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Carter L, Mankad A, Hobman EV, Weynberg KD, Kaksonen AH, Cooper C. Three synthetic biology applications and their paths to impact in Australia: Cane toads, bacteriophages and biomining microbes. Biotechnol J 2022; 17:e2200009. [DOI: 10.1002/biot.202200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Lucy Carter
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Aditi Mankad
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Elizabeth V. Hobman
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Karen D. Weynberg
- Australian Centre for Ecogenomics School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Anna H. Kaksonen
- CSIRO Land and Water Brisbane QLD Australia
- Land and Water CSIRO Floreat WA Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Caitlin Cooper
- The University of California Davis California United States
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Gordillo Altamirano FL, Kostoulias X, Subedi D, Korneev D, Peleg AY, Barr JJ. Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study. EBioMedicine 2022; 80:104045. [PMID: 35537278 PMCID: PMC9097682 DOI: 10.1016/j.ebiom.2022.104045] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/30/2022] [Accepted: 04/22/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Clinical phage therapy is often delivered alongside antibiotics. However, the phenomenon of phage-antibiotic synergy has been mostly studied in vitro. Here, we assessed the in vivo bactericidal effect of a phage-antibiotic combination on Acinetobacter baumannii AB900 using phage øFG02, which binds to capsular polysaccharides and leads to antimicrobial resensitisation in vitro. METHODS We performed a two-stage preclinical study using a murine model of severe A. baumannii AB900 bacteraemia. In the first stage, with an endpoint of 11 h, mice (n = 4 per group) were treated with either PBS, ceftazidime, phage øFG02, or the combination of phage and ceftazidime. The second stage involved only the latter two groups (n = 5 per group), with a prolonged endpoint of 16 h. The primary outcome was the average bacterial burden from four body sites (blood, liver, kidney, and spleen). Bacterial colonies from phage-treated mice were retrieved and screened for phage-resistance. FINDINGS In the first stage, the bacterial burden (CFU/g of tissue) of the combination group (median: 4.55 × 105; interquartile range [IQR]: 2.79 × 105-2.81 × 106) was significantly lower than the PBS (median: 2.42 × 109; IQR: 1.97 × 109-3.48 × 109) and ceftazidime groups (median: 3.86 × 108; IQR: 2.15 × 108-6.35 × 108), but not the phage-only group (median: 1.28 × 107; IQR: 4.71 × 106-7.13 × 107). In the second stage, the combination treatment (median: 1.72 × 106; IQR: 5.11 × 105-4.00 × 106) outperformed the phage-only treatment (median: 7.46 × 107; IQR: 1.43 × 107-1.57 × 108). Phage-resistance emerged in 96% of animals receiving phages, and all the tested isolates (n = 11) had loss-of-function mutations in genes involved in capsule biosynthesis and increased sensitivity to ceftazidime. INTERPRETATION øFG02 reliably drives the in vivo evolution of A. baumannii AB900 towards a capsule-deficient, phage-resistant phenotype that is resensitised to ceftazidime. This mechanism highlights the clinical potential of using phage therapy to target A. baumannii and restore antibiotic activity. FUNDING National Health and Medical Research Council (Australia).
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Affiliation(s)
- Fernando L Gordillo Altamirano
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia; Centre to Impact AMR, Monash University, Clayton, Victoria, Australia; Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Xenia Kostoulias
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia; Infection Program, Department of Microbiology Monash University, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Dinesh Subedi
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia; Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - Denis Korneev
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Faculty of Science, School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Anton Y Peleg
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia; Infection Program, Department of Microbiology Monash University, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia; Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia.
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia; Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
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Díaz-Galián MV, Vega-Rodríguez MA, Molina F. PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106865. [PMID: 35576688 DOI: 10.1016/j.cmpb.2022.106865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND OBJECTIVE Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks. METHODS This R package includes four different methods for designing phage cocktails: ExhaustiveSearch, ExhaustivePhi, ClusteringSearch, and ClusteringPhi. These four methods are explained in detail and are evaluated using 13 empirical phage-bacteria infection networks. More specifically, runtime and expected success (fraction of lysed bacteria) are analyzed. RESULTS The four methods have variations in terms of runtime and quality of the results. ExhaustiveSearch always provides the best possible phage cocktail, but its runtime could be long. ExhaustivePhi only focuses on one cocktail size, the one estimated as the best; thus, its runtime is less than ExhaustiveSearch, but it can produce cocktails with more phages than necessary. ClusteringSearch and ClusteringPhi are very fast (generally, less than one millisecond), providing always immediate results due to clustering techniques, but their accuracies can be lower, yielding cocktails with lower expected successes. CONCLUSIONS The larger the phage-bacteria infection network is, the more complex its analysis is. Thus, this tool eases this task for scientists and other users while designing phage cocktails of good quality. This R package includes four different methods; therefore, users may choose among them, considering their preferences in speed and accuracy of results.
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Affiliation(s)
- María Victoria Díaz-Galián
- Escuela Politécnica, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de la Universidad s/n, Cáceres, 10003, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de la Universidad s/n, Cáceres, 10003, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de Elvas s/n, Badajoz, 06006, Spain.
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Abd-Allah IM, El-Housseiny GS, Alshahrani MY, El-Masry SS, Aboshanab KM, Hassouna NA. An Anti-MRSA Phage From Raw Fish Rinse: Stability Evaluation and Production Optimization. Front Cell Infect Microbiol 2022; 12:904531. [PMID: 35656033 PMCID: PMC9152141 DOI: 10.3389/fcimb.2022.904531] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022] Open
Abstract
Accumulating evidence has denoted the danger of resistance in tenacious organisms like methicillin-resistant Staphylococcus aureus (MRSA). MRSA, a supple bacterium that adopts a variety of antibiotic resistance mechanisms, is the cause of multiple life-threatening conditions. Approaching a post-antibiotic era, bacteria-specific natural predators, bacteriophages, are now given the chance to prove eligible for joining the antibacterial weaponry. Considering the foregoing, this study aimed at isolating bacteriophages with promising anti-MRSA lytic activity, followed by characterization and optimization of the production of the bacteriophage with the broadest host range. Five phages were isolated from different environmental sources including the rinse of raw chicken egg, raw milk, and, remarkably, the raw meat rinses of chicken and fish. Examined for lytic activity against a set of 23 MRSA isolates collected from various clinical specimens, all five phages showed relatively broad host ranges with the bacteriophage originally isolated from raw fish rinse showing lytic activity against all the isolates tested. This phage is suggested to be a member of Siphoviridae family, order Caudovirales, as revealed by electron microscopy. It also exhibited good thermal stability and viability at different pH grades. Moreover, it showed reasonable stability against UV light and all viricidal organic solvents tested. Optimization using D-optimal design by response surface methodology was carried out to enhance the phage yield. The optimum conditions suggested by the generated model were a pH value of 7, a carbon source of 0.5% w/v sucrose, and a nitrogen source of 0.1% w/v peptone, at a temperature of 28°C and a bacterial inoculum size of 107 CFU/ml, resulting in a 2 log-fold increase in the produced bacteriophage titer. Overall, the above findings indicate the lytic ability inflicted by this virus on MRSA. Apparently, its stability under some of the extreme conditions tested implies its potential to be a candidate for pharmaceutical formulation as an anti-MRSA therapeutic tool. We hope that bacteriophages could tip the balance in favor of the human front in their battle against multidrug-resistant pathogens.
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Affiliation(s)
- Israa M. Abd-Allah
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ghadir S. El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Samar S. El-Masry
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nadia A. Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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Mutalik VK, Arkin AP. A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)-viruses targeting bacteria-offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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Affiliation(s)
- Vivek K. Mutalik
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adam P. Arkin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
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Barr HL, Bihouee T, Zwitserloot AM. A year in review: Real world evidence, functional monitoring and emerging therapeutics in 2021. J Cyst Fibros 2022; 21:191-196. [PMID: 35272931 PMCID: PMC8900606 DOI: 10.1016/j.jcf.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022]
Affiliation(s)
- H L Barr
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; Nottingham Respiratory Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.
| | - T Bihouee
- Chronic Childhood Diseases unit, Pediatric Department, Nantes University Hospital, Nantes, France
| | - A M Zwitserloot
- University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
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57
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Mitigation of evolved bacterial resistance to phage therapy. Curr Opin Virol 2022; 53:101201. [PMID: 35180532 DOI: 10.1016/j.coviro.2022.101201] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022]
Abstract
The ease with which bacteria can evolve resistance to phages is a key consideration for development of phage therapy. Here, we review recent work on the different evolutionary and ecological approaches to mitigate the problem. The approaches are broadly categorised into two areas: Minimising evolved phage resistance; and Directing phage-resistance evolution towards therapeutically beneficial outcomes.
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58
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Molina F, Menor-Flores M, Fernández L, Vega-Rodríguez MA, García P. Systematic analysis of putative phage-phage interactions on minimum-sized phage cocktails. Sci Rep 2022; 12:2458. [PMID: 35165352 PMCID: PMC8844382 DOI: 10.1038/s41598-022-06422-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
The application of bacteriophages as antibacterial agents has many benefits in the “post-antibiotic age”. To increase the number of successfully targeted bacterial strains, phage cocktails, instead of a single phage, are commonly formulated. Nevertheless, there is currently no consensus pipeline for phage cocktail development. Thus, although large cocktails increase the spectrum of activity, they could produce side effects such as the mobilization of virulence or antibiotic resistance genes. On the other hand, coinfection (simultaneous infection of one host cell by several phages) might reduce the potential for bacteria to evolve phage resistance, but some antagonistic interactions amongst phages might be detrimental for the outcome of phage cocktail application. With this in mind, we introduce here a new method, which considers the host range and each individual phage-host interaction, to design the phage mixtures that best suppress the target bacteria while minimizing the number of phages to restrict manufacturing costs. Additionally, putative phage-phage interactions in cocktails and phage-bacteria networks are compared as the understanding of the complex interactions amongst bacteriophages could be critical in the development of realistic phage therapy models in the future.
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59
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Würstle S, Stender J, Hammerl JA, Vogele K, Rothe K, Willy C, Bugert JJ. Practical Assessment of an Interdisciplinary Bacteriophage Delivery Pipeline for Personalized Therapy of Gram-Negative Bacterial Infections. Pharmaceuticals (Basel) 2022; 15:186. [PMID: 35215298 PMCID: PMC8879309 DOI: 10.3390/ph15020186] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/24/2022] Open
Abstract
Despite numerous advances in personalized phage therapy, smooth logistics are challenging, particularly for multidrug-resistant Gram-negative bacterial infections requiring high numbers of specific lytic phages. We conducted this study to pave the way for efficient logistics for critically ill patients by (1) closely examining and improving a current pipeline under realistic conditions, (2) offering guidelines for each step, leading to safe and high-quality phage supplies, and (3) providing a tool to evaluate the pipeline's efficiency. Due to varying stipulations for quality and safety in different countries, we focused the pipeline on all steps up to a required phage product by a cell-free extract system. The first of three study runs included patients with respiratory bacterial infections from four intensive care units, and it revealed a cumulative time of up to 23 days. Ultimately, adjustment of specific set points of the vulnerable components of the pipeline, phage isolation, and titration increased the pipeline's efficiency by 15% and decreased the maximum required time to 13 days. We present a site-independent practical approach to establish and optimize pipelines for personalized phage delivery, the co-organization of pipeline components between different institutions, non-binding guidelines for every step, and an efficiency check for phage laboratories.
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Affiliation(s)
- Silvia Würstle
- Department of Internal Medicine II, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Jana Stender
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany;
| | - Jens André Hammerl
- Unit Epidemiology, Zoonoses and Antimicrobial Resistances, Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | - Kilian Vogele
- Physics of Synthetic Biological Systems-E14, Physics-Department and ZNN, Technical University Munich, 85748 Munich, Germany;
| | - Kathrin Rothe
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
| | - Christian Willy
- Trauma & Orthopaedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Bundeswehr (Military) Academic Hospital Berlin, 10115 Berlin, Germany;
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Namonyo S, Carvalho G, Guo J, Weynberg KD. Novel Bacteriophages Show Activity against Selected Australian Clinical Strains of Pseudomonas aeruginosa. Microorganisms 2022; 10:microorganisms10020210. [PMID: 35208664 PMCID: PMC8875357 DOI: 10.3390/microorganisms10020210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Multi-drug resistant (MDR) clinical strains of Pseudomonas aeruginosa are the most prevalent bacteria in the lungs of patients with cystic fibrosis (CF) and burn wounds and among the most common in immunocompromised hospital patients in Australia. There are currently no promising antibiotics in the pipeline being developed against these strains. Phage therapy, which uses viruses known as bacteriophages to infect and kill pathogenic bacteria, could be a possible alternative treatment. To this end, we isolated and characterised four novel phages against Australian clinical strains of P. aeruginosa isolated from patients with cystic fibrosis, from infected blood and joint aspirate in Southeast Queensland, Australia. Activated sludge was enriched for phages using the clinical strains, and four bacteriophages were isolated. The phages were able to cause lysis in a further three identified clinical isolates. Morphology showed that they were all tailed phages (of the order Caudovirales), two belonging to the family Myoviridae and the others assigned to the Podoviridae and Siphoviridae. Their genomes were sequenced to reveal a doubled stranded DNA topology with genome sizes ranging from 42 kb to 65 kb. In isolating and characterising these novel phages, we directed our efforts toward the development and use of these phages as candidates for phage therapy as an alternative strategy for the management or elimination of these pathogenic strains. Here we describe novel phage candidates for potential therapeutic treatment of MDR Australian clinical isolates of P. aeruginosa.
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Affiliation(s)
- Samuel Namonyo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
- Queensland Alliance for Environmental Health Services, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Gilda Carvalho
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
- Correspondence: (G.C.); (K.D.W.)
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
| | - Karen D. Weynberg
- Australian Centre for Ecogenomics, School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: (G.C.); (K.D.W.)
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Onsea J, Post V, Buchholz T, Schwegler H, Zeiter S, Wagemans J, Pirnay JP, Merabishvili M, D’Este M, Rotman SG, Trampuz A, Verhofstad MHJ, Obremskey WT, Lavigne R, Richards RG, Moriarty TF, Metsemakers WJ. Bacteriophage Therapy for the Prevention and Treatment of Fracture-Related Infection Caused by Staphylococcus aureus: a Preclinical Study. Microbiol Spectr 2021; 9:e0173621. [PMID: 34908439 PMCID: PMC8672900 DOI: 10.1128/spectrum.01736-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022] Open
Abstract
Although several studies have shown promising clinical outcomes of phage therapy in patients with orthopedic device-related infections, questions remain regarding the optimal application protocol, systemic effects, and the impact of the immune response. This study provides a proof-of-concept of phage therapy in a clinically relevant rabbit model of fracture-related infection (FRI) caused by Staphylococcus aureus. In a prevention setting, phage in saline (without any biomaterial-based carrier) was highly effective in the prevention of FRI, compared to systemic antibiotic prophylaxis alone. In the subsequent study involving treatment of established infection, daily administration of phage in saline through a subcutaneous access tube was compared to a single intraoperative application of a phage-loaded hydrogel and a control group receiving antibiotics only. In this setting, although a possible trend of bacterial load reduction on the implant was observed with the phage-loaded hydrogel, no superior effect of phage therapy was found compared to antibiotic treatment alone. The application of phage in saline through a subcutaneous access tube was, however, complicated by superinfection and the development of neutralizing antibodies. The latter was not found in the animals that received the phage-loaded hydrogel, which may indicate that encapsulation of phages into a carrier such as a hydrogel limits their exposure to the adaptive immune system. These studies show phage therapy can be useful in targeting orthopedic device-related infection, however, further research and improvements of these application methods are required for this complex clinical setting. IMPORTANCE Because of the growing spread of antimicrobial resistance, the use of alternative prevention and treatment strategies is gaining interest. Although the therapeutic potential of bacteriophages has been demonstrated in a number of case reports and series over the past decade, many unanswered questions remain regarding the optimal application protocol. Furthermore, a major concern during phage therapy is the induction of phage neutralizing antibodies. This study aimed at providing a proof-of-concept of phage therapy in a clinically relevant rabbit model of fracture-related infection caused by Staphylococcus aureus. Phage therapy was applied as prophylaxis in a first phase, and as treatment of an established infection in a second phase. The development of phage neutralizing antibodies was evaluated in the treatment study. This study demonstrates that phage therapy can be useful in targeting orthopedic device-related infection, especially as prophylaxis; however, further research and improvements of these application methods are required.
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Affiliation(s)
- Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - 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
| | | | | | - Andrej Trampuz
- Center for Musculoskeletal Surgery, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Michael H. J. Verhofstad
- Trauma Research Unit Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - William T. Obremskey
- Department of Orthopaedic Surgery and Rehabilitation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | | | - Willem-Jan Metsemakers
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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Rosas NC, Lithgow T. Targeting bacterial outer-membrane remodelling to impact antimicrobial drug resistance. Trends Microbiol 2021; 30:544-552. [PMID: 34872824 DOI: 10.1016/j.tim.2021.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022]
Abstract
The cell envelope is essential for survival and adaptation of bacteria. Bacterial membrane proteins include the major porins that mediate the influx of nutrients and several classes of antimicrobial drugs. Consequently, membrane remodelling is closely linked to antimicrobial resistance (AMR). Knowledge of bacterial membrane protein biogenesis and turnover underpins our understanding of bacterial membrane remodelling and the consequences that this process have in the evolution of AMR phenotypes. At the population level, the evolution of phenotypes is a reversible process, and we can use these insights to deploy evolutionary principles to resensitize bacteria to existing antimicrobial drugs. In our opinion, fundamental knowledge is opening a new way of thinking towards sustainable solutions to the mounting crisis in AMR. Here we discuss what is known about outer-membrane remodelling in bacteria and how the process could be targeted as a means to restore sensitivity to antimicrobial drugs. Bacteriophages are highlighted as a powerful means to exert this control over membrane remodelling but they require careful selection so as to reverse, and not exacerbate, AMR phenotypes.
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Affiliation(s)
- Natalia C Rosas
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia.
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Wang X, Loh B, Altamirano FG, Yu Y, Hua X, Leptihn S. Colistin- phage combinations decrease antibiotic resistance in A. baumannii via changes in envelope architecture. Emerg Microbes Infect 2021; 10:2205-2219. [PMID: 34736365 PMCID: PMC8648044 DOI: 10.1080/22221751.2021.2002671] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Multidrug-resistant bacterial infections are becoming increasingly common, with only few last-resort antibiotics such as colistin available for clinical therapy. An alternative therapeutic strategy gaining momentum is phage therapy, which has the advantage of not being affected by bacterial resistance to antibiotics. However, a major challenge in phage therapy is the rapid emergence of phage-resistant bacteria. In this work, our main aim was to understand the mechanisms of phage-resistance used by the top priority pathogen Acinetobacter baumannii. We isolated the novel phage Phab24, capable of infecting colistin-sensitive and -resistant strains of A. baumannii. After co-incubating Phab24 with its hosts, we obtained phage-resistant mutants which were characterized on both genotypic and phenotypic levels. Using whole genome sequencing, we identified phage-resistant strains that displayed mutations in genes that alter the architecture of the bacterial envelope at two levels: the capsule and the outer membrane. Using an adsorption assay, we confirmed that phage Phab24 uses the bacterial capsule as its primary receptor, with the outer membrane possibly serving as the secondary receptor. Interestingly, the phage-resistant isolates were less virulent compared to the parental strains in a Galleria mellonella infection model. Most importantly, we observed that phage-resistant bacteria that evolved in the absence of antibiotics exhibited an increased sensitivity to colistin, even though the antibiotic resistance mechanism per se remained unaltered. This increase in antibiotic sensitivity is a direct consequence of the phage-resistance mechanism, and could potentially be exploited in the clinical setting.
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Affiliation(s)
- Xiaoqing Wang
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, Haining, China.,Medical school, Lishui University, Lishui, China
| | | | - Fernando Gordillo Altamirano
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, Haining, China.,Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China .,University of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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64
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Loose M, Sáez Moreno D, Mutti M, Hitzenhammer E, Visram Z, Dippel D, Schertler S, Tišáková LP, Wittmann J, Corsini L, Wagenlehner F. Natural Bred ε 2-Phages Have an Improved Host Range and Virulence against Uropathogenic Escherichia coli over Their Ancestor Phages. Antibiotics (Basel) 2021; 10:1337. [PMID: 34827275 PMCID: PMC8614997 DOI: 10.3390/antibiotics10111337] [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: 08/30/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 12/22/2022] Open
Abstract
Alternative treatments for Escherichia coli infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 E. coli strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of E. coli strains. The bred phages, which we termed evolution-squared ε2-phages, of a mixture of Myoviridae have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, Myoviridae ε2-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε2-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε2-phages with the broadest host range reveals that they are mosaic intercrossings of 2-3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε2-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε2-phages are remarkably more suitable than the wild-type phages for phage therapy.
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Affiliation(s)
- Maria Loose
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
| | - David Sáez Moreno
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Michele Mutti
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Eva Hitzenhammer
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Zehra Visram
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - David Dippel
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
| | - Susanne Schertler
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Lenka Podpera Tišáková
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Johannes Wittmann
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Lorenzo Corsini
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Florian Wagenlehner
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
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65
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Arbatsky NP, Popova AV, Shneider MM, Shashkov AS, Hall RM, Kenyon JJ, Knirel YA. Structure of the K87 capsular polysaccharide and KL87 gene cluster of Acinetobacter baumannii LUH5547 reveals a heptasaccharide repeating unit. Carbohydr Res 2021; 509:108439. [PMID: 34555685 DOI: 10.1016/j.carres.2021.108439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022]
Abstract
K87 capsular polysaccharide (CPS) was isolated from Acinetobacter baumannii isolate LUH5547 that carries the KL87 capsule biosynthesis gene cluster at the chromosomal K locus. Studies by sugar analysis, selective chemical cleavages, and 1D and 2D 1H and 13C NMR spectroscopy showed that the CPS has a branched heptasaccharide repeat (K unit) containing one residue each of d-glucose (d-Glсp), d-glucuronic acid (d-GlсpA), N-acetyl-d-glucosamine (d-GlсpNAc), 6-deoxy-l-talose (l-6dTalp), and three residues of l-rhamnose (l-Rhap). The following structure of the CPS was established: →3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-6dTalp-(1→3)-β-D-GlcpNAc-(1→2↑1β-D-GlcpA-(4←1)-α-D-Glcp(2←1)-α-L-Rhap The position of a minor O-acetyl group present in the CPS was not determined. Functions of enzymes coded by genes in the KL87 gene cluster were tentatively assigned and found to be consistent with the CPS structure.
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Affiliation(s)
- Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V Popova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology. Brisbane, Australia.
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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66
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Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
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67
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Kenyon JJ, Kasimova AA, Sviridova AN, Shpirt AM, Shneider MM, Mikhaylova YV, Shelenkov AA, Popova AV, Perepelov AV, Shashkov AS, Dmitrenok AS, Chizov AO, Knirel YA. Correlation of Acinetobacter baumannii K144 and K86 capsular polysaccharide structures with genes at the K locus reveals the involvement of a novel multifunctional rhamnosyltransferase for structural synthesis. Int J Biol Macromol 2021; 193:1294-1300. [PMID: 34757131 DOI: 10.1016/j.ijbiomac.2021.10.178] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/24/2021] [Indexed: 10/19/2022]
Abstract
Whole genome sequence from Acinetobacter baumannii isolate Ab-46-1632 reveals a novel KL144 capsular polysaccharide (CPS) biosynthesis gene cluster, which carries genes for d-glucuronic acid (D-GlcA) and l-rhamnose (l-Rha) synthesis. The CPS was extracted from Ab-46-1632 and studied by 1H and 13C NMR spectroscopy, including a two-dimensional 1H,13C HMBC experiment and Smith degradation. The CPS was found to have a hexasaccharide repeat unit composed of four l-Rhap residues and one residue each of d-GlcpA and N-acetyl-d-glucosamine (D-GlcpNAc) consistent with sugar synthesis genes present in KL144. The K144 CPS structure was established and found to be related to those of A. baumannii K55, K74, K85, and K86. A comparison of the corresponding gene clusters to KL144 revealed a number of shared glycosyltransferase genes correlating to shared glycosidic linkages in the structures. One from the enzymes, encoded by only KL144 and KL86, is proposed to be a novel multifunctional rhamnosyltransfaerase likely responsible for synthesis of a shared α-l-Rhap-(1 → 2)-α-L-Rhap-(1 → 3)-L-Rhap trisaccharide fragment in the K144 and K86 structures.
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Affiliation(s)
- Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology. Brisbane, Australia
| | - Anastasiya A Kasimova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | | | - Anna M Shpirt
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia.
| | - Mikhail M Shneider
- M.M. Shemyakin and Y.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | | | | | - Anastasiya V Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow, Region, Russia
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Andrei S Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Alexander O Chizov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
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68
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Affiliation(s)
- Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
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69
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The Potential of Phage Therapy against the Emerging Opportunistic Pathogen Stenotrophomonas maltophilia. Viruses 2021; 13:v13061057. [PMID: 34204897 PMCID: PMC8228603 DOI: 10.3390/v13061057] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
The isolation and characterization of bacteriophages for the treatment of infections caused by the multidrug resistant pathogen Stenotrophomonas maltophilia is imperative as nosocomial and community-acquired infections are rapidly increasing in prevalence. This increase is largely due to the numerous virulence factors and antimicrobial resistance genes encoded by this bacterium. Research on S. maltophilia phages to date has focused on the isolation and in vitro characterization of novel phages, often including genomic characterization, from the environment or by induction from bacterial strains. This review summarizes the clinical significance, virulence factors, and antimicrobial resistance mechanisms of S. maltophilia, as well as all phages isolated and characterized to date and strategies for their use. We further address the limited in vivo phage therapy studies conducted against this bacterium and discuss the future research needed to spearhead phages as an alternative treatment option against multidrug resistant S. maltophilia.
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70
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Holger D, Kebriaei R, Morrisette T, Lev K, Alexander J, Rybak M. Clinical Pharmacology of Bacteriophage Therapy: A Focus on Multidrug-Resistant Pseudomonas aeruginosa Infections. Antibiotics (Basel) 2021; 10:556. [PMID: 34064648 PMCID: PMC8151982 DOI: 10.3390/antibiotics10050556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most common causes of healthcare-associated diseases and is among the top three priority pathogens listed by the World Health Organization (WHO). This Gram-negative pathogen is especially difficult to eradicate because it displays high intrinsic and acquired resistance to many antibiotics. In addition, growing concerns regarding the scarcity of antibiotics against multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa infections necessitate alternative therapies. Bacteriophages, or phages, are viruses that target and infect bacterial cells, and they represent a promising candidate for combatting MDR infections. The aim of this review was to highlight the clinical pharmacology considerations of phage therapy, such as pharmacokinetics, formulation, and dosing, while addressing several challenges associated with phage therapeutics for MDR P. aeruginosa infections. Further studies assessing phage pharmacokinetics and pharmacodynamics will help to guide interested clinicians and phage researchers towards greater success with phage therapy for MDR P. aeruginosa infections.
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Affiliation(s)
- Dana Holger
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; (D.H.); (R.K.); (T.M.); (K.L.)
| | - Razieh Kebriaei
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; (D.H.); (R.K.); (T.M.); (K.L.)
| | - Taylor Morrisette
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; (D.H.); (R.K.); (T.M.); (K.L.)
| | - Katherine Lev
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; (D.H.); (R.K.); (T.M.); (K.L.)
| | - Jose Alexander
- Department of Microbiology, Virology and Immunology, AdventHealth Central Florida, Orlando, FL 32803, USA;
| | - Michael Rybak
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; (D.H.); (R.K.); (T.M.); (K.L.)
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- Detroit Medical Center, Department of Pharmacy, Detroit, MI 48201, USA
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71
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Goswami A, Sharma PR, Agarwal R. Combatting intracellular pathogens using bacteriophage delivery. Crit Rev Microbiol 2021; 47:461-478. [PMID: 33818246 DOI: 10.1080/1040841x.2021.1902266] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Intracellular pathogens reside in specialised compartments within the host cells restricting the access of antibiotics. Insufficient intracellular delivery of antibiotics along with several other resistance mechanisms weaken the efficacy of current therapies. An alternative to antibiotic therapy could be bacteriophage (phage) therapy. Although phage therapy has been in practice for a century against various bacterial infections, the efficacy of phages against intracellular bacteria is still being explored. In this review, we will discuss the advancement and challenges in phage therapy, particularly against intracellular bacterial pathogens. Finally, we will highlight the uptake mechanisms and approaches to overcome the challenges to phage therapy against intracellular bacteria.
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Affiliation(s)
- Avijit Goswami
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Pallavi Raj Sharma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rachit Agarwal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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72
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Niu YD, Liu H, Du H, Meng R, Sayed Mahmoud E, Wang G, McAllister TA, Stanford K. Efficacy of Individual Bacteriophages Does Not Predict Efficacy of Bacteriophage Cocktails for Control of Escherichia coli O157. Front Microbiol 2021; 12:616712. [PMID: 33717006 PMCID: PMC7943454 DOI: 10.3389/fmicb.2021.616712] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/18/2021] [Indexed: 01/21/2023] Open
Abstract
Effectiveness of bacteriophages AKFV33 (Tequintavirus, T5) and AHP24 (Rogunavirus, T1), wV7 (Tequatrovirus, T4), and AHP24S (Vequintavirus, rV5), as well as 11 cocktails of combinations of the four phages, were evaluated in vitro for biocontrol of six common phage types of Escherichia coli O157 (human and bovine origins) at different multiplicities of infection (MOIs; 0.01–1,000), temperatures (37 or 22°C), and exposure times (10–22 h). Phage efficacy against O157 was highest at MOI 1,000 (P < 0.001) and after 14-18 h of exposure at 22°C (P < 0.001). The activity of individual phages against O157 did not predict the activity of a cocktail of these phages even at the same temperature and MOI. Combinations of phages were neutral (no better or worse than the most effective constituent phages acting alone), displayed facilitation (greater efficacy than the most effective constituent phages acting alone), or antagonistic (lower efficacy than the most effective constituent phages acting alone). Across MOIs, temperatures, exposure time, and O157 strains, a cocktail of T1, T4, and rV5 was most effective (P < 0.05) against O157, although T1 and rV5 were less effective (P < 0.001) than other individual phages. T5 was the most effective individual phages (P < 0.05), but was antagonistic to other phages, particularly rV5 and T4 + rV5. Interactions among phages were influenced by phage genera and phage combination, O157 strains, MOIs, incubation temperatures, and times. Based on this study, future development of phage cocktails should, as a minimum, include confirmation of a lack of antagonism among constituent phages and preferably confirmation of facilitation or synergistic effects.
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Affiliation(s)
- Yan D Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hui Liu
- Hohhot Bureau of Ecology and Environment, Hohhot, China.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Hechao Du
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.,College of Animal Science and Technology, Jinling Institute of Technology, Nanjing, China
| | - Ruiqiang Meng
- Inner Mongolia C. P. Livestock Husbandry Co., Ltd., Hohhot, China
| | - El Sayed Mahmoud
- School of Applied Computing, Faculty of Applied Science and Technology, Sheridan College, Oakville, ON, Canada
| | - Guihua Wang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kim Stanford
- Department of Biological Science, University of Lethbridge, Lethbridge, AB, Canada
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