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Ponce Benavente L, Wagemans J, Hinkel D, Aguerri Lajusticia A, Lavigne R, Trampuz A, Gonzalez Moreno M. Targeted enhancement of bacteriophage activity against antibiotic-resistant Staphylococcus aureus biofilms through an evolutionary assay. Front Microbiol 2024; 15:1372325. [PMID: 39040906 PMCID: PMC11260789 DOI: 10.3389/fmicb.2024.1372325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/28/2024] [Indexed: 07/24/2024] Open
Abstract
Staphylococcus aureus´ biofilm-forming ability and rapid resistance development pose a significant challenge to successful treatment, particularly in postoperative complications, emphasizing the need for enhanced therapeutic strategies. Bacteriophage (phage) therapy has reemerged as a promising and safe option to combat multidrug-resistant bacteria. However, questions regarding the efficacy of phages against biofilms and the development of phage resistance require further evaluation. Expanding on the adaptable and evolutionary characteristics of phages, we introduce an evolutionary approach to enhance the activity of S. aureus phages against biofilms. Unlike other in vitro directed evolution methods performed in planktonic cultures, we employed pre-stablished biofilms to do a serial-passage assay to evolve phages monitored by real-time isothermal microcalorimetry (IMC). The evolved phages demonstrated an expanded host range, with the CUB_MRSA-COL_R9 phage infecting 83% of strains in the collection (n = 72), surpassing the ISP phage, which represented the widest host range (44%) among the ancestral phages. In terms of antimicrobial efficacy, IMC data revealed superior suppression of bacterial growth by the evolved phages compared to the ancestral CUB-M and/or ISP phages against the respective bacterial strain. The phage cocktail exhibited higher efficacy, achieving over 90% suppression relative to the growth control even after 72 h of monitoring. Biofilm cell-counts, determined by RT-qPCR, confirmed the enhanced antibiofilm performance of evolved phages with no biofilm regrowth up to 48 h in treated MRSA15 and MRSA-COL strains. Overall, our results underscore the potential of biofilm-adapted phage cocktails to improve clinical outcomes in biofilm-associated infections, minimizing the emergence of resistance and lowering the risk of infection relapse. However, further investigation is necessary to evaluate the translatability of our results from in vitro to in vivo models, especially in the context of combination therapy with the current standard of care treatment.
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Affiliation(s)
- Luis Ponce Benavente
- Corporate Member of Freie Universität Berlin and Humboldt, Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Dennis Hinkel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Alba Aguerri Lajusticia
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Andrej Trampuz
- Corporate Member of Freie Universität Berlin and Humboldt, Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mercedes Gonzalez Moreno
- Corporate Member of Freie Universität Berlin and Humboldt, Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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3
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Podlacha M, Węgrzyn G, Węgrzyn A. Bacteriophages-Dangerous Viruses Acting Incognito or Underestimated Saviors in the Fight against Bacteria? Int J Mol Sci 2024; 25:2107. [PMID: 38396784 PMCID: PMC10889324 DOI: 10.3390/ijms25042107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The steadily increasing number of drug-resistant bacterial species has prompted the search for alternative treatments, resulting in a growing interest in bacteriophages. Although they are viruses infecting bacterial cells, bacteriophages are an extremely important part of the human microbiota. By interacting with eukaryotic cells, they are able to modulate the functioning of many systems, including the immune and nervous systems, affecting not only the homeostasis of the organism, but potentially also the regulation of pathological processes. Therefore, the aim of this review is to answer the questions of (i) how animal/human immune systems respond to bacteriophages under physiological conditions and under conditions of reduced immunity, especially during bacterial infection; (ii) whether bacteriophages can induce negative changes in brain functioning after crossing the blood-brain barrier, which could result in various disorders or in an increase in the risk of neurodegenerative diseases; and (iii) how bacteriophages can modify gut microbiota. The crucial dilemma is whether administration of bacteriophages is always beneficial or rather if it may involve any risks.
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Affiliation(s)
- Magdalena Podlacha
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (G.W.)
| | - Alicja Węgrzyn
- Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Kładki 24, 80-822 Gdansk, Poland
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4
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Zhao Y, Shu M, Zhang L, Zhong C, Liao N, Wu G. Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum. ISME COMMUNICATIONS 2024; 4:ycae039. [PMID: 38616926 PMCID: PMC11014889 DOI: 10.1093/ismeco/ycae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Phage therapy faces challenges against multidrug-resistant (MDR) Salmonella due to rapid phage-resistant mutant emergence. Understanding the intricate interplay between antibiotics and phages is essential for shaping Salmonella evolution and advancing phage therapy. In this study, MDR Salmonella anatum (S. anatum) 2089b coevolved with phage JNwz02 for 30 passages (60 days), then the effect of coevolution on the trade-off between phage and antibiotic resistance in bacteria was investigated. Our results demonstrated antagonistic coevolution between bacteria and phages, transitioning from arms race dynamics (ARD) to fluctuating selection dynamics (FSD). The fitness cost of phage resistance, manifested as reduced competitiveness, was observed. Bacteria evolved phage resistance while simultaneously regaining sensitivity to amoxicillin, ampicillin, and gentamicin, influenced by phage selection pressure and bacterial competitiveness. Moreover, the impact of phage selection pressure on the trade-off between antibiotic and phage resistance was more pronounced in the ARD stage than in the FSD stage. Whole genome analysis revealed mutations in the btuB gene in evolved S. anatum strains, with a notably higher mutation frequency in the ARD stage compared to the FSD stage. Subsequent knockout experiments confirmed BtuB as a receptor for phage JNwz02, and the deletion of btuB resulted in reduced bacterial competitiveness. Additionally, the mutations identified in the phage-resistant strains were linked to multiple single nucleotide polymorphisms (SNPs) associated with membrane components. This correlation implies a potential role of these SNPs in reinstating antibiotic susceptibility. These findings significantly advance our understanding of phage-host interactions and the impact of bacterial adaptations on antibiotic resistance.
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Affiliation(s)
- Yuanyang Zhao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Mei Shu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Ling Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Chan Zhong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Ningbo Liao
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Guoping Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
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El Ghali A, Stamper K, Kunz Coyne AJ, Holger D, Kebriaei R, Alexander J, Lehman SM, Rybak MJ. Ciprofloxacin in combination with bacteriophage cocktails against multi-drug resistant Pseudomonas aeruginosa in ex vivo simulated endocardial vegetation models. Antimicrob Agents Chemother 2023; 67:e0072823. [PMID: 37877697 PMCID: PMC10649104 DOI: 10.1128/aac.00728-23] [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: 06/01/2023] [Accepted: 08/18/2023] [Indexed: 10/26/2023] Open
Abstract
Pseudomonas aeruginosa-associated infective endocarditis represents difficult-to-treat, deep-seated infections. Phage-antibiotic combinations have shown to eradicate multi-drug resistant (MDR) P. aeruginosa, limit the development of phage resistance, and restore antibiotic sensitivity. The objective of this study was to evaluate the activity of phage-ciprofloxacin (CIP) combinations in 4-day ex vivo simulated endocardial vegetation (SEV) models against drug-resistant P. aeruginosa isolates. Two P. aeruginosa isolates, extensively drug-resistant AR351 and MDR I0003-1, were selected for their drug resistance and sensitivity to phage. Three phages [LL-5504721-AH (LL), E2005-C (EC), and 109] and CIP were evaluated alone and in combination for their activity and influence on drug and phage resistance using 24-h time-kill analysis. The three-phage cocktail (q24h) in combination with CIP (400 mg q12h) was then tested in dynamic 4-day ex vivo SEV models, with reduction of log10 CFU/mL compared using ANOVA with Bonferroni analysis. Compared to other combinations, CIP-LL-EC-109 demonstrated synergistic and bactericidal activity from starting CFU/g against AR351 and I0003-1 (-Δ5.65 and 6.60 log10 CFU/g, respectively; P < 0.001). Additionally, CIP-LL-EC-109 mitigated phage resistance, while all other therapies had a high degree of resistance to >1 phages, and all phage-containing regimens prevented CIP mean inhibitory concentration increases compared to CIP alone for both AR351 and I0003-1 at 96 h.
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Affiliation(s)
- Amer El Ghali
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Kyle Stamper
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Ashlan J. Kunz Coyne
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Dana Holger
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Razieh Kebriaei
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
| | - Jose Alexander
- Department of Microbiology, Virology and Immunology, AdventHealth Central Florida, Orlando, Florida, USA
| | - Susan M. Lehman
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael J. Rybak
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Detroit, Michigan, USA
- Department of Medicine, Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
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6
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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: 15] [Impact Index Per Article: 15.0] [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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7
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McGee LW, Barhoush Y, Shima R, Hennessy M. Phage-resistant mutations impact bacteria susceptibility to future phage infections and antibiotic response. Ecol Evol 2023; 13:e9712. [PMID: 36620417 PMCID: PMC9817185 DOI: 10.1002/ece3.9712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
Bacteriophage (phage) therapy in combination with antibiotic treatment serves as a potential strategy to overcome the continued rise in antibiotic resistance across bacterial pathogens. Understanding the impacts of evolutionary and ecological processes to the phage-antibiotic-resistance dynamic could advance the development of such combinatorial therapy. We tested whether the acquisition of mutations conferring phage resistance may have antagonistically pleiotropic consequences for antibiotic resistance. First, to determine the robustness of phage resistance across different phage strains, we infected resistant Escherichia coli cultures with phage that were not previously encountered. We found that phage-resistant E. coli mutants that gained resistance to a single phage strain maintain resistance to other phages with overlapping adsorption methods. Mutations underlying the phage-resistant phenotype affects lipopolysaccharide (LPS) structure and/or synthesis. Because LPS is implicated in both phage infection and antibiotic response, we then determined whether phage-resistant trade-offs exist when challenged with different classes of antibiotics. We found that only 1 out of the 4 phage-resistant E. coli mutants yielded trade-offs between phage and antibiotic resistance. Surprisingly, when challenged with novobiocin, we uncovered evidence of synergistic pleiotropy for some mutants allowing for greater antibiotic resistance, even though antibiotic resistance was never selected for. Our results highlight the importance of understanding the role of selective pressures and pleiotropic interactions in the bacterial response to phage-antibiotic combinatorial therapy.
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Affiliation(s)
| | - Yazid Barhoush
- Biology DepartmentEarlham CollegeRichmondIndianaUSA,Department of Epidemiology and BiostatisticsDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Rafaella Shima
- Biology DepartmentEarlham CollegeRichmondIndianaUSA,Department of Physiology and Institute of Diabetes, Obesity, and Metabolism, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Delesalle VA, Tomko BE, Vill AC, Lichty KB, Krukonis GP. Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative. Viruses 2022; 14:2106. [PMID: 36298661 PMCID: PMC9607348 DOI: 10.3390/v14102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2023] Open
Abstract
SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage-host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more genes than SPP1. We identified a new putative gene in SPP1 based on a conserved sequence found in all phages. Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. Patterns of divergence point to genes or gene domains likely involved in adaptation to diverse hosts or different environments. Ultimately, comparative genomics of related phages provides insight into the long-term selective pressures that affect phage-bacteria interactions and alter phage genome content.
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Affiliation(s)
- Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Brianne E. Tomko
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Albert C. Vill
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd., Ithaca, NY 14850, USA
| | - Katherine B. Lichty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biological Sciences, University of Delaware, Wolf Hall, Newark, DE 19716, USA
| | - Greg P. Krukonis
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA
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Debray R, De Luna N, Koskella B. Historical contingency drives compensatory evolution and rare reversal of phage resistance. Mol Biol Evol 2022; 39:6673247. [PMID: 35994371 PMCID: PMC9447851 DOI: 10.1093/molbev/msac182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
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Affiliation(s)
- Reena Debray
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nina De Luna
- Department of Immunology, Pennsylvania State University, State College, PA, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg BioHub, San Francisco, CA, USA
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A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)—viruses targeting bacteria—offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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Castledine M, Padfield D, Sierocinski P, Soria Pascual J, Hughes A, Mäkinen L, Friman VP, Pirnay JP, Merabishvili M, de Vos D, Buckling A. Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro. eLife 2022; 11:73679. [PMID: 35188102 PMCID: PMC8912922 DOI: 10.7554/elife.73679] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/20/2022] [Indexed: 12/02/2022] Open
Abstract
With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolves to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct ‘in vitro evolutionary simulations’ using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria—evolved in vitro and in vivo—had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and how in vitro experiments may give useful insights for clinical evolutionary outcomes.
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Affiliation(s)
- Meaghan Castledine
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Daniel Padfield
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Pawel Sierocinski
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Jesica Soria Pascual
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Adam Hughes
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Lotta Mäkinen
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | | | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel de Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Angus Buckling
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
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12
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Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View. Antibiotics (Basel) 2022; 11:antibiotics11020163. [PMID: 35203766 PMCID: PMC8868336 DOI: 10.3390/antibiotics11020163] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
Aeromonas species often cause disease in farmed fish and are responsible for causing significant economic losses worldwide. Although vaccination is the ideal method to prevent infectious diseases, there are still very few vaccines commercially available in the aquaculture field. Currently, aquaculture production relies heavily on antibiotics, contributing to the global issue of the emergence of antimicrobial-resistant bacteria and resistance genes. Therefore, it is essential to develop effective alternatives to antibiotics to reduce their use in aquaculture systems. Bacteriophage (or phage) therapy is a promising approach to control pathogenic bacteria in farmed fish that requires a heavy understanding of certain factors such as the selection of phages, the multiplicity of infection that produces the best bacterial inactivation, bacterial resistance, safety, the host’s immune response, administration route, phage stability and influence. This review focuses on the need to advance phage therapy research in aquaculture, its efficiency as an antimicrobial strategy and the critical aspects to successfully apply this therapy to control Aeromonas infection in fish.
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13
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Dewald-Wang EA, Parr N, Tiley K, Lee A, Koskella B. Multiyear Time-Shift Study of Bacteria and Phage Dynamics in the Phyllosphere. Am Nat 2022; 199:126-140. [DOI: 10.1086/717181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Application of Bacteriophages on Shiga Toxin-Producing Escherichia coli (STEC) Biofilm. Antibiotics (Basel) 2021; 10:antibiotics10111423. [PMID: 34827361 PMCID: PMC8614735 DOI: 10.3390/antibiotics10111423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Shiga toxin-producing Escherichia coli are pathogenic bacteria able to form biofilms both on abiotic surfaces and on food, thus increasing risks for food consumers. Moreover, biofilms are difficult to remove and more resistant to antimicrobial agents compared to planktonic cells. Bacteriophages, natural predators of bacteria, can be used as an alternative to prevent biofilm formation or to remove pre-formed biofilm. In this work, four STEC able to produce biofilm were selected among 31 different strains and tested against single bacteriophages and two-phage cocktails. Results showed that our phages were able to reduce biofilm formation by 43.46% both when used as single phage preparation and as a cocktail formulation. Since one of the two cocktails had a slightly better performance, it was used to remove pre-existing biofilms. In this case, the phages were unable to destroy the biofilms and reduce the number of bacterial cells. Our data confirm that preventing biofilm formation in a food plant is better than trying to remove a preformed biofilm and the continuous presence of bacteriophages in the process environment could reduce the number of bacteria able to form biofilms and therefore improve the food safety.
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Bono LM, Mao S, Done RE, Okamoto KW, Chan BK, Turner PE. Advancing phage therapy through the lens of virus host-breadth and emergence potential. Adv Virus Res 2021; 111:63-110. [PMID: 34663499 DOI: 10.1016/bs.aivir.2021.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phages are viruses that specifically infect bacteria, and their biodiversity contributes to historical and current development of phage therapy to treat myriad bacterial infections. Phage therapy holds promise as an alternative to failing chemical antibiotics, but there are benefits and costs of this technology. Here, we review the rich history of phage therapy, highlighting reasons (often political) why it was widely rejected by Western medicine until recently. One longstanding idea involves mixing different phages together in cocktails, to increase the probability of killing target pathogenic bacteria without pre-screening for phage susceptibility. By challenging 30 lytic phages to infect 14 strains of the bacteria Pseudomonas aeruginosa, we showed that some phages were "generalists" with broad host-ranges, emphasizing that extreme host-specificity of phages was not necessarily a liability. Using a "greedy algorithm" analysis, we identified the best cocktail mixture of phages to achieve broad bacteria killing. Additionally, we review how virus host-range can evolve and connect lessons learned from virus emergence-including contributions of elevated virus mutation rates in promoting emergence and virus evolutionary transitions from specialized to generalized host-use-as cautionary tales for avoiding risk of "off-target" phage emergence on commensal bacteria in microbiomes. Throughout, we highlight how fundamental understanding of virus ecology and evolution is vital for developing phage therapy; heeding these principles should help in designing therapeutic strategies that do not recapitulate consequences of virus selection to emerge on novel hosts.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, Emory University, Atlanta, GA, United States.
| | - Stephanie Mao
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel E Done
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, United States; Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Kenichi W Okamoto
- Department of Biology, University of St. Thomas, St. Paul, MN, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Microbiology Program, Yale School of Medicine, New Haven, CT, United States
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Abstract
Control of pathogenic bacteria by deliberate application of predatory phages has potential as a powerful therapy against antibiotic-resistant bacteria. The key advantages of phage biocontrol over antibacterial chemotherapy are: (1) an ability to self-propagate inside host bacteria, (2) targeted predation of specific species or strains of bacteria, (3) adaptive molecular machinery to overcome resistance in target bacteria. However, realizing the potential of phage biocontrol is dependent on harnessing or adapting these responses, as many phage species switch between lytic infection cycles (resulting in lysis) and lysogenic infection cycles (resulting in genomic integration) that increase the likelihood of survival of the phage in response to external stress or host depletion. Similarly, host range will need to be optimized to make phage therapy medically viable whilst avoiding the potential for deleteriously disturbing the commensal microbiota. Phage training is a new approach to produce efficient phages by capitalizing on the evolved response of wild-type phages to bacterial resistance. Here we will review recent studies reporting successful trials of training different strains of phages to switch into lytic replication mode, overcome bacterial resistance, and increase their host range. This review will also highlight the current knowledge of phage training and future implications in phage applications and phage therapy and summarize the recent pipeline of the magistral preparation to produce a customized phage for clinical trials and medical applications.
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Squires RA. Bacteriophage therapy for challenging bacterial infections: achievements, limitations and prospects for future clinical use by veterinary dermatologists. Vet Dermatol 2021; 32:587-e158. [PMID: 33870572 DOI: 10.1111/vde.12958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Bacteriophages were discovered just over 100 years ago and have been used to treat bacterial infections in animals since the 1920s. The antimicrobial resistance crisis has led to a new surge of interest in the use of bacteriophage therapy as an alternative or supplement to antimicrobial therapy in humans and other animals. OBJECTIVES To describe the nature of bacteriophages and provide a critical review and update on the clinical use of bacteriophages in the treatment of challenging bacterial infections, with an emphasis on companion animal veterinary applications. METHODS AND MATERIALS The scientific literature on the subject was critically evaluated. Findings from the most pertinent papers have been presented in summary form and critiqued. RESULTS Over the last 20 years there has been a considerable increase in the volume and quality of publications dealing with bacteriophage therapy. Some recent papers build on excellent work published in the 1980s and describe promising veterinary applications. Challenges related particularly to the registration and approval of phage remedies will need to be overcome before phage therapy can become a mainstream tool for use in veterinary settings. Considerably more research, particularly controlled clinical trials, needs to be done. CONCLUSIONS AND CLINICAL IMPORTANCE Bacteriophage therapy is one of the most promising approaches to tackling the looming antimicrobial resistance crisis, yet substantial regulatory challenges will need to be overcome before it enters widespread use. Phage therapy also may, in the future, improve the management of challenging bacterial infections that are not necessarily multidrug-resistant.
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Affiliation(s)
- Richard Adrian Squires
- Discipline of Veterinary Science, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4814, Australia
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18
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Majkowska-Skrobek G, Markwitz P, Sosnowska E, Lood C, Lavigne R, Drulis-Kawa Z. The evolutionary trade-offs in phage-resistant Klebsiella pneumoniae entail cross-phage sensitization and loss of multidrug resistance. Environ Microbiol 2021; 23:7723-7740. [PMID: 33754440 DOI: 10.1111/1462-2920.15476] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Bacteriophage therapy is currently being evaluated as a critical complement to traditional antibiotic treatment. However, the emergence of phage resistance is perceived as a major hurdle to the sustainable implementation of this antimicrobial strategy. By combining comprehensive genomics and microbiological assessment, we show that the receptor-modification resistance to capsule-targeting phages involves either escape mutation(s) in the capsule biosynthesis cluster or qualitative changes in exopolysaccharides, converting clones to mucoid variants. These variants introduce cross-resistance to phages specific to the same receptor yet sensitize to phages utilizing alternative ones. The loss/modification of capsule, the main Klebsiella pneumoniae virulence factor, did not dramatically impact population fitness, nor the ability to protect bacteria against the innate immune response. Nevertheless, the introduction of phage drives bacteria to expel multidrug resistance clusters, as observed by the large deletion in K. pneumoniae 77 plasmid containing blaCTX-M , ant(3″), sul2, folA, mph(E)/mph(G) genes. The emerging bacterial resistance to viral infection steers evolution towards desired population attributes and highlights the synergistic potential for combined antibiotic-phage therapy against K. pneumoniae.
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Affiliation(s)
- Grazyna Majkowska-Skrobek
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
| | - Pawel Markwitz
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
| | - Ewelina Sosnowska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
| | - Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium.,Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
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Hill T, Unckless RL. Recurrent evolution of high virulence in isolated populations of a DNA virus. eLife 2020; 9:e58931. [PMID: 33112738 PMCID: PMC7685711 DOI: 10.7554/elife.58931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/28/2020] [Indexed: 12/30/2022] Open
Abstract
Hosts and viruses are constantly evolving in response to each other: as a host attempts to suppress a virus, the virus attempts to evade and suppress the host's immune system. Here, we describe the recurrent evolution of a virulent strain of a DNA virus, which infects multiple Drosophila species. Specifically, we identified two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar differences observed in multiple species. Our analysis suggests that one of the viral types recurrently evolved at least four times in the past ~30,000 years, three times in Arizona and once in another geographically distinct species. This recurrent evolution may be facilitated by an effective mutation rate which increases as each prior mutation increases viral titer and effective population size. The higher titer viral type suppresses the host-immune system and an increased virulence compared to the low viral titer type.
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Affiliation(s)
- Tom Hill
- The Department of Molecular Biosciences, University of KansasLawrenceUnited States
| | - Robert L Unckless
- The Department of Molecular Biosciences, University of KansasLawrenceUnited States
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20
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Bacteriophage biocontrol to fight Listeria outbreaks in seafood. Food Chem Toxicol 2020; 145:111682. [PMID: 32805341 DOI: 10.1016/j.fct.2020.111682] [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: 02/29/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is a well-known pathogen responsible for the severe foodborne disease listeriosis. The control of L. monocytogenes occurrence in seafood products and seafood processing environments is an important challenge for the seafood industry and the public health sector. However, bacteriophage biocontrol shows great potential to be used as safety control measure in seafood. This review provides an update on Listeria-specific bacteriophages, focusing on their application as a safe and natural strategy to prevent L. monocytogenes contamination and growth in seafood products and seafood processing environments. Furthermore, the main properties required from bacteriophages intended to be used as biocontrol tools are summarized and emerging strategies to overcome the current limitations are considered. Also, major aspects relevant for bacteriophage production at industrial scale, their access to the market, as well as the current regulatory status of bacteriophage-based solutions for Listeria biocontrol are discussed.
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21
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Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-550. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
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22
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Ferriol-González C, Domingo-Calap P. Phages for Biofilm Removal. Antibiotics (Basel) 2020; 9:antibiotics9050268. [PMID: 32455536 PMCID: PMC7277876 DOI: 10.3390/antibiotics9050268] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Biofilms are clusters of bacteria that live in association with surfaces. Their main characteristic is that the bacteria inside the biofilms are attached to other bacterial cells and to the surface by an extracellular polymeric matrix. Biofilms are capable of adhering to a wide variety of surfaces, both biotic and abiotic, including human tissues, medical devices, and other materials. On these surfaces, biofilms represent a major threat causing infectious diseases and economic losses. In addition, current antibiotics and common disinfectants have shown limited ability to remove biofilms adequately, and phage-based treatments are proposed as promising alternatives for biofilm eradication. This review analyzes the main advantages and challenges that phages can offer for the elimination of biofilms, as well as the most important factors to be taken into account in order to design effective phage-based treatments.
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Affiliation(s)
| | - Pilar Domingo-Calap
- Department of Genetics, Universitat de València, 46100 Valencia, Spain;
- Institute for Integrative Systems Biology, ISysBio, Universitat de València-CSIC, 46910 Valencia, Spain
- Correspondence: ; Tel.: +34-963-543-261
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23
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Pleiotropy complicates a trade-off between phage resistance and antibiotic resistance. Proc Natl Acad Sci U S A 2020; 117:11207-11216. [PMID: 32424102 PMCID: PMC7260982 DOI: 10.1073/pnas.1919888117] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages (“phages,” viruses that infect bacteria) are an important source of selection for bacterial populations. Phages use various structures to infect bacterial cells, and bacteria often evolve phage resistance by losing or modifying these structures. We examine a phage that uses two structures that also provide Escherichia coli cells with antibiotic resistance. We show that phage selection can result in bacteria evolving phage resistance by losing or modifying the structures. When phage resistance evolves, the bacteria sometimes also show increased antibiotic sensitivity. This result indicates an evolutionary trade-off between phage resistance and antibiotic resistance. However, we also discovered bacterial mutations that avoid the trade-off. We discuss the potential use of phage selection and evolutionary trade-offs in treating bacterial infections. Bacteria frequently encounter selection by both antibiotics and lytic bacteriophages. However, the evolutionary interactions between antibiotics and phages remain unclear, in particular, whether and when phages can drive evolutionary trade-offs with antibiotic resistance. Here, we describe Escherichia coli phage U136B, showing it relies on two host factors involved in different antibiotic resistance mechanisms: 1) the efflux pump protein TolC and 2) the structural barrier molecule lipopolysaccharide (LPS). Since TolC and LPS contribute to antibiotic resistance, phage U136B should select for their loss or modification, thereby driving a trade-off between phage resistance and either of the antibiotic resistance mechanisms. To test this hypothesis, we used fluctuation experiments and experimental evolution to obtain phage-resistant mutants. Using these mutants, we compared the accessibility of specific mutations (revealed in the fluctuation experiments) to their actual success during ecological competition and coevolution (revealed in the evolution experiments). Both tolC and LPS-related mutants arise readily during fluctuation assays, with tolC mutations becoming more common during the evolution experiments. In support of the trade-off hypothesis, phage resistance via tolC mutations occurs with a corresponding reduction in antibiotic resistance in many cases. However, contrary to the hypothesis, some phage resistance mutations pleiotropically confer increased antibiotic resistance. We discuss the molecular mechanisms underlying this surprising pleiotropic result, consideration for applied phage biology, and the importance of ecology in evolution of phage resistance. We envision that phages may be useful for the reversal of antibiotic resistance, but such applications will need to account for unexpected pleiotropy and evolutionary context.
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24
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Caflisch KM, Suh GA, Patel R. Biological challenges of phage therapy and proposed solutions: a literature review. Expert Rev Anti Infect Ther 2019; 17:1011-1041. [PMID: 31735090 DOI: 10.1080/14787210.2019.1694905] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: In light of the emergence of antibiotic-resistant bacteria, phage (bacteriophage) therapy has been recognized as a potential alternative or addition to antibiotics in Western medicine for use in humans.Areas covered: This review assessed the scientific literature on phage therapy published between 1 January 2007 and 21 October 2019, with a focus on the successes and challenges of this prospective therapeutic.Expert opinion: Efficacy has been shown in animal models and experimental findings suggest promise for the safety of human phagotherapy. Significant challenges remain to be addressed prior to the standardization of phage therapy in the West, including the development of phage-resistant bacteria; the pharmacokinetic complexities of phage; and any potential human immune response incited by phagotherapy.
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Affiliation(s)
- Katherine M Caflisch
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Gina A Suh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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25
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Sutton TDS, Hill C. Gut Bacteriophage: Current Understanding and Challenges. Front Endocrinol (Lausanne) 2019; 10:784. [PMID: 31849833 PMCID: PMC6895007 DOI: 10.3389/fendo.2019.00784] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.
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Affiliation(s)
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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26
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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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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Resistance Evolution against Phage Combinations Depends on the Timing and Order of Exposure. mBio 2019; 10:e01652-19. [PMID: 31551330 PMCID: PMC6759759 DOI: 10.1128/mbio.01652-19] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/29/2019] [Indexed: 01/07/2023] Open
Abstract
Phage therapy is a promising alternative to chemotherapeutic antibiotics for the treatment of bacterial infections. However, despite recent clinical uses of combinations of phages to treat multidrug-resistant infections, a mechanistic understanding of how bacteria evolve resistance against multiple phages is lacking, limiting our ability to deploy phage combinations optimally. Here, we show, using Pseudomonas aeruginosa and pairs of phages targeting shared or distinct surface receptors, that the timing and order of phage exposure determine the strength, cost, and mutational basis of resistance. Whereas sequential exposure allowed bacteria to acquire multiple resistance mutations effective against both phages, this evolutionary trajectory was prevented by simultaneous exposure, resulting in quantitatively weaker resistance. The order of phage exposure determined the fitness costs of sequential resistance, such that certain sequential orders imposed much higher fitness costs than the same phage pair in the reverse order. Together, these data suggest that phage combinations can be optimized to limit the strength of evolved resistances while maximizing their associated fitness costs to promote the long-term efficacy of phage therapy.IMPORTANCE Globally rising rates of antibiotic resistance have renewed interest in phage therapy where combinations of phages have been successfully used to treat multidrug-resistant infections. To optimize phage therapy, we first need to understand how bacteria evolve resistance against combinations of multiple phages. Here, we use simple laboratory experiments and genome sequencing to show that the timing and order of phage exposure determine the strength, cost, and mutational basis of resistance evolution in the opportunistic pathogen Pseudomonas aeruginosa These findings suggest that phage combinations can be optimized to limit the emergence and persistence of resistance, thereby promoting the long-term usefulness of phage therapy.
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Affiliation(s)
- Rosanna C T Wright
- Department of Biology, University of York, York, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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28
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Scanlan JG, Hall AR, Scanlan PD. Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01. INFECTION GENETICS AND EVOLUTION 2019; 73:425-432. [DOI: 10.1016/j.meegid.2019.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 01/21/2023]
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29
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Cebriá-Mendoza M, Sanjuán R, Domingo-Calap P. Directed Evolution of a Mycobacteriophage. Antibiotics (Basel) 2019; 8:antibiotics8020046. [PMID: 31027152 PMCID: PMC6627502 DOI: 10.3390/antibiotics8020046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/03/2022] Open
Abstract
Bacteriophages represent an alternative strategy to combat pathogenic bacteria. Currently, Mycobacterium tuberculosis infections constitute a major public health problem due to extensive antibiotic resistance in some strains. Using a non-pathogenic species of the same genus as an experimental model, Mycobacterium smegmatis, here we have set up a basic methodology for mycobacteriophage growth and we have explored directed evolution as a tool for increasing phage infectivity and lytic activity. We demonstrate mycobacteriophage adaptation to its host under different conditions. Directed evolution could be used for the development of future phage therapy applications against mycobacteria.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
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Moulton‐Brown CE, Friman V. Rapid evolution of generalized resistance mechanisms can constrain the efficacy of phage-antibiotic treatments. Evol Appl 2018; 11:1630-1641. [PMID: 30344632 PMCID: PMC6183449 DOI: 10.1111/eva.12653] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance has been estimated to be responsible for over 700,000 deaths per year; therefore, new antimicrobial therapies are urgently needed. One way to increase the efficiency of antibiotics is to use them in combination with bacteria-specific parasitic viruses, phages, which have been shown to exert additive or synergistic effects in controlling bacteria. However, it is still unclear to what extent these combinatory effects are limited by rapid evolution of resistance, especially when the pathogen grows as biofilm on surfaces typical for many persistent and chronic infections. To study this, we used a microcosm system, where genetically isogenic populations of Pseudomonas aeruginosa PAO1 bacterial pathogen were exposed to a phage 14/1, gentamycin or a combination of them both in a spatially structured environment. We found that even though antibiotic and phage-antibiotic treatments were equally effective at controlling bacteria in the beginning of the experiment, combination treatment rapidly lost its efficacy in both planktonic and biofilm populations. In a mechanistic manner, this was due to rapid resistance evolution: While both antibiotic and phage selected for increased resistance on their own, phage selection correlated positively with increase in antibiotic resistance, while biofilm growth, which provided generalized resistance mechanism, was favoured most in the combination treatment. Only relatively small cost of resistance and weak evidence for coevolutionary dynamics were observed. Together, these results suggest that spatial heterogeneity can promote rapid evolution of generalized resistance mechanisms without corresponding increase in phage infectivity, which could potentially limit the effectiveness of phage-antibiotic treatments in the evolutionary timescale.
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Domingo-Calap P, Delgado-Martínez J. Bacteriophages: Protagonists of a Post-Antibiotic Era. Antibiotics (Basel) 2018; 7:E66. [PMID: 30060506 PMCID: PMC6163168 DOI: 10.3390/antibiotics7030066] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022] Open
Abstract
Despite their long success for more than half a century, antibiotics are currently under the spotlight due to the emergence of multidrug-resistant bacteria. The development of new alternative treatments is of particular interest in the fight against bacterial resistance. Bacteriophages (phages) are natural killers of bacteria and are an excellent tool due to their specificity and ecological safety. Here, we highlight some of their advantages and drawbacks as potential therapeutic agents. Interestingly, phages are not only attractive from a clinical point of view, but other areas, such as agriculture, food control, or industry, are also areas for their potential application. Therefore, we propose phages as a real alternative to current antibiotics.
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Affiliation(s)
- Pilar Domingo-Calap
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
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Parallel Evolution of Host-Attachment Proteins in Phage PP01 Populations Adapting to Escherichia coli O157:H7. Pharmaceuticals (Basel) 2018; 11:ph11020060. [PMID: 29925767 PMCID: PMC6027323 DOI: 10.3390/ph11020060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
The emergence of antibiotic resistance has sparked interest in phage therapy, which uses virulent phages as antibacterial agents. Bacteriophage PP01 has been studied for potential bio-control of Escherichia coli O157:H7, its natural host, but in the laboratory, PP01 can be inefficient at killing this bacterium. Thus, the goal of this study was to improve the therapeutic potential of PP01 through short-term experimental evolution. Four replicate populations of PP01 were serially passaged 21 times on non-evolving E. coli O157:H7 with the prediction that the evolved phage populations would adsorb faster and more efficiently kill the host bacteria. Dead-cell adsorption assays and in vitro killing assays confirmed that evolved viruses improved their adsorption ability on E. coli O157:H7, and adapted to kill host bacteria faster than the wildtype ancestor. Sequencing of candidate tail-fiber genes revealed that the phage populations evolved in parallel; the lineages shared two point mutations in gp38 that encodes a host recognition protein, and surprisingly shared a ~600 bp deletion in gp37 that encodes the distal tail fibers. In contrast, no mutations were observed in the gp12 gene encoding PP01’s short tail fibers. We discuss the functional role of the observed mutations, including the possible adaptive role of the evolved deletions. This study demonstrates how experimental evolution can be used to select for viral traits that improve phage attack of an important bacterial pathogen, and that the molecular targets of selection include loci contributing to cell attachment and phage virulence.
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Torres-Barceló C. Phage Therapy Faces Evolutionary Challenges. Viruses 2018; 10:v10060323. [PMID: 29895791 PMCID: PMC6024868 DOI: 10.3390/v10060323] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/09/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance evolution in bacteria indicates that one of the challenges faced by phage therapy is that, sooner or later, bacteria will evolve resistance to phages. Evidently, this is the case of every known antimicrobial therapy, but here this is also part of a ubiquitous natural process of co-evolution between phages and bacteria. Fundamental evolutionary studies hold some clues that are crucial to limit the problematic process of bacterial resistance during phage applications. First, I discuss here the importance of defining evolutionary and ecological factors influencing bacterial resistance and phage counter-defense mechanisms. Then, I comment on the interest of determining the co-evolutionary dynamics between phages and bacteria that may allow for selecting the conditions that will increase the probability of therapeutic success. I go on to suggest the varied strategies that may ensure the long-term success of phage therapy, including analysis of internal phage parameters and personalized treatments. In practical terms, these types of approaches will define evolutionary criteria regarding how to develop, and when to apply, therapeutic phage cocktails. Integrating this perspective in antimicrobial treatments, such as phage therapy, is among the necessary steps to expand its use in the near future, and to ensure its durability and success.
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Affiliation(s)
- Clara Torres-Barceló
- University of Reunion Island, UMR Plant populations and bio-agressors in tropical environment (PVBMT), Saint-Pierre 97410, Reunion, France.
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Protein Expression Modifications in Phage-Resistant Mutants of Aeromonas salmonicida after AS-A Phage Treatment. Antibiotics (Basel) 2018. [PMID: 29518018 PMCID: PMC5872132 DOI: 10.3390/antibiotics7010021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The occurrence of infections by pathogenic bacteria is one of the main sources of financial loss for the aquaculture industry. This problem often cannot be solved with antibiotic treatment or vaccination. Phage therapy seems to be an alternative environmentally-friendly strategy to control infections. Recognizing the cellular modifications that bacteriophage therapy may cause to the host is essential in order to confirm microbial inactivation, while understanding the mechanisms that drive the development of phage-resistant strains. The aim of this work was to detect cellular modifications that occur after phage AS-A treatment in A. salmonicida, an important fish pathogen. Phage-resistant and susceptible cells were subjected to five successive streak-plating steps and analysed with infrared spectroscopy, a fast and powerful tool for cell study. The spectral differences of both populations were investigated and compared with a phage sensitivity profile, obtained through the spot test and efficiency of plating. Changes in protein associated peaks were found, and these results were corroborated by 1-D electrophoresis of intracellular proteins analysis and by phage sensitivity profiles. Phage AS-A treatment before the first streaking-plate step clearly affected the intracellular proteins expression levels of phage-resistant clones, altering the expression of distinct proteins during the subsequent five successive streak-plating steps, making these clones recover and be phenotypically more similar to the sensitive cells.
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Long-term genomic coevolution of host-parasite interaction in the natural environment. Nat Commun 2017; 8:111. [PMID: 28740072 PMCID: PMC5524643 DOI: 10.1038/s41467-017-00158-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage-bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size. We identified two CRISPR loci in the bacterial host: a type II-C locus and a type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appear in the variable ends of both loci over time. The spacers mostly target the terminal end of the phage genomes, which also exhibit the most variation across time, resulting in arms-race-like changes in the protospacers of the coevolving phage population.Arms races between phage and bacteria are well known from lab experiments, but insight from field systems is limited. Here, the authors show changes in the resistance and CRISPR loci of bacteria and the infectivity, host range and genome size of phage over multiple years in an aquaculture environment.
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Oechslin F, Piccardi P, Mancini S, Gabard J, Moreillon P, Entenza JM, Resch G, Que YA. Synergistic Interaction Between Phage Therapy and Antibiotics Clears Pseudomonas Aeruginosa Infection in Endocarditis and Reduces Virulence. J Infect Dis 2017; 215:703-712. [PMID: 28007922 PMCID: PMC5388299 DOI: 10.1093/infdis/jiw632] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
Background. Increasing antibiotic resistance warrants therapeutic alternatives. Here we investigated the efficacy of bacteriophage-therapy (phage) alone or combined with antibiotics against experimental endocarditis (EE) due to Pseudomonas aeruginosa, an archetype of difficult-to-treat infection. Methods. In vitro fibrin clots and rats with aortic EE were treated with an antipseudomonas phage cocktail alone or combined with ciprofloxacin. Phage pharmacology, therapeutic efficacy, and resistance were determined. Results. In vitro, single-dose phage therapy killed 7 log colony-forming units (CFUs)/g of fibrin clots in 6 hours. Phage-resistant mutants regrew after 24 hours but were prevented by combination with ciprofloxacin (2.5 × minimum inhibitory concentration). In vivo, single-dose phage therapy killed 2.5 log CFUs/g of vegetations in 6 hours (P < .001 vs untreated controls) and was comparable with ciprofloxacin monotherapy. Moreover, phage/ciprofloxacin combinations were highly synergistic, killing >6 log CFUs/g of vegetations in 6 hours and successfully treating 64% (n = 7/11) of rats. Phage-resistant mutants emerged in vitro but not in vivo, most likely because resistant mutations affected bacterial surface determinants important for infectivity (eg, the pilT and galU genes involved in pilus motility and LPS formation). Conclusions. Single-dose phage therapy was active against P. aeruginosa EE and highly synergistic with ciprofloxacin. Phage-resistant mutants had impaired infectivity. Phage-therapy alone or combined with antibiotics merits further clinical consideration.
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Affiliation(s)
- Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Philippe Piccardi
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Stefano Mancini
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | | | - Philippe Moreillon
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - José M Entenza
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Bern University Hospital, Switzerland
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Bacteria-Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality. Trends Microbiol 2017; 25:614-623. [PMID: 28342597 DOI: 10.1016/j.tim.2017.02.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/24/2017] [Indexed: 02/08/2023]
Abstract
Antagonistic coevolution (AC) between bacteria and bacteriophages plays a key role in driving and maintaining microbial diversity. Consequently, AC is predicted to affect all levels of biological organisation, from the individual to ecosystem scales. Nonetheless, we know nothing about bacteria-bacteriophage AC in perhaps the most important and clinically relevant microbial ecosystem known to humankind - the human gut microbiome. In this opinion piece I review current research on bacteria-phage AC in in vitro and natural populations of microbes. I then examine the evidence and discuss the potential role of AC in driving observed patterns of intra- and interindividual variation in the gut microbiome together with detailing the potential functional consequences of such AC-driven microbial variation for human health and disease.
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Analyses of Short-Term Antagonistic Evolution of Pseudomonas aeruginosa Strain PAO1 and Phage KPP22 (Myoviridae Family, PB1-Like Virus Genus). Appl Environ Microbiol 2016; 82:4482-4491. [PMID: 27208109 DOI: 10.1128/aem.00090-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/02/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa causes serious intractable infections in humans and animals. Bacteriophage (phage) therapy has been applied to treat P. aeruginosa infections, and phages belonging to the PB1-like virus genus in the Myoviridae family have been used as therapeutic phages. To achieve safer and more effective phage therapy, the use of preadapted phages is proposed. To understand in detail such phage preadaptation, the short-term antagonistic evolution of bacteria and phages should be studied. In this study, the short-term antagonistic evolution of bacteria and PB1-like phage was examined by studying phage-resistant clones of P. aeruginosa strain PAO1 and mutant PB1-like phages that had recovered their infectivity. First, phage KPP22 was isolated and characterized; it was classified as belonging to the PB1-like virus genus in the Myoviridae family. Subsequently, three KPP22-resistant PAO1 clones and three KPP22 mutant phages capable of infecting these clones were isolated in three sets of in vitro experiments. It was shown that the bacterial resistance to phage KPP22 was caused by significant decreases in phage adsorption and that the improved infectivity of KPP22 mutant phages was caused by significant increases in phage adsorption. The KPP22-resistant PAO1 clones and the KPP22 mutant phages were then analyzed genetically. All three KPP22-resistant PAO1 clones, which were deficient for the O5 antigen, had a common nonsense mutation in the wzy gene. All the KPP22 mutant phage genomes showed the same four missense mutations in the open reading frames orf060, orf065, and orf086 The information obtained in this study should be useful for further development of safe and efficient phage therapy. IMPORTANCE Pseudomonas aeruginosa causes serious intractable infections in humans and animals; bacteriophage (phage) therapy has been utilized to treat P. aeruginosa infections, and phages that belong to the PB1-like virus genus in the family Myoviridae have been used as therapeutic phages. The preadapted phage is trained in advance through the antagonistic evolution of bacteria and phage and is proposed to be used to achieve safer and more effective phage therapy. In this study, to understand the phage preadaptation, the in vitro short-term antagonistic evolution was studied using P. aeruginosa strain PAO1 and the newly isolated PB1-like phage KPP22. Phage KPP22 was characterized, and the molecular framework regarding the phage preadaptation of KPP22 was elucidated. The importance of study of antagonistic evolution of bacteria and phage in phage therapy is discussed.
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