1
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Asgharzadeh Kangachar S, Logel DY, Trofimova E, Zhu HX, Zaugg J, Schembri MA, Weynberg KD, Jaschke PR. Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology 2024; 597:110148. [PMID: 38941748 DOI: 10.1016/j.virol.2024.110148] [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: 01/31/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Antimicrobial resistance is an escalating threat with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are prone to becoming recurrent and antibiotic resistant. We discovered and characterized six novel Autographiviridae and Guernseyvirinae bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), a leading cause of UTIs. The phage genomes were between 39,471 bp - 45,233 bp, with 45.0%-51.0% GC%, and 57-84 predicted coding sequences per genome. We show that tail fiber domain structure, predicted host capsule type, and host antiphage repertoire correlate with phage host range. In vitro characterisation of phage cocktails showed synergistic improvement against a mixed UPEC strain population and when sequentially dosed. Together, these phage are a new set extending available treatments for UTI from UPEC, and phage vM_EcoM_SHAK9454 represents a promising candidate for further improvement through engineering.
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Affiliation(s)
- Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Queensland, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Karen D Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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2
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Dave R, Banerjee D. Bacteriophage therapy- a refurbished age-old potential strategy to treat antibiotic and multidrug resistant bacterial infections in future. Braz J Microbiol 2024:10.1007/s42770-024-01434-7. [PMID: 38951476 DOI: 10.1007/s42770-024-01434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
The worldwide prevalence of antimicrobial resistance coupled with the unavailability of newer antibiotics, has brought the sharp focus back among the scientific community, towards the discovery of novel alternative therapeutics to tackle the menace. Consequently, in the current post-antibiotic era, 'Bacteriophage Therapy' has emerged as one of the most promising option to address this problem. Bacteriophages, actually discovered long back, has shown greater potential to kill various bacterial pathogens, including the resistant clinical ones. Some of the other advantages for the use of bacteriophage therapy to treat infectious diseases include, wider availability of these microorganisms in nature, host-specific action, absence of any significant side-effects in humans and most often also exhibiting a broader anti-bacterial potential. In the recent times, the potential of phage therapy has been demonstrated in various treatments, clinical trials and infection models across the globe, where even antibiotics have completely failed. To address the global threat of AMR, WHO and UN have jointly illustrated "One Health" approach, recently extending the context to bacteriophage therapy. Many pharmaceutical companies have also recently started employing bacteriophages for developing different kinds of formulations for catering to medical and other industries. It has even shown great effect as combinatorial therapy along with antibiotics, to treat or manage various critical antibiotic resistant clinical infections. This continuously expanding potential of the bacteriophages holds great promise in the future, in the fight against the rising threat of AMR globally.
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Affiliation(s)
- Rajal Dave
- Department of Microbiology, Faculty of Science, Atmiya University, "Yogidham Gurukul", Kalawad Road, Rajkot, 360005, Gujarat, India
| | - Debashis Banerjee
- Dept. Of Biotechnology, Faculty of Science, Atmiya University, "Yogidham Gurukul", Kalawad Road, Rajkot, 360005, Gujarat, India.
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3
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Hourigan D, Stefanovic E, Hill C, Ross RP. Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol 2024; 24:103. [PMID: 38539119 PMCID: PMC10976773 DOI: 10.1186/s12866-024-03243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Affiliation(s)
- David Hourigan
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - Ewelina Stefanovic
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland.
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland.
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland.
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4
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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5
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Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, Whitehead N, Soothill J, Michell S, Temperton B. The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK. Microorganisms 2024; 12:253. [PMID: 38399657 PMCID: PMC10893117 DOI: 10.3390/microorganisms12020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
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Affiliation(s)
- Julie Fletcher
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Robyn Manley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christian Fitch
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christina Bugert
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Michelle Michelsen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Shayma Alathari
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Nicola Senior
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Alice Mills
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - Natalie Whitehead
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - James Soothill
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - Stephen Michell
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Ben Temperton
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
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6
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Piya D, Nolan N, Moore ML, Ramirez Hernandez LA, Cress BF, Young R, Arkin AP, Mutalik VK. Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages. PLoS Biol 2023; 21:e3002416. [PMID: 38048319 PMCID: PMC10695390 DOI: 10.1371/journal.pbio.3002416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023] Open
Abstract
Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.
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Affiliation(s)
- Denish Piya
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
| | - Nicholas Nolan
- Department of Bioengineering, University of California-Berkeley, Berkeley, California, United States of America
| | - Madeline L. Moore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luis A. Ramirez Hernandez
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Brady F. Cress
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California, United States of America
| | - Ry Young
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
| | - Adam P. Arkin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California-Berkeley, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Vivek K. Mutalik
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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7
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Usman SS, Uba AI, Christina E. Bacteriophage genome engineering for phage therapy to combat bacterial antimicrobial resistance as an alternative to antibiotics. Mol Biol Rep 2023; 50:7055-7067. [PMID: 37392288 DOI: 10.1007/s11033-023-08557-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Bacteriophages (phages) are viruses that mainly infect bacteria and are ubiquitously distributed in nature, especially to their host. Phage engineering involves nucleic acids manipulation of phage genome for antimicrobial activity directed against pathogens through the applications of molecular biology techniques such as synthetic biology methods, homologous recombination, CRISPY-BRED and CRISPY-BRIP recombineering, rebooting phage-based engineering, and targeted nucleases including CRISPR/Cas9, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Management of bacteria is widely achieved using antibiotics whose mechanism of action has been shown to target both the genetic dogma and the metabolism of pathogens. However, the overuse of antibiotics has caused the emergence of multidrug-resistant (MDR) bacteria which account for nearly 5 million deaths as of 2019 thereby posing threats to the public health sector, particularly by 2050. Lytic phages have drawn attention as a strong alternative to antibiotics owing to the promising efficacy and safety of phage therapy in various models in vivo and human studies. Therefore, harnessing phage genome engineering methods, particularly CRISPR/Cas9 to overcome the limitations such as phage narrow host range, phage resistance or any potential eukaryotic immune response for phage-based enzymes/proteins therapy may designate phage therapy as a strong alternative to antibiotics for combatting bacterial antimicrobial resistance (AMR). Here, the current trends and progress in phage genome engineering techniques and phage therapy are reviewed.
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Affiliation(s)
- Sani Sharif Usman
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144401, Punjab, India
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, 34537, Istanbul, Türkiye
| | - Evangeline Christina
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144401, Punjab, India.
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8
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Nir-Paz R, Kuijper EJ. Bacteriophage therapy in humans. Clin Microbiol Infect 2023:S1198-743X(23)00125-8. [PMID: 36914071 DOI: 10.1016/j.cmi.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 03/15/2023]
Affiliation(s)
- Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center and the Hebrew University of Jerusalem, Israel.
| | - Ed J Kuijper
- Department of Medical Microbiology, Center for Microbiota Analysis and Therapeutics Leiden University Medical Center, the Netherlands
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9
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Huss P, Chen J, Raman S. High-throughput approaches to understand and engineer bacteriophages. Trends Biochem Sci 2023; 48:187-197. [PMID: 36180320 PMCID: PMC9868059 DOI: 10.1016/j.tibs.2022.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Bacteriophage research has been vital to fundamental aspects of modern biology. Advances in metagenomics have revealed treasure troves of new and uncharacterized bacteriophages ('phages') that are not yet understood. However, our ability to find new phages has outpaced our understanding of how sequence encodes function in phages. Traditional approaches for characterizing phages are limited in scale and face hurdles in determining how changes in sequence drive function. We describe powerful emerging technologies that can be used to clarify sequence-function relationships in phages through high-throughput genome engineering. Using these approaches, up to 105 variants can be characterized through pooled selection experiments and deep sequencing. We describe caveats when using these tools and provide examples of basic science and engineering goals that are pursuable using these approaches.
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Affiliation(s)
- Phil Huss
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jackie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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10
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 135.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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11
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Shaidullina A, Harms A. Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions. Curr Opin Microbiol 2022; 70:102225. [PMID: 36327691 DOI: 10.1016/j.mib.2022.102225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 01/25/2023]
Abstract
Bacteriophages are abundant and diverse predators that drive community dynamics in many ecosystems and hold great potential for biotechnology and as therapeutics for bacterial infections. Previous research has largely explored phage-host interactions one-by-one, which limited our ability to observe phenotypic patterns, to uncover their genetic basis, and to unravel the underlying molecular mechanisms. However, the famous 'toothpicks and logic' were recently joined by large-scale sequencing of phage genomes and bacterial genome-wide screens that enable us to systematically investigate phage-host interactions. In this article, we highlight recent breakthroughs from the molecular basis of phage host range and receptor recognition over new insights into bacterial immunity to the serendipitous discovery of a new bacterial surface glycan. Future work will enable the understanding, prediction, and engineering of more complicated phage traits for new applications and extend the scope of these studies from simple test tube experiments to natural communities of phages and hosts.
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12
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Liyanagedera SBW, Williams J, Wheatley JP, Biketova AY, Hasan M, Sagona AP, Purdy KJ, Puxty RJ, Feher T, Kulkarni V. SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies. ACS Synth Biol 2022; 11:3330-3342. [PMID: 36194543 DOI: 10.1021/acssynbio.2c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The past decade has seen the emergence of multidrug resistant pathogens as a leading cause of death worldwide, reigniting interest in the field of phage therapy. Modern advances in the genetic engineering of bacteriophages have enabled several useful results including host range alterations, constitutive lytic growth, and control over phage replication. However, the slow licensing process of genetically modified organisms clearly inhibits the rapid therapeutic application of novel engineered variants necessary to fight mutant pathogens that emerge throughout the course of a pandemic. As a solution to this problem, we propose the SpyPhage system where a "scaffold" bacteriophage is engineered to incorporate a SpyTag moiety on its capsid head to enable rapid postsynthetic modification of their surfaces with SpyCatcher-fused therapeutic proteins. As a proof of concept, through CRISPR/Cas-facilitated phage engineering and whole genome assembly, we targeted a SpyTag capsid fusion to K1F, a phage targeting the pathogenic strain Escherichia coli K1. We demonstrate for the first time the cell-free assembly and decoration of the phage surface with two alternative fusion proteins, SpyCatcher-mCherry-EGF and SpyCatcher-mCherry-Rck, both of which facilitate the endocytotic uptake of the phages by a urinary bladder epithelial cell line. Overall, our work presents a cell-free phage production pipeline for the generation of multiple phenotypically distinct phages with a single underlying "scaffold" genotype. These phages could become the basis of next-generation phage therapies where the knowledge-based engineering of numerous phage variants would be quickly achievable without the use of live bacteria or the need to repeatedly license novel genetic alterations.
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Affiliation(s)
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Joseph P Wheatley
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alona Yu Biketova
- Institute of Biochemistry, Eötvös Lóránd Research Network, Szeged Biological Research Centre, Szeged 6726, Hungary.,Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Muhammad Hasan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tamas Feher
- Institute of Biochemistry, Eötvös Lóránd Research Network, Szeged Biological Research Centre, Szeged 6726, Hungary
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13
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Serwer P. A Perspective on Studies of Phage DNA Packaging Dynamics. Int J Mol Sci 2022; 23:ijms23147854. [PMID: 35887200 PMCID: PMC9324371 DOI: 10.3390/ijms23147854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/05/2022] Open
Abstract
The Special Issue “DNA Packaging Dynamics of Bacteriophages” is focused on an event that is among the physically simplest known events with biological character. Thus, phage DNA (and RNA) packaging is used as a relatively accessible model for physical analysis of all biological events. A similar perspective motivated early phage-directed work, which was a major contributor to early molecular biology. However, analysis of DNA packaging encounters the limitation that phages vary in difficulty of observing various aspects of their packaging. If a difficult-to-access aspect arises while using a well-studied phage, a counterstrategy is to (1) look for and use phages that provide a better access “window” and (2) integrate multi-phage-accessed information with the help of chemistry and physics. The assumption is that all phages are characterized by the same evolution-derived themes, although with variations. Universal principles will emerge from the themes. A spin-off of using this strategy is the isolation and characterization of the diverse phages needed for biomedicine. Below, I give examples in the areas of infectious disease, cancer, and neurodegenerative disease.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Center at San Antonio, San Antonio, TX 78229, USA
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