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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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Kelly A, Went SC, Mariano G, Shaw LP, Picton DM, Duffner SJ, Coates I, Herdman-Grant R, Gordeeva J, Drobiazko A, Isaev A, Lee YJ, Luyten Y, Morgan RD, Weigele P, Severinov K, Wenner N, Hinton JCD, Blower TR. Diverse Durham collection phages demonstrate complex BREX defense responses. Appl Environ Microbiol 2023; 89:e0062323. [PMID: 37668405 PMCID: PMC10537673 DOI: 10.1128/aem.00623-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023] Open
Abstract
Bacteriophages (phages) outnumber bacteria ten-to-one and cause infections at a rate of 1025 per second. The ability of phages to reduce bacterial populations makes them attractive alternative antibacterials for use in combating the rise in antimicrobial resistance. This effort may be hindered due to bacterial defenses such as Bacteriophage Exclusion (BREX) that have arisen from the constant evolutionary battle between bacteria and phages. For phages to be widely accepted as therapeutics in Western medicine, more must be understood about bacteria-phage interactions and the outcomes of bacterial phage defense. Here, we present the annotated genomes of 12 novel bacteriophage species isolated from water sources in Durham, UK, during undergraduate practical classes. The collection includes diverse species from across known phylogenetic groups. Comparative analyses of two novel phages from the collection suggest they may be founding members of a new genus. Using this Durham phage collection, we determined that particular BREX defense systems were likely to confer a varied degree of resistance against an invading phage. We concluded that the number of BREX target motifs encoded in the phage genome was not proportional to the degree of susceptibility. IMPORTANCE Bacteriophages have long been the source of tools for biotechnology that are in everyday use in molecular biology research laboratories worldwide. Phages make attractive new targets for the development of novel antimicrobials. While the number of phage genome depositions has increased in recent years, the expected bacteriophage diversity remains underrepresented. Here we demonstrate how undergraduates can contribute to the identification of novel phages and that a single City in England can provide ample phage diversity and the opportunity to find novel technologies. Moreover, we demonstrate that the interactions and intricacies of the interplay between bacterial phage defense systems such as Bacteriophage Exclusion (BREX) and phages are more complex than originally thought. Further work will be required in the field before the dynamic interactions between phages and bacterial defense systems are fully understood and integrated with novel phage therapies.
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Affiliation(s)
- Abigail Kelly
- Department of Biosciences, Durham University, Durham, UK
| | - Sam C. Went
- Department of Biosciences, Durham University, Durham, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Liam P. Shaw
- Department of Biosciences, Durham University, Durham, UK
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Isabel Coates
- Department of Biosciences, Durham University, Durham, UK
| | | | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yan-Jiun Lee
- New England Biolabs, Ipswich, Massachusetts, USA
| | | | | | | | | | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R. Blower
- Department of Biosciences, Durham University, Durham, UK
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