aureus isolates from three swine farms, two slaughterhouses, and four markets (Yangzhou, China) were evaluated. The biological characteristics of four lytic S. aureus phages were compared and the lytic activity of phage SapYZU15 against MDR S. aureus was assessed using milk, fresh pork and a mouse model of subcutaneous abscess. The results showed that 28 S. aureus isolates (59.6%, 28/47) exhibited multiple antibiotic resistance to at least three different classes of antibiotics. Compared to SapYZU01, SapYZU02, and SapYZU03, SapYZU15 had a shorter latent period (10 min), larger burst size (322.00 PFU/cell), broader host range, wider temperature stability (-80 to 50 °C), and pH stability. Furthermore, SapYZU15 significantly reduces the counts of S. aureus in milk and pork (5.69 and 1.16 log colony-forming unit/mL, respectively) at 25 °C and controls the growth of S. aureus at 4 °C. Compared to the mice infected with S. aureus MRSA JCSC 4744 and cocktail (S. aureus YZUsa1, YZUsa4, YZUsa12, YZUsa14, and MRSA JCSC 4744), treatment with SapYZU15 led to faster tissue healing, less weight loss, and lower viable S. aureus counts in the murine abscess model. Moreover, prevention with SapYZU15 effectively inhibited abscess formation through a synergistic effect with pro-inflammatory cytokines. Consequently, our results suggest that SapYZU15 is an effective strategy for controlling S. aureus contamination in food products, and possesses an immense potential to treat and prevent clinic infection caused by MDR S. aureus strains. The interactions and mechanisms between SapYZU15 and its bacterial host differed depending on the model, temperature, and multiplicity of infection (MOI).
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Affiliation(s)
- Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Ying Wu
- School of Public Health and Emergency Management, Southern University of Science and Technology, ShenZhen, Guangdong 518055, China
| | - Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhenwen Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuewen Gu
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Cuimei Wang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
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11
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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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12
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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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13
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Gómez MC, Mondragon EI, Molano EL, Hidalgo-Troya A, Mármol-Martínez MA, Guerrero-Ceballos DL, Pantoja MA, Paz-García C, Gómez-Arrieta J, Burbano-Rosero M. Mathematical model of interaction Escherichia coli and Coliphages. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9712-9727. [PMID: 37322908 DOI: 10.3934/mbe.2023426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We propose a mathematical model based in ordinary differential equations between bacterial pathogen and Bacteriophages to describe the infection dynamics of these populations, for which we use a nonlinear function with an inhibitory effect. We study the stability of the model using the Lyapunov theory and the second additive compound matrix and perform a global sensitivity analysis to elucidate the most influential parameters in the model, besides we make a parameter estimation using growth data of Escherichia coli (E.coli) bacteria in presence of Coliphages (bacteriophages that infect E.coli) with different multiplicity of infection. We found a threshold that indicates whether the bacteriophage concentration will coexist with the bacterium (the coexistence equilibrium) or become extinct (phages extinction equilibrium), the first equilibrium is locally asymptotically stable while the other is globally asymptotically stable depending on the magnitude of this threshold. Beside we found that the dynamics of the model is particularly affected by infection rate of bacteria and Half-saturation phages density. Parameter estimation show that all multiplicities of infection are effective in eliminating infected bacteria but the smaller one leaves a higher number of bacteriophages at the end of this elimination.
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Affiliation(s)
- Miller Cerón Gómez
- Department of Mathematics, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | | | - Eddy Lopez Molano
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | | | | | | | - Mario A Pantoja
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | - Camilo Paz-García
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | - Jenny Gómez-Arrieta
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
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14
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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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15
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Marchi J, Zborowsky S, Debarbieux L, Weitz JS. The dynamic interplay of bacteriophage, bacteria and the mammalian host during phage therapy. iScience 2023; 26:106004. [PMID: 36818291 PMCID: PMC9932479 DOI: 10.1016/j.isci.2023.106004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
For decades, biomedically centered studies of bacteria have focused on mechanistic drivers of disease in their mammalian hosts. Likewise, molecular studies of bacteriophage have centered on understanding mechanisms by which bacteriophage exploit the intracellular environment of their bacterial hosts. These binary interactions - bacteriophage infect bacteria and bacteria infect eukaryotic hosts - have remained largely separate lines of inquiry. However, recent evidence demonstrates how tripartite interactions between bacteriophage, bacteria and the eukaryotic host shape the dynamics and fate of each component. In this perspective, we provide an overview of different ways in which bacteriophage ecology modulates bacterial infections along a spectrum of positive to negative impacts on a mammalian host. We also examine how coevolutionary processes over longer timescales may change the valence of these interactions. We argue that anticipating both ecological and evolutionary dynamics is key to understand and control tripartite interactions and ultimately to the success or failure of phage therapy.
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Affiliation(s)
- Jacopo Marchi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sophia Zborowsky
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France
- Corresponding author
| | - Joshua S. Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Institut de Biologie, École Normale Supérieure, 75005 Paris, France
- Corresponding author
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16
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Nilsson AS. Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses 2022; 14:v14112483. [PMID: 36366581 PMCID: PMC9695944 DOI: 10.3390/v14112483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Cocktail is an easy-to-use computer program for mathematical modelling of bacteriophage (phage) infection kinetics in a chemostat. The infection of bacteria by phages results in complicated dynamic processes as both have the ability to multiply and change during the course of an infection. There is a need for a simple way to visualise these processes, not least due to the increased interest in phage therapy. Cocktail is completely self-contained and runs on a Windows 64-bit operating system. By changing the publicly available source code, the program can be developed in the directions that users see fit. Cocktail's models consist of coupled differential equations that describe the infection of a bacterium in a vessel by one or two (interfering) phages. In the models, the bacterial population can be controlled by sixteen parameters, for example, through different growth rates, phage resistance, metabolically inactive cells or biofilm formation. The phages can be controlled by eight parameters each, such as different adsorption rates or latency periods. As the models in Cocktail describe the infection kinetics of phages in vitro, the program is primarily intended to generate hypotheses, but the results can however be indicative in the application of phage therapy.
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Affiliation(s)
- Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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17
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Igler C. Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack. Virus Evol 2022; 8:veac086. [PMID: 36225237 PMCID: PMC9547521 DOI: 10.1093/ve/veac086] [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: 01/25/2022] [Revised: 08/11/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, the viruses of bacteria, have been studied for over a century. They were not only instrumental in laying the foundations of molecular biology, but they are also likely to play crucial roles in shaping our biosphere and may offer a solution to the control of drug-resistant bacterial infections. However, it remains challenging to predict the conditions for bacterial eradication by phage predation, sometimes even under well-defined laboratory conditions, and, most curiously, if the majority of surviving cells are genetically phage-susceptible. Here, I propose that even clonal phage and bacterial populations are generally in a state of continuous 'phenotypic flux', which is caused by transient and nongenetic variation in phage and bacterial physiology. Phenotypic flux can shape phage infection dynamics by reducing the force of infection to an extent that allows for coexistence between phages and susceptible bacteria. Understanding the mechanisms and impact of phenotypic flux may be key to providing a complete picture of phage-bacteria coexistence. I review the empirical evidence for phenotypic variation in phage and bacterial physiology together with the ways they have been modeled and discuss the potential implications of phenotypic flux for ecological and evolutionary dynamics between phages and bacteria, as well as for phage therapy.
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Affiliation(s)
- Claudia Igler
- Department of Environmental Systems Science, ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zurich 8092, Switzerland
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18
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Minimizing Foaming and Bulking in Activated Sludge with Bacteriophage Treatment: A Review of Mathematical Modeling. Processes (Basel) 2022. [DOI: 10.3390/pr10081600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture, and the food industry. In particular, several authors have proposed using bacteriophages as an alternative method to control foaming and bulking in wastewater treatment. This strategy has shown successful results at the laboratory scale. However, this technology is still in development, and there are several challenges to overcome before bacteriophages can be widely used to control foaming and bulking in pilot or larger-scale treatment plants. Several models of the infection mechanisms in individual bacteria–phage pairs have been reported, i.e., for controlled systems with only one bacterium species in the presence of one phage species. However, activated sludge treatment systems largely differ from this situation, which opens a large horizon for future research. Mathematical models will play a key role in this development process, and this review offers an overview of the proposed models: their applications, potential, and challenges. A particular focus is placed on the model properties, such as parameter identifiability and states’ observability, which are essential for process prediction, monitoring, or dynamic optimization.
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19
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Glonti T, Pirnay JP. In Vitro Techniques and Measurements of Phage Characteristics That Are Important for Phage Therapy Success. Viruses 2022; 14:1490. [PMID: 35891470 PMCID: PMC9323186 DOI: 10.3390/v14071490] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023] Open
Abstract
Validated methods for phage selection, host range expansion, and lytic activity determination are indispensable for maximizing phage therapy outcomes. In this review, we describe some relevant methods, highlighting their advantages and disadvantages, and categorize them as preliminary or confirmatory methods where appropriate. Experimental conditions, such as the composition and consistency of culture media, have an impact on bacterial growth and, consequently, phage propagation and the selection of phage-resistant mutants. The phages require different experimental conditions to be tested to fully reveal their characteristics and phage therapy potential in view of their future use in therapy. Phage lytic activity or virulence should be considered as a result of the phage, its host, and intracellular/environmental factors, including the ability of a phage to recognize receptors on the bacterial cell surface. In vitro quantitative and qualitative measurements of phage characteristics, further validated by in vivo experiments, could be incorporated into one system or mathematical model/formula, which could predict a potential successful outcome of clinical applications.
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Affiliation(s)
- Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, B-1120 Brussels, Belgium;
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20
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PhREEPred: Phage Resistance Emergence Prediction web to foresee encapsulated bacterial escape from phage cocktail treatment. J Mol Biol 2022; 434:167670. [PMID: 35671831 DOI: 10.1016/j.jmb.2022.167670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/06/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
Abstract
Phages, as well as phage-derived proteins, especially lysins and depolymerases, are intensively studied to become prospective alternatives or supportive antibacterials used alone or in combination. In the common phage therapy approach, the unwanted emergence of phage-resistant variants from the treated bacterial population can be postponed or reduced by the utilization of an effective phage cocktail. In this work, we present a publicly available web tool PhREEPred (Phage Resistance Emergence Prediction) (https://phartner.shinyapps.io/PhREEPred/), which will allow an informed choice of the composition of phage cocktails by predicting the outcome of phage cocktail or phage/depolymerase combination treatments given a mutating population that escapes single phage treatment. PhREEPred simulates solutions of our mathematical model calibrated and tested on the experimental Klebsiella pneumoniae setup and Klebsiella-specific lytic phages: K63 type-specific phage KP34 equipped with a capsule-degrading enzyme (KP34p57), capsule-independent myoviruses KP15 and KP27, and recombinant capsule depolymerase KP34p57. The model can calculate the phage-resistance emergence depending on the bacterial growth rate and initial density, the multiplicity of infection, phage latent period, its infectiveness and the cocktail composition, as well as initial depolymerase concentration and activity rate. This model reproduced the experimental results and showed that (i) the phage cocktail of parallelly infecting phages is less effective than the one composed of sequentially infecting phages; (ii) depolymerase can delay or prevent bacterial resistance by unveiling an alternative receptor for initially inactive phages. In our opinion, this customer-friendly web tool will allow for the primary design of the phage cocktail and phage-depolymerase combination effectiveness against encapsulated pathogens.
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21
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Delattre R, Seurat J, Haddad F, Nguyen TT, Gaborieau B, Kane R, Dufour N, Ricard JD, Guedj J, Debarbieux L. Combination of in vivo phage therapy data with in silico model highlights key parameters for pneumonia treatment efficacy. Cell Rep 2022; 39:110825. [PMID: 35584666 DOI: 10.1016/j.celrep.2022.110825] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/19/2021] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
The clinical (re)development of bacteriophage (phage) therapy to treat antibiotic-resistant infections faces the challenge of understanding the dynamics of phage-bacteria interactions in the in vivo context. Here, we develop a general strategy coupling in vitro and in vivo experiments with a mathematical model to characterize the interplay between phage and bacteria during pneumonia induced by a pathogenic strain of Escherichia coli. The model allows the estimation of several key parameters for phage therapeutic efficacy. In particular, it quantifies the impact of dose and route of phage administration as well as the synergism of phage and the innate immune response on bacterial clearance. Simulations predict a limited impact of the intrinsic phage characteristics in agreement with the current semi-empirical choices of phages for compassionate treatments. Model-based approaches will foster the deployment of future phage-therapy clinical trials.
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Affiliation(s)
- Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Jérémy Seurat
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Feyrouz Haddad
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Thu-Thuy Nguyen
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Baptiste Gaborieau
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France; APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Rokhaya Kane
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France
| | - Nicolas Dufour
- Centre Hospitalier René Dubos, Médecine Intensive Réanimation, Cergy Pontoise 95503, France
| | - Jean-Damien Ricard
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France; APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Jérémie Guedj
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France.
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France.
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22
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Kowalski J, Górska R, Cieślik M, Górski A, Jończyk-Matysiak E. What Are the Potential Benefits of Using Bacteriophages in Periodontal Therapy? Antibiotics (Basel) 2022; 11:antibiotics11040446. [PMID: 35453197 PMCID: PMC9027636 DOI: 10.3390/antibiotics11040446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/16/2023] Open
Abstract
Periodontitis, which may result in tooth loss, constitutes both a serious medical and social problem. This pathology, if not treated, can contribute to the development of, among others, pancreatic cancer, cardiovascular diseases or Alzheimer’s disease. The available treatment methods are expensive but not always fully effective. For this reason, the search for and isolation of bacteriophages specific to bacterial strains causing periodontitis seems to be a great opportunity to target persistent colonization by bacterial pathogens and lower the use of antibiotics consequently limiting further development of antibiotic resistance. Furthermore, antimicrobial resistance (AMR) constitutes a growing challenge in periodontal therapy as resistant pathogens may be isolated from more than 70% of patients with periodontitis. The aim of this review is to present the perspective of phage application in the prevention and/or treatment of periodontitis alongside its complicated multifactorial aetiology and emphasize the challenges connecting composition and application of effective phage preparation.
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Affiliation(s)
- Jan Kowalski
- Department of Periodontology and Oral Diseases, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.K.); (R.G.)
| | - Renata Górska
- Department of Periodontology and Oral Diseases, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.K.); (R.G.)
| | - Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (A.G.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (A.G.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (A.G.)
- Correspondence:
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23
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Olson EG, Micciche AC, Rothrock MJ, Yang Y, Ricke SC. Application of Bacteriophages to Limit Campylobacter in Poultry Production. Front Microbiol 2022; 12:458721. [PMID: 35069459 PMCID: PMC8766974 DOI: 10.3389/fmicb.2021.458721] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Campylobacter is a major foodborne pathogen with over a million United States cases a year and is typically acquired through the consumption of poultry products. The common occurrence of Campylobacter as a member of the poultry gastrointestinal tract microbial community remains a challenge for optimizing intervention strategies. Simultaneously, increasing demand for antibiotic-free products has led to the development of several alternative control measures both at the farm and in processing operations. Bacteriophages administered to reduce foodborne pathogens are one of the alternatives that have received renewed interest. Campylobacter phages have been isolated from both conventionally and organically raised poultry. Isolated and cultivated Campylobacter bacteriophages have been used as an intervention in live birds to target colonized Campylobacter in the gastrointestinal tract. Application of Campylobacter phages to poultry carcasses has also been explored as a strategy to reduce Campylobacter levels during poultry processing. This review will focus on the biology and ecology of Campylobacter bacteriophages in poultry production followed by discussion on current and potential applications as an intervention strategy to reduce Campylobacter occurrence in poultry production.
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Affiliation(s)
- Elena G. Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Andrew C. Micciche
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Michael J. Rothrock
- Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
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24
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Steffan SM, Shakeri G, Hammerl JA, Kehrenberg C, Peh E, Rohde M, Jackel C, Plotz M, Kittler S. Isolation and Characterization of Group III Campylobacter jejuni-Specific Bacteriophages From Germany and Their Suitability for Use in Food Production. Front Microbiol 2021; 12:761223. [PMID: 34956123 PMCID: PMC8696038 DOI: 10.3389/fmicb.2021.761223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Campylobacter spp. are a major cause of bacterial foodborne diarrhea worldwide. While thermophilic Campylobacter species asymptomatically colonize the intestines of chickens, most human infections in industrial countries have been attributed to consumption of chicken meat or cross-contaminated products. Bacteriophages (phages) are natural predators of bacteria and their use at different stages of the food production chain has been shown to reduce the public health burden of human campylobacteriosis. However, regarding regulatory issues, the use of lytic phages in food is still under discussion and evaluation. This study aims to identify lytic phages suitable for reducing Campylobacter bacteria along the food production chain. Therefore, four of 19 recently recovered phages were further characterized in detail for their lytic efficacy against different Campylobacter field strains and their suitability under food production settings at different temperatures and pH values. Based on the results of this study, the phages vB_CjM-LmqsCP1-4 and vB_CjM-LmqsCP1-5 appear to be promising candidates for the reduction of Campylobacter jejuni in food production settings.
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Affiliation(s)
- Severin Michael Steffan
- Institute for Food Quality and Food Safety, Foundation University of Veterinary Medicine Hannover, Hanover, Germany
| | - Golshan Shakeri
- Department of Food Hygiene and Aquaculture, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig-University Giessen, Giessen, Germany
| | - Elisa Peh
- Institute for Food Quality and Food Safety, Foundation University of Veterinary Medicine Hannover, Hanover, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research GmbH, Braunschweig, Germany
| | - Claudia Jackel
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Madeleine Plotz
- Institute for Food Quality and Food Safety, Foundation University of Veterinary Medicine Hannover, Hanover, Germany
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, Foundation University of Veterinary Medicine Hannover, Hanover, Germany
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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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Kaur S, Kumari A, Kumari Negi A, Galav V, Thakur S, Agrawal M, Sharma V. Nanotechnology Based Approaches in Phage Therapy: Overcoming the Pharmacological Barriers. Front Pharmacol 2021; 12:699054. [PMID: 34675801 PMCID: PMC8524003 DOI: 10.3389/fphar.2021.699054] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
With the emergence and spread of global antibiotic resistance and the need for searching safer alternatives, there has been resurgence in exploring the use of bacteriophages in the treatment of bacterial infections referred as phage therapy. Although modern phage therapy has come a long way as demonstrated by numerous efficacy studies but the fact remains that till date, phage therapy has not received regulatory approval for human use (except for compassionate use).Thus, to hit the clinical market, the roadblocks need to be seriously addressed and gaps mended with modern solution based technologies. Nanotechnology represents one such ideal and powerful tool for overcoming the pharmacological barriers (low stability, poor in-vivo retention, targeted delivery, neutralisation by immune system etc.) of administered phage preparations.In literature, there are many review articles on nanotechnology and bacteriophages but these are primarily focussed on highlighting the use of lytic and temperate phages in different fields of nano-medicine such as nanoprobes, nanosensors, cancer diagnostics, cancer cell targeting, drug delivery through phage receptors, phage display etc. Reviews specifically focused on the use of nanotechnology driven techniques strictly to improve phage therapy are however limited. Moreover, these review if present have primarily focussed on discussing encapsulation as a primary method for improving the stability and retention of phage(s) in the body.With new advances made in the field of nanotechnology, approaches extend from mere encapsulation to recently adopted newer strategies. The present review gives a detailed insight into the more recent strategies which include 1) use of lipid based nano-carriers (liposomes, transfersomes etc.) 2) adopting microfluidic based approach, surface modification methods to further enhance the efficiency and stability of phage loaded liposomes 3) Nano- emulsification approach with integration of microfluidics for producing multiple emulsions (suitable for phage cocktails) with unique control over size, shape and drop morphology 4) Phage loaded nanofibers produced by electro-spinning and advanced core shell nanofibers for immediate, biphasic and delayed release systems and 5) Smart release drug delivery platforms that allow superior control over dosing and phage release as and when required. All these new advances are aimed at creating a suitable housing system for therapeutic bacteriophage preparations while targeting the multiple issues of phage therapy i.e., improving phage stability and titers, improving in-vivo retention times, acting as suitable delivery systems for sustained release at target site of infection, improved penetration into biofilms and protection from immune cell attack. The present review thus aims at giving a complete insight into the recent advances (2010 onwards) related to various nanotechnology based approaches to address the issues pertaining to phage therapy. This is essential for improving the overall therapeutic index and success of phage therapy for future clinical approval.
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Affiliation(s)
- Sandeep Kaur
- Department of Food Science, Mehr Chand Mahajan DAV College for Women, Chandigarh, India
| | - Anila Kumari
- Department of Food Science, Mehr Chand Mahajan DAV College for Women, Chandigarh, India
| | - Anjana Kumari Negi
- Department of Biochemistry, Dr. Rajendra Prasad Government Medical College, Himachal Pradesh, India
| | - Vikas Galav
- Department of Veterinary Pathology, Post Graduate Institute of Veterinary Education and Research (RAJUVAS), Jaipur, India
| | - Shikha Thakur
- Department of Biotechnology, Kumaun University, Uttarakhand, India
| | - Manish Agrawal
- Department of Veterinary Pathology, Post Graduate Institute of Veterinary Education and Research (RAJUVAS), Jaipur, India
| | - Vandana Sharma
- Department of Food Science, Mehr Chand Mahajan DAV College for Women, Chandigarh, India
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Styles KM, Brown AT, Sagona AP. A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions. Front Microbiol 2021; 12:724767. [PMID: 34621252 PMCID: PMC8490754 DOI: 10.3389/fmicb.2021.724767] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
Phage therapy, the therapeutic usage of viruses to treat bacterial infections, has many theoretical benefits in the ‘post antibiotic era.’ Nevertheless, there are currently no approved mainstream phage therapies. One reason for this is a lack of understanding of the complex interactions between bacteriophage, bacteria and eukaryotic hosts. These three-component interactions are complex, with non-linear or synergistic relationships, anatomical barriers and genetic or phenotypic heterogeneity all leading to disparity between performance and efficacy in in vivo versus in vitro environments. Realistic computer or mathematical models of these complex environments are a potential route to improve the predictive power of in vitro studies for the in vivo environment, and to streamline lab work. Here, we introduce and review the current status of mathematical modeling and highlight that data on genetic heterogeneity and mutational stochasticity, time delays and population densities could be critical in the development of realistic phage therapy models in the future. With this in mind, we aim to inform and encourage the collaboration and sharing of knowledge and expertise between microbiologists and theoretical modelers, synergising skills and smoothing the road to regulatory approval and widespread use of phage therapy.
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Affiliation(s)
- Kathryn M Styles
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aidan T Brown
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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The lytic siphophage vB_StyS-LmqsSP1 reduces Salmonella Typhimurium isolates on chicken skin. Appl Environ Microbiol 2021; 87:e0142421. [PMID: 34586906 DOI: 10.1128/aem.01424-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Phage-based biocontrol of bacteria is considered as a natural approach to combat food-borne pathogens. Salmonella spp. are notifiable and highly prevalent pathogens that cause foodborne diseases globally. In this study, six bacteriophages were isolated and further characterized that infect food-derived Salmonella isolates from different meat sources. The siphovirus VB_StyS-LmqsSP1, which was isolated from a cow´s nasal swab, was further subjected to in-depth characterization. Phage-host interaction investigations in liquid medium showed that vB_StyS-LmqsSP1 can suppress the growth of Salmonella spp. isolates at 37°C for ten hours and reduce the bacterial titer at 4°C significantly. A reduction of 1.4 to 3 log units was observed in investigations with two food-derived Salmonella isolates and one reference strain under cooling conditions using MOIs of 104 and 105. Phage application on chicken skin resulted in a reduction of about 2 log units in the tested Salmonella isolates from the first three hours throughout a one-week experiment at cooling temperature and an MOI of 105. The one-step growth curve analysis using vB_StyS-LmqsSP1 demonstrated a 60-min latent period and a burst size of 50-61 PFU/infected cell for all tested hosts. Furthermore, the genome of the phage was determined to be free from genes causing undesired effects. Based on the phenotypic and genotypic properties, LmqsSP1 was assigned as a promising candidate for biocontrol of Salmonella Typhimurium in food. Importance: Salmonella enterica is one of the major global causes of foodborne enteritis in humans. The use of chemical sanitizers for reducing bacterial pathogens in the food chain can result in the spread of bacterial resistance. Targeted and clean label intervention strategies can reduce Salmonella contamination in food. The significance of our research demonstrates the suitability of a bacteriophage (vB_StyS-LmqsSP1) for biocontrol of Salmonella enterica serovar Typhimurium on poultry due to its lytic efficacy under conditions prevailing in food production environments.
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Tuomala H, Verkola M, Meller A, Van der Auwera J, Patpatia S, Järvinen A, Skurnik M, Heikinheimo A, Kiljunen S. Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. Viruses 2021; 13:1888. [PMID: 34696318 PMCID: PMC8539482 DOI: 10.3390/v13101888] [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: 08/19/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
The increase of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) causes a threat to human health. LA-MRSA can be transmitted from animals to animal caretakers, which may further spread MRSA to communities and health care facilities. The objective of this work was to study the efficacy of phage treatment in the eradication of LA-MRSA from healthy carrier pigs. A total of 19 MRSA -positive weanling pigs were assigned to a test (n = 10) and a control group (n = 9). A phage cocktail containing three Staphylococcus phages, or a control buffer was administered to the nares and skin of the pigs three times every two days, after which the phage and MRSA levels in nasal and skin swab samples were monitored for a three-week period. The sensitivity of the strains isolated during the follow-up period to the phage cocktail and each phage individually was analyzed and the pig sera were tested for antibodies against the phages used in the cocktail. The phage treatment did not cause any side effects to the pigs. Phages were found in the skin and nasal samples on the days following the phage applications, but there was no reduction in the MRSA levels in the sampled animals. Phage-resistant strains or phage-specific antibodies were not detected during the experiment. The MRSA load in these healthy carrier animals was only 10-100 CFU/swab or nasal sample, which was likely below the replication threshold of phages. The effectiveness of phage treatment to eradicate MRSA from the pigs could thus not be (reliably) determined.
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Affiliation(s)
- Henni Tuomala
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland; (H.T.); (M.S.)
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland; (J.V.d.A.); (S.P.)
| | - Marie Verkola
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland; (M.V.); (A.H.)
| | - Anna Meller
- Laboratory Animal Center, University of Helsinki, 00014 Helsinki, Finland;
| | - Jasper Van der Auwera
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland; (J.V.d.A.); (S.P.)
| | - Sheetal Patpatia
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland; (J.V.d.A.); (S.P.)
| | - Asko Järvinen
- Department of Infectious Diseases, Inflammation Center, Helsinki University Central Hospital and University of Helsinki, Haartmaninkatu 4, 00029 Helsinki, Finland;
| | - Mikael Skurnik
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland; (H.T.); (M.S.)
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland; (J.V.d.A.); (S.P.)
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland; (M.V.); (A.H.)
- Finnish Food Authority, Laboratory and Research Division, Microbiology Unit, P.O. Box 200, 00027 Helsinki, Finland
| | - Saija Kiljunen
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland; (H.T.); (M.S.)
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland; (J.V.d.A.); (S.P.)
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D’Angelantonio D, Scattolini S, Boni A, Neri D, Di Serafino G, Connerton P, Connerton I, Pomilio F, Di Giannatale E, Migliorati G, Aprea G. Bacteriophage Therapy to Reduce Colonization of Campylobacter jejuni in Broiler Chickens before Slaughter. Viruses 2021; 13:v13081428. [PMID: 34452294 PMCID: PMC8402772 DOI: 10.3390/v13081428] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
Campylobacteriosis is the most commonly reported gastrointestinal disease in humans. Campybacter jejuni is the main cause of the infection, and bacterial colonization in broiler chickens is widespread and difficult to prevent, leading to high risk of occurrence in broiler meat. Phage therapy represents an alternative strategy to control Campylobacter in poultry. The aim of this work was to assess the efficacy of two field-isolated bacteriophages against experimental infections with an anti-microbial resistant (AMR) Campylobacter jejuni strain. A two-step phage application was tested according to a specific combination between chickens’ rearing time and specific multiplicities of infections (MOIs), in order to reduce the Campylobacter load in the animals at slaughtering and to limit the development of phage-resistant mutants. In particular, 75 broilers were divided into three groups (A, B and C), and phages were administered to animals of groups B and C at day 38 (Φ 16-izsam) and 39 (Φ 7-izsam) at MOI 0.1 (group B) and 1 (group C). All broilers were euthanized at day 40, and Campylobacter jejuni was enumerated in cecal contents. Reductions in Campylobacter counts were statistically significant in both group B (1 log10 colony forming units (cfu)/gram (gr)) and group C (2 log10 cfu/gr), compared to the control group. Our findings provide evidence about the ability of phage therapy to reduce the Campylobacter load in poultry before slaughtering, also associated with anti-microbial resistance pattern.
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Affiliation(s)
- Daniela D’Angelantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
| | - Silvia Scattolini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
| | - Arianna Boni
- Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Diana Neri
- Local Health Unit of Ferrara (USL Ferrara), 44121 Ferrara, Italy;
| | | | - Philippa Connerton
- Division of Food Science, School of Bioscience, The University of Nottingham, Nottingham LE12 5RD, UK; (P.C.); (I.C.)
| | - Ian Connerton
- Division of Food Science, School of Bioscience, The University of Nottingham, Nottingham LE12 5RD, UK; (P.C.); (I.C.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
| | - Elisabetta Di Giannatale
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
| | - Giacomo Migliorati
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
| | - Giuseppe Aprea
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (D.D.); (S.S.); (F.P.); (E.D.G.); (G.M.)
- Correspondence: ; Tel.: +39-0861-33-2-469
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Pourtois JD, Kratochvil MJ, Chen Q, Haddock NL, Burgener EB, De Leo GA, Bollyky PL. Filamentous Bacteriophages and the Competitive Interaction between Pseudomonas aeruginosa Strains under Antibiotic Treatment: a Modeling Study. mSystems 2021; 6:e0019321. [PMID: 34156288 PMCID: PMC8269214 DOI: 10.1128/msystems.00193-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa (Pa) is a major bacterial pathogen responsible for chronic lung infections in cystic fibrosis patients. Recent work has implicated Pf bacteriophages, nonlytic filamentous viruses produced by Pa, in the chronicity and severity of Pa infections. Pf phages act as structural elements in Pa biofilms and sequester aerosolized antibiotics, thereby contributing to antibiotic tolerance. Consistent with a selective advantage in this setting, the prevalence of Pf-positive (Pf+) bacteria increases over time in these patients. However, the production of Pf phages comes at a metabolic cost to bacteria, such that Pf+ strains grow more slowly than Pf-negative (Pf-) strains in vitro. Here, we use a mathematical model to investigate how these competing pressures might influence the relative abundance of Pf+ versus Pf- strains in different settings. Our model suggests that Pf+ strains of Pa cannot outcompete Pf- strains if the benefits of phage production falls onto both Pf+ and Pf- strains for a majority of parameter combinations. Further, phage production leads to a net positive gain in fitness only at antibiotic concentrations slightly above the MIC (i.e., concentrations for which the benefits of antibiotic sequestration outweigh the metabolic cost of phage production) but which are not lethal for Pf+ strains. As a result, our model suggests that frequent administration of intermediate doses of antibiotics with low decay rates and high killing rates favors Pf+ over Pf- strains. These models inform our understanding of the ecology of Pf phages and suggest potential treatment strategies for Pf+ Pa infections. IMPORTANCE Filamentous phages are a frontier in bacterial pathogenesis, but the impact of these phages on bacterial fitness is unclear. In particular, Pf phages produced by Pa promote antibiotic tolerance but are metabolically expensive to produce, suggesting that competing pressures may influence the prevalence of Pf+ versus Pf- strains of Pa in different settings. Our results identify conditions likely to favor Pf+ strains and thus antibiotic tolerance. This study contributes to a better understanding of the unique ecology of filamentous phages in both environmental and clinical settings and may facilitate improved treatment strategies for combating antibiotic tolerance.
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Affiliation(s)
- Julie D. Pourtois
- Department of Biology, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, California, USA
| | - Michael J. Kratochvil
- Department of Materials Science and Engineering, Stanford University, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Giulio A. De Leo
- Department of Biology, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, California, USA
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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Sandhu SK, Bayliss CD, Morozov AY. How does feedback from phage infections influence the evolution of phase variation in Campylobacter? PLoS Comput Biol 2021; 17:e1009067. [PMID: 34125841 PMCID: PMC8224891 DOI: 10.1371/journal.pcbi.1009067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Campylobacter jejuni (C. jejuni) causes gastroenteritis following the consumption of contaminated poultry meat, resulting in a large health and economic burden worldwide. Phage therapy is a promising technique for eradicating C. jejuni from poultry flocks and chicken carcasses. However, C. jejuni can resist infections by some phages through stochastic, phase-variable ON/OFF switching of the phage receptors mediated by simple sequence repeats (SSR). While selection strength and exposure time influence the evolution of SSR-mediated phase variation (PV), phages offer a more complex evolutionary environment as phage replication depends on having a permissive host organism. Here, we build and explore several continuous culture bacteria-phage computational models, each analysing different phase-variable scenarios calibrated to the experimental SSR rates of C. jejuni loci and replication parameters for the F336 phage. We simulate the evolution of PV rates via the adaptive dynamics framework for varying levels of selective pressures that act on the phage-resistant state. Our results indicate that growth reducing counter-selection on a single PV locus results in the stable maintenance of the phage, while compensatory selection between bacterial states affects the evolutionary stable mutation rates (i.e. very high and very low mutation rates are evolutionarily disadvantageous), whereas, in the absence of either selective pressure the evolution of PV rates results in mutation rates below the basal values. Contrastingly, a biologically-relevant model with two phase-variable loci resulted in phage extinction and locking of the bacteria into a phage-resistant state suggesting that another counter-selective pressure is required, instance, the use of a distinct phage whose receptor is an F336-phage-resistant state. We conclude that a delicate balance between counter-selection and phage-attack can result in both the evolution of phase-variable phage receptors and persistence of PV-receptor-specific phage. Globally rising rates of antibiotic resistance have renewed interest in phage therapy. Bacteriophages (phages) act on bacteria to select for resistance mechanisms such as loss of phage receptors by phase variation (PV). Phase-variable genes mediate rapid adaption by stochastic switching of gene expression. Campylobacter jejuni is a common commensal of birds but also causes serious gastrointestinal infections in humans. Optimisation of phage therapy against C. jejuni requires an in-depth understanding of how PV has evolved and mediates phage resistance. Here, we use a detailed continuous culture model for nutrient-limited bacteria-phage interactions, with PV rates calibrated to match the experimental observations for C.jejuni and phage F336. Evolution within a model accounting for two phase-variable loci closely matches the experimental results when growth reducing counter-selection is imposed on all phage-resistant states, but, not when restricted to the particular states associated with resistance to immune effectors. Our results emphasize that delicate balancing of selective pressures, imposed by single and multiple distinct phages, are necessary for effective use of phage therapy against C. jejuni.
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Affiliation(s)
- Simran K. Sandhu
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
| | - Christopher D. Bayliss
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Andrew Yu. Morozov
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Shi Y, Peng Y, Zhang Y, Chen Y, Zhang C, Luo X, Chen Y, Yuan Z, Chen J, Gong Y. Safety and Efficacy of a Phage, kpssk3, in an in vivo Model of Carbapenem-Resistant Hypermucoviscous Klebsiella pneumoniae Bacteremia. Front Microbiol 2021; 12:613356. [PMID: 34093455 PMCID: PMC8175031 DOI: 10.3389/fmicb.2021.613356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most significant threats to global public health. As antibiotic failure is increasing, phages are gradually becoming important agents in the post-antibiotic era. In this study, the therapeutic effects and safety of kpssk3, a previously isolated phage infecting carbapenem-resistant hypermucoviscous Klebsiella pneumoniae (CR-HMKP), were evaluated in a mouse model of systemic CR-HMKP infection. The therapeutic efficacy experiment showed that intraperitoneal injection with a single dose of phage kpssk3 (1 × 107 PFU/mouse) 3 h post infection protected 100% of BALB/c mice against bacteremia induced by intraperitoneal challenge with a 2 × LD100 dose of NY03, a CR-HMKP clinical isolate. In addition, mice were treated with antibiotics from three classes (polymyxin B, tigecycline, and ceftazidime/avibactam plus aztreonam), and the 7 days survival rates of the treated mice were 20, 20, and 90%, respectively. The safety test consisted of 2 parts: determining the cytotoxicity of kpssk3 and evaluating the short- and long-term impacts of phage therapy on the mouse gut microbiota. Phage kpssk3 was shown to not be cytotoxic to mammalian cells in vitro or in vivo. Fecal samples were collected from the phage-treated mice at 3 time points before (0 day) and after (3 and 10 days) phage therapy to study the change in the gut microbiome via high-throughput 16S rDNA sequence analysis, which revealed no notable alterations in the gut microbiota except for decreases in the Chao1 and ACE indexes.
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Affiliation(s)
- Yunlong Shi
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuan Peng
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yixin Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Cheng Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaoqiang Luo
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yajie Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhiqiang Yuan
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jing Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yali Gong
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Huang C, Mahboubat BY, Ding Y, Yang Q, Wang J, Zhou M, Wang X. Development of a rapid Salmonella detection method via phage-conjugated magnetic bead separation coupled with real-time PCR quantification. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Scattolini S, D’Angelantonio D, Boni A, Mangone I, Marcacci M, Battistelli N, D’Agostino K, Pomilio F, Camma C, Migliorati G, Aprea G. Characterization and In Vitro Efficacy against Listeria monocytogenes of a Newly Isolated Bacteriophage, ɸIZSAM-1. Microorganisms 2021; 9:731. [PMID: 33807487 PMCID: PMC8065603 DOI: 10.3390/microorganisms9040731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
Listeria monocytogenes is a bacterial pathogen responsible of listeriosis, a disease that in humans is often related to the contamination of ready-to-eat foods. Phages are candidate biodecontaminants of pathogenic bacteria thanks to their ability to lyse prokaryotes while being safe for eukaryotic cells. In this study, ɸIZSAM-1 was isolated from the drain-waters of an Italian blue cheese plant and showed lytic activity against antimicrobial resistant Listeria monocytogenes strains. This phage was subjected to purification and in vitro efficacy tests. The results showed that at multiplicities of infection (MOIs) ≤ 1, phages were able to keep Listeria monocytogenes at low optical density values up to 8 h, with bacterial counts ranging from 1.02 to 3.96 log10 units lower than the control. Besides, ɸIZSAM-1 was further characterized, showing 25 principal proteins (sodium dodecyl sulfate polyacrylamide gel electrophoresis profile) and a genome of approximately 50 kilo base pairs. Moreover, this study describes a new approach to phage isolation for applications in Listeriamonocytogenes biocontrol in food production. In particular, the authors believe that the selection of phages from the same environments where pathogens live could represent a new approach to successfully integrating the control measures in an innovative, cost effective, safe and environmentally friendly way.
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Affiliation(s)
- Silvia Scattolini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Daniela D’Angelantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Arianna Boni
- Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Noemi Battistelli
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy;
| | - Krizia D’Agostino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Giacomo Migliorati
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Giuseppe Aprea
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
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Molina F, Simancas A, Ramírez M, Tabla R, Roa I, Rebollo JE. A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks. Front Microbiol 2021; 12:564532. [PMID: 33664712 PMCID: PMC7920989 DOI: 10.3389/fmicb.2021.564532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.
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Affiliation(s)
- Felipe Molina
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Manuel Ramírez
- Microbiology, Department of Biomedical Sciences, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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Li M, Chang RYK, Lin Y, Morales S, Kutter E, Chan HK. Phage cocktail powder for Pseudomonas aeruginosa respiratory infections. Int J Pharm 2021; 596:120200. [PMID: 33486032 DOI: 10.1016/j.ijpharm.2021.120200] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/30/2022]
Abstract
Phage cocktail broadens the host range compared with a single phage and minimizes the development of phage-resistant bacteria thereby promoting the long-term usefulness of inhaled phage therapy. In this study, we produced a phage cocktail powder by spray drying three Pseudomonas phages PEV2 (podovirus), PEV1 and PEV20 (both myovirus) with lactose (80 wt%) and leucine (20 wt%) as excipients. Our results showed that the phages remained viable in the spray dried powder, with little to mild titer reduction (ranging from 0.11 to 1.3 logs) against each of their specific bacterial strains. The powder contained spherical particles with a small volume median diameter of 1.9 µm (span 1.5), a moisture content of 3.5 ± 0.2 wt%., and was largely amorphous with some crystalline peaks, which were assigned to the excipient leucine, as shown in the X-ray diffraction pattern. When the powder was dispersed using the low- and high-resistance Osmohalers, the fine particle fraction (FPF, wt. % of particles < 5 µm in the aerosols relative to the loaded dose) values were 45.37 ± 0.27% and 62.69 ± 2.1% at the flow rate of 100 and 60 L/min, respectively. In conclusion, the PEV phage cocktail powder produced was stable, inhalable and efficacious in vitro against various MDR P. aeruginosa strains that cause pulmonary infections. This formulation will broaden the bactericidal spectrum and reduce the emergence of resistance in bacteria compared with single-phage formulations reported previously.
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Affiliation(s)
- Mengyu Li
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Rachel Yoon Kyung Chang
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Yu Lin
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | | | | | - Hak-Kim Chan
- Advanced Drug Delivery Group, School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
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Schmalstig AA, Freidy S, Hanafin PO, Braunstein M, Rao GG. Reapproaching Old Treatments: Considerations for PK/PD Studies on Phage Therapy for Bacterial Respiratory Infections. Clin Pharmacol Ther 2021; 109:1443-1456. [PMID: 33615463 DOI: 10.1002/cpt.2214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023]
Abstract
Antibiotic resistant bacterial respiratory infections are a significant global health burden, and new therapeutic strategies are needed to control the problem. For bacterial respiratory infections, this need is emphasized by the rise in antibiotic resistance and a lean drug development pipeline. Bacteriophage (phage) therapy is a promising alternative to antibiotics. Phage are viruses that infect and kill bacteria. Because phage and antibiotics differ in their bactericidal mechanisms, phage are a treatment option for antibiotic-resistant bacteria. Here, we review the history of phage therapy and highlight recent preclinical and clinical case reports of its use for treating antibiotic-resistant respiratory infections. The ability of phage to replicate while killing the bacteria is both a benefit for treatment and a challenge for pharmacokinetic (PK) and pharmacodynamic (PD) studies. In this review, we will discuss how the phage lifecycle and associated bidirectional interactions between phage and bacteria can impact treatment. We will also highlight PK/PD considerations for designing studies of phage therapy to optimize the efficacy and feasibility of the approach.
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Affiliation(s)
- Alan A Schmalstig
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Soha Freidy
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Patrick O Hanafin
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Shetru MN, Karched M, Agsar D. Locally isolated broad host-range bacteriophage kills methicillin-resistant Staphylococcus aureus in an in vivo skin excisional wound model in mice. Microb Pathog 2021; 152:104744. [PMID: 33484806 DOI: 10.1016/j.micpath.2021.104744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/28/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
From the perspective of an ever-increasing multidrug resistance among bacterial pathogens, bacteriophages are receiving renewed interest as potential alternative to antibiotics. We investigated the potential of a locally isolated species-specific phage against Staphylococcus aureus infection in a skin excisional wound model in mice. A significant time-dependent increase (P < 0.05) in wound healing was observed in the phage-treated mice groups. The animals treated with the phage ΦDMSA-2 exhibited a faster re-epithelialization and faster tissue re-modelling. Bacterial load in the infected tissue in all phage-treated groups diminished. The mean ± SD CFU per ml decreased from 3.3 × 108 ± 3.5 × 106 at day 1-1.43 × 103 ± 8.48 × 102 at day 16 (P < 0.05). The highest reduction in the bacterial load was observed in G5 (povidine-iodine treated) and G6 (povidine iodine + phage 107 PFU) groups as no bacterial counts were detected by day 12 in both groups. Interestingly, group G3, which was treated with a lower phage concentration (5 × 106 PFU), resulted in total clearing of the inoculated bacteria by day 16; while bacterial counts were still detected by that time in group G4, which was treated with a higher phage concentration of 107 PFU. Animals from phage-treated group G3 survived 100%, while those from the infected wound control group survived at a rate of 34% at day 9 and reached 0% by the end of day 22 (P < 0.001). The data from this study convincingly showed that phage treatment of the S. aureus-infected wounds resulted in a faster wound healing and a 100% survival of the animals. The results emphasize the utility of locally isolated species-specific phages in treatment against multidrug-resistant MRSA infections.
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Affiliation(s)
- Manjunath Nandihalli Shetru
- Department of Biotechnology and Research Centre, Bapuji Institute of Engineering and Technology, Davangere, 577 004, Karnataka, India.
| | - Maribasappa Karched
- Oral Microbiology Research Laboratory, Faculty of Dentistry, Kuwait University, Kuwait.
| | - Dayanand Agsar
- DBT Research Laboratory, Department of Microbiology, Gulbarga University, Gulbarga, 585 106, Karnataka, India.
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Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft JU, Hobman JL, Stekel DJ. A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiol Ecol 2020; 96:5850753. [PMID: 32490523 DOI: 10.1093/femsec/fiaa100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/02/2020] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a major global challenge. Of particular concern are mobilizable elements that can transfer resistance genes between bacteria, leading to pathogens with new combinations of resistance. To date, mathematical models have largely focussed on transfer of resistance by plasmids, with fewer studies on transfer by bacteriophages. We aim to understand how best to model transfer of resistance by transduction by lytic phages. We show that models of lytic bacteriophage infection with empirically derived realistic phage parameters lead to low numbers of bacteria, which, in low population or localised environments, lead to extinction of bacteria and phage. Models that include antagonistic co-evolution of phage and bacteria produce more realistic results. Furthermore, because of these low numbers, stochastic dynamics are shown to be important, especially to spread of resistance. When resistance is introduced, resistance can sometimes be fixed, and at other times die out, with the probability of each outcome sensitive to bacterial and phage parameters. Specifically, that outcome most strongly depends on the baseline death rate of bacteria, with phage-mediated spread favoured in benign environments with low mortality over more hostile environments. We conclude that larger-scale models should consider spatial compartmentalisation and heterogeneous microenviroments, while encompassing stochasticity and co-evolution.
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Affiliation(s)
- Sankalp Arya
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Henry Todman
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michelle Baker
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Steven Hooton
- Division of Food Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jan-Ulrich Kreft
- School of Biosciences & Institute of Microbiology and Infection & Centre for Computational Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jon L Hobman
- Division of Food Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Dov J Stekel
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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Echeverría-Vega A, Morales-Vicencio P, Saez-Saavedra C, Alvarez MA, Gordillo F, Del-Valle R, Solís ME, Araya R. Characterization of the Bacteriophage vB_VorS-PVo5 Infection on Vibrio ordalii: A Model for Phage-Bacteria Adsorption in Aquatic Environments. Front Microbiol 2020; 11:550979. [PMID: 33193133 PMCID: PMC7661435 DOI: 10.3389/fmicb.2020.550979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 09/11/2020] [Indexed: 01/24/2023] Open
Abstract
A mathematical first-order difference equation was designed to predict the dynamics of the phage-bacterium adsorption process in aquatic environments, under laboratory conditions. Our model requires knowledge of bacteria and bacteriophage concentrations and the measurements of bacterial size and velocity to predict both the number of bacteriophages adsorbed onto their bacterial host and the number of infected bacteria in a given specific time. It does not require data from previously performed adhesion experiments. The predictions generated by our model were validated in laboratory. Our model was initially conceived as an estimator for the effectiveness of the inoculation of phages as antibacterial therapy for aquaculture, is also suitable for a wide range of potential applications.
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Affiliation(s)
- Alex Echeverría-Vega
- Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | - Pablo Morales-Vicencio
- Laboratorio de Microbiología Costera, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Camila Saez-Saavedra
- Laboratorio de Microbiología Costera, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - María Alejandra Alvarez
- Departamento de Matemáticas, Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Felipe Gordillo
- Centro de Biotecnología de los Recursos Naturales, Facultad de Agronomía y Ciencias Forestales, Universidad Católica del Maule, Talca, Chile
| | - Rodrigo Del-Valle
- Departamento de Matemática, Física y Estadística, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | - Ma. Eugenia Solís
- Departamento de Matemática, Física y Estadística, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | - Rubén Araya
- Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Saucedo-Uriarte JA, Honorio-Javes CE, Vallenas-Sánchez YPA, Acuña-Leiva A. Bacteriófagos: aliados para combatir enfermedades bacterianas en acuicultura. Un primer punto de partida en la acuicultura ecológica. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2020. [DOI: 10.36610/j.jsaas.2020.070200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Saucedo-Uriarte JA, Honorio-Javes CE, Vallenas-Sánchez YPA, Acuña-Leiva A. Bacteriophages: allies to combat bacterial diseases in aquaculture. A first starting point in organic aquaculture. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2020. [DOI: 10.36610/j.jsaas.2020.070200107x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Loessner H, Schlattmeier I, Anders-Maurer M, Bekeredjian-Ding I, Rohde C, Wittmann J, Pokalyuk C, Krut O, Kamp C. Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy. Antibiotics (Basel) 2020; 9:E408. [PMID: 32674401 PMCID: PMC7400656 DOI: 10.3390/antibiotics9070408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022] Open
Abstract
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage-host pair during the course of infection. We have elaborated such a kinetic fingerprint for a human urinary tract Klebsiella pneumoniae isolate and its phage vB_KpnP_Lessing by a modeling approach based on data from in vitro co-culture. We found a faster depletion of the initially sensitive bacterial population than expected from simple mass action kinetics. A possible explanation for the rapid decline of the bacterial population is a synergistic interaction of phages which can be a favorable feature for phage therapies. In addition to this interaction characteristic, analysis of the kinetic fingerprint of this bacteria and phage combination revealed several relevant aspects of their population dynamics: A reduction of the bacterial concentration can be achieved only at high multiplicity of infection whereas bacterial extinction is hardly accomplished. Furthermore the binding affinity of the phage to bacteria is identified as one of the most crucial parameters for the reduction of the bacterial population size. Thus, kinetic fingerprinting can be used to infer phage-host interactions and to explore emergent dynamics which facilitates a rational design of phage therapies.
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Affiliation(s)
- Holger Loessner
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Insea Schlattmeier
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Marie Anders-Maurer
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | | | - Christine Rohde
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Cornelia Pokalyuk
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Oleg Krut
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Christel Kamp
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
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Rajnovic D, Mas J. Fluorometric detection of phages in liquid media: Application to turbid samples. Anal Chim Acta 2020; 1111:23-30. [DOI: 10.1016/j.aca.2020.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 02/07/2023]
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Chinivasagam HN, Estella W, Maddock L, Mayer DG, Weyand C, Connerton PL, Connerton IF. Bacteriophages to Control Campylobacter in Commercially Farmed Broiler Chickens, in Australia. Front Microbiol 2020; 11:632. [PMID: 32395115 PMCID: PMC7197261 DOI: 10.3389/fmicb.2020.00632] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
This study describes the development and use of bacteriophage cocktails to control Campylobacter in broiler chickens, in a commercial setting, in Queensland Australia, following the birds from farm to the processing plant. The components of the bacteriophage cocktails were selected to be effective against the maximum number of Campylobacter jejuni and Campylobacter coli isolates encountered on SE Queensland farms. Farms were identified that had suitable Campylobacter target populations and phage were undetectable 1 week prior to the intended treatment. Cocktails of phages were administered at 47 days of age. Groups of study birds were slaughtered the following day, on-farm, at the end of flock transport to the plant, and at processing (approximately 28 h post-treatment). On Farm A, the phage treatment significantly reduced Campylobacter levels in the ceca at the farm in the range of 1-3 log10 CFU/g (p = 0.007), compared to mock treated controls. However, individual birds sampled on farm (1/10) or following transport (2/10) exhibited high cecal Campylobacter counts with low phage titers, suggesting that treatment periods > 24 h may be required to ensure phage replication for effective biocontrol in vivo. At the time of the trial the control birds in Farm B were phage positive despite having been negative one week earlier. There was no significant difference in the cecal Campylobacter counts between the treatment and control groups following treatment but a fall of 1.7 log10 CFU/g was observed from that determined from birds collected the previous week (p = 0.0004). Campylobacter isolates from both farms retained sensitivity to the treatment phages. These trials demonstrated bacteriophages sourced from Queensland farms have the potential to reduce intestinal Campylobacter levels in market ready broiler chickens.
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Affiliation(s)
- Helene N. Chinivasagam
- EcoSciences Precinct, Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - Wiyada Estella
- EcoSciences Precinct, Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - Lance Maddock
- EcoSciences Precinct, Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - David G. Mayer
- EcoSciences Precinct, Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - Caitlin Weyand
- EcoSciences Precinct, Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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Hobley L, Summers JK, Till R, Milner DS, Atterbury RJ, Stroud A, Capeness MJ, Gray S, Leidenroth A, Lambert C, Connerton I, Twycross J, Baker M, Tyson J, Kreft JU, Sockett RE. Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot. J Bacteriol 2020; 202:e00629-19. [PMID: 31907203 PMCID: PMC7043672 DOI: 10.1128/jb.00629-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023] Open
Abstract
Bacteria are preyed upon by diverse microbial predators, including bacteriophage and predatory bacteria, such as Bdellovibrio bacteriovorus While bacteriophage are used as antimicrobial therapies in Eastern Europe and are being applied for compassionate use in the United States, predatory bacteria are only just beginning to reveal their potential therapeutic uses. However, predation by either predator type can falter due to different adaptations arising in the prey bacteria. When testing poultry farm wastewater for novel Bdellovibrio isolates on Escherichia coli prey lawns, individual composite plaques were isolated containing both an RTP (rosette-tailed-phage)-like-phage and a B. bacteriovorus strain and showing central prey lysis and halos of extra lysis. Combining the purified phage with a lab strain of B. bacteriovorus HD100 recapitulated haloed plaques and increased killing of the E. coli prey in liquid culture, showing an effective side-by-side action of these predators compared to their actions alone. Using approximate Bayesian computation to select the best fitting from a variety of different mathematical models demonstrated that the experimental data could be explained only by assuming the existence of three prey phenotypes: (i) sensitive to both predators, (ii) genetically resistant to phage only, and (iii) plastic resistant to B. bacteriovorus only. Although each predator reduces prey availability for the other, high phage numbers did not abolish B. bacteriovorus predation, so both predators are competent to coexist and are causing different selective pressures on the bacterial surface while, in tandem, controlling prey bacterial numbers efficiently. This suggests that combinatorial predator therapy could overcome problems of phage resistance.IMPORTANCE With increasing levels of antibiotic resistance, the development of alternative antibacterial therapies is urgently needed. Two potential alternatives are bacteriophage and predatory bacteria. Bacteriophage therapy has been used, but prey/host specificity and the rapid acquisition of bacterial resistance to bacteriophage are practical considerations. Predatory bacteria are of interest due to their broad Gram-negative bacterial prey range and the lack of simple resistance mechanisms. Here, a bacteriophage and a strain of Bdellovibrio bacteriovorus, preyed side by side on a population of E. coli, causing a significantly greater decrease in prey numbers than either alone. Such combinatorial predator therapy may have greater potential than individual predators since prey surface changes selected for by each predator do not protect prey against the other predator.
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Affiliation(s)
- Laura Hobley
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J Kimberley Summers
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rob Till
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David S Milner
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert J Atterbury
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Amy Stroud
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Michael J Capeness
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie Gray
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andreas Leidenroth
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ian Connerton
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jamie Twycross
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Michelle Baker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - R Elizabeth Sockett
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Abstract
This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa. In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes. The spread of multidrug-resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or “phage therapy”) constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage, and antibiotics for in vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage sensitive (and antibiotic resistant) and one which is antibiotic sensitive (and phage resistant). We find that combination therapy outperforms either phage or antibiotic alone and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes. IMPORTANCE This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa. In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes.
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Abstract
Phage-bacteria interaction is a classic example of competitive coevolution in nature. Mathematical modeling of such interactions furnishes new insight into the dynamics of phage and bacteria. Besides its intrinsic value, a somewhat underutilized aspect of such insight is that it can provide beneficial inputs toward better experimental design. In this chapter, we discuss several modeling techniques that can be used to study the dynamics between phages and their host bacteria. Monte Carlo simulations and differential equations (both ordinary and delay differential equations) can be used to successfully model phage-bacteria dynamics in well-mixed populations. The presence of spatial restrictions in the interaction media significantly affects the dynamics of phage-bacteria interactions. For such cases, techniques like cellular automata and reaction-diffusion equations can be used to capture these effects adequately. We discuss details of the modeling techniques with specific examples.
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Affiliation(s)
| | | | - Soumen Roy
- Department of Physics, Bose Institute, Kolkata, India.
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Dąbrowska K, Abedon ST. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies. Microbiol Mol Biol Rev 2019; 83:e00012-19. [PMID: 31666296 PMCID: PMC6822990 DOI: 10.1128/mmbr.00012-19] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The use of viruses infecting bacteria (bacteriophages or phages) to treat bacterial infections has been ongoing clinically for approximately 100 years. Despite that long history, the growing international crisis of resistance to standard antibiotics, abundant anecdotal evidence of efficacy, and one successful modern clinical trial of efficacy, this phage therapy is not yet a mainstream approach in medicine. One explanation for why phage therapy has not been subject to more widespread implementation is that phage therapy research, both preclinical and clinical, can be insufficiently pharmacologically aware. Consequently, here we consider the pharmacological obstacles to phage therapy effectiveness, with phages in phage therapy explicitly being considered to serve as drug equivalents. The study of pharmacology has traditionally been differentiated into pharmacokinetic and pharmacodynamic aspects. We therefore separately consider the difficulties that phages as virions can have in traveling through body compartments toward reaching their target bacteria (pharmacokinetics) and the difficulties that phages can have in exerting antibacterial activity once they have reached those bacteria (pharmacodynamics). The latter difficulties, at least in part, are functions of phage host range and bacterial resistance to phages. Given the apparently low toxicity of phages and the minimal side effects of phage therapy as practiced, phage therapy should be successful so long as phages can reach the targeted bacteria in sufficiently high numbers, adsorb, and then kill those bacteria. Greater awareness of what obstacles to this success generally or specifically can exist, as documented in this review, should aid in the further development of phage therapy toward wider use.
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Affiliation(s)
- Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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