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Dharmaraj T, Kratochvil MJ, Pourtois JD, Chen Q, Hajfathalian M, Hargil A, Lin YH, Evans Z, Oromí-Bosch A, Berry JD, McBride R, Haddock NL, Holman DR, van Belleghem JD, Chang TH, Barr JJ, Lavigne R, Heilshorn SC, Blankenberg FG, Bollyky PL. Rapid assessment of changes in phage bioactivity using dynamic light scattering. PNAS NEXUS 2023; 2:pgad406. [PMID: 38111822 PMCID: PMC10726995 DOI: 10.1093/pnasnexus/pgad406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/02/2023] [Indexed: 12/20/2023]
Abstract
Extensive efforts are underway to develop bacteriophages as therapies against antibiotic-resistant bacteria. However, these efforts are confounded by the instability of phage preparations and a lack of suitable tools to assess active phage concentrations over time. In this study, we use dynamic light scattering (DLS) to measure changes in phage physical state in response to environmental factors and time, finding that phages tend to decay and form aggregates and that the degree of aggregation can be used to predict phage bioactivity. We then use DLS to optimize phage storage conditions for phages from human clinical trials, predict bioactivity in 50-y-old archival stocks, and evaluate phage samples for use in a phage therapy/wound infection model. We also provide a web application (Phage-Estimator of Lytic Function) to facilitate DLS studies of phages. We conclude that DLS provides a rapid, convenient, and nondestructive tool for quality control of phage preparations in academic and commercial settings.
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Affiliation(s)
- Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael J Kratochvil
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Julie D Pourtois
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Aviv Hargil
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Yung-Hao Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Zoe Evans
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | | | - Joel D Berry
- Felix Biotechnology, South SanFrancisco, CA 94080, USA
| | | | - Naomi L Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Derek R Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonas D van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Tony H Chang
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
| | - Sarah C Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Francis G Blankenberg
- Division of Pediatric Radiology and Nuclear Medicine, Department of Radiology, Lucile Packard Children's Hospital, Stanford, CA 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center for Molecular and Genetic Medicine, Stanford, CA 94305, USA
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Dharmaraj T, Kratochvil MJ, Pourtois JD, Chen Q, Hajfathalian M, Hargil A, Lin YH, Evans Z, Oromí-Bosch A, Berry JD, McBride R, Haddock NL, Holman DR, van Belleghem JD, Chang TH, Barr JJ, Lavigne R, Heilshorn SC, Blankenberg FG, Bollyky PL. Rapid assessment of changes in phage bioactivity using dynamic light scattering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547396. [PMID: 37425882 PMCID: PMC10327207 DOI: 10.1101/2023.07.02.547396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Extensive efforts are underway to develop bacteriophages as therapies against antibiotic-resistant bacteria. However, these efforts are confounded by the instability of phage preparations and a lack of suitable tools to assess active phage concentrations over time. Here, we use Dynamic Light Scattering (DLS) to measure changes in phage physical state in response to environmental factors and time, finding that phages tend to decay and form aggregates and that the degree of aggregation can be used to predict phage bioactivity. We then use DLS to optimize phage storage conditions for phages from human clinical trials, predict bioactivity in 50-year-old archival stocks, and evaluate phage samples for use in a phage therapy/wound infection model. We also provide a web-application (Phage-ELF) to facilitate DLS studies of phages. We conclude that DLS provides a rapid, convenient, and non-destructive tool for quality control of phage preparations in academic and commercial settings.
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Affiliation(s)
- Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael J. Kratochvil
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305
| | - Julie D. Pourtois
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aviv Hargil
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yung-Hao Lin
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Zoe Evans
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Derek R. Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonas D. van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tony H. Chang
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeremy J. Barr
- School of Biological Sciences, Monash University, Clayton, 3800, VIC, Australia
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Sarah C. Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305
| | - Francis G. Blankenberg
- Division of Pediatric Radiology and Nuclear Medicine, Department of Radiology, Lucile Packard Children’s Hospital, Stanford, CA 94305, USA
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Bleriot I, Blasco L, Pacios O, Fernández-García L, López M, Ortiz-Cartagena C, Barrio-Pujante A, Fernández-Cuenca F, Pascual Á, Martínez-Martínez L, Oteo-Iglesias J, Tomás M. Proteomic Study of the Interactions between Phages and the Bacterial Host Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0397422. [PMID: 36877024 PMCID: PMC10100988 DOI: 10.1128/spectrum.03974-22] [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: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Phages and bacteria have acquired resistance mechanisms for protection. In this context, the aims of the present study were to analyze the proteins isolated from 21 novel lytic phages of Klebsiella pneumoniae in search of defense mechanisms against bacteria and also to determine the infective capacity of the phages. A proteomic study was also conducted to investigate the defense mechanisms of two clinical isolates of K. pneumoniae infected by phages. For this purpose, the 21 lytic phages were sequenced and de novo assembled. The host range was determined in a collection of 47 clinical isolates of K. pneumoniae, revealing the variable infective capacity of the phages. Genome sequencing showed that all of the phages were lytic phages belonging to the order Caudovirales. Phage sequence analysis revealed that the proteins were organized in functional modules within the genome. Although most of the proteins have unknown functions, multiple proteins were associated with defense mechanisms against bacteria, including the restriction-modification system, the toxin-antitoxin system, evasion of DNA degradation, blocking of host restriction and modification, the orphan CRISPR-Cas system, and the anti-CRISPR system. Proteomic study of the phage-host interactions (i.e., between isolates K3574 and K3320, which have intact CRISPR-Cas systems, and phages vB_KpnS-VAC35 and vB_KpnM-VAC36, respectively) revealed the presence of several defense mechanisms against phage infection (prophage, defense/virulence/resistance, oxidative stress and plasmid proteins) in the bacteria, and of the Acr candidate (anti-CRISPR protein) in the phages. IMPORTANCE Researchers, including microbiologists and infectious disease specialists, require more knowledge about the interactions between phages and their bacterial hosts and about their defense mechanisms. In this study, we analyzed the molecular mechanisms of viral and bacterial defense in phages infecting clinical isolates of K. pneumoniae. Viral defense mechanisms included restriction-modification system evasion, the toxin-antitoxin (TA) system, DNA degradation evasion, blocking of host restriction and modification, and resistance to the abortive infection system, anti-CRISPR and CRISPR-Cas systems. Regarding bacterial defense mechanisms, proteomic analysis revealed expression of proteins involved in the prophage (FtsH protease modulator), plasmid (cupin phosphomannose isomerase protein), defense/virulence/resistance (porins, efflux pumps, lipopolysaccharide, pilus elements, quorum network proteins, TA systems, and methyltransferases), oxidative stress mechanisms, and Acr candidates (anti-CRISPR protein). The findings reveal some important molecular mechanisms involved in the phage-host bacterial interactions; however, further study in this field is required to improve the efficacy of phage therapy.
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Affiliation(s)
- Inés Bleriot
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Olga Pacios
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Laura Fernández-García
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Concha Ortiz-Cartagena
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Antonio Barrio-Pujante
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Felipe Fernández-Cuenca
- Clinical Unit of Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville (University Hospital Virgen Macarena/CSIC/University of Seville), Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Pascual
- Clinical Unit of Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville (University Hospital Virgen Macarena/CSIC/University of Seville), Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Clinical Unit of Microbiology, Reina Sofía University Hospital, Department of Agricultural Chemistry, Edaphology and Microbiology, University of Cordoba, Maimonides Biomedical Research Institute (IMIBIC), Cordoba, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
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