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Attrill EL, Łapińska U, Westra ER, Harding SV, Pagliara S. Slow growing bacteria survive bacteriophage in isolation. ISME COMMUNICATIONS 2023; 3:95. [PMID: 37684358 PMCID: PMC10491631 DOI: 10.1038/s43705-023-00299-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The interactions between bacteria and bacteriophage have important roles in the global ecosystem; in turn changes in environmental parameters affect the interactions between bacteria and phage. However, there is a lack of knowledge on whether clonal bacterial populations harbour different phenotypes that respond to phage in distinct ways and whether the abundance of such phenotypes within bacterial populations is affected by variations in environmental parameters. Here we study the impact of variations in nutrient availability, bacterial growth rate and phage abundance on the interactions between the phage T4 and individual Escherichia coli cells confined in spatial refuges. Surprisingly, we found that fast growing bacteria survive together with all of their clonal kin cells, whereas slow growing bacteria survive in isolation. We also discovered that the number of bacteria that survive in isolation decreases at increasing phage doses possibly due to lysis inhibition in the presence of secondary adsorptions. We further show that these changes in the phenotypic composition of the E. coli population have important consequences on the bacterial and phage population dynamics and should therefore be considered when investigating bacteria-phage interactions in ecological, health or food production settings in structured environments.
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Affiliation(s)
- Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK.
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Attrill EL, Claydon R, Łapińska U, Recker M, Meaden S, Brown AT, Westra ER, Harding SV, Pagliara S. Individual bacteria in structured environments rely on phenotypic resistance to phage. PLoS Biol 2021; 19:e3001406. [PMID: 34637438 PMCID: PMC8509860 DOI: 10.1371/journal.pbio.3001406] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages represent an avenue to overcome the current antibiotic resistance crisis, but evolution of genetic resistance to phages remains a concern. In vitro, bacteria evolve genetic resistance, preventing phage adsorption or degrading phage DNA. In natural environments, evolved resistance is lower possibly because the spatial heterogeneity within biofilms, microcolonies, or wall populations favours phenotypic survival to lytic phages. However, it is also possible that the persistence of genetically sensitive bacteria is due to less efficient phage amplification in natural environments, the existence of refuges where bacteria can hide, and a reduced spread of resistant genotypes. Here, we monitor the interactions between individual planktonic bacteria in isolation in ephemeral refuges and bacteriophage by tracking the survival of individual cells. We find that in these transient spatial refuges, phenotypic resistance due to reduced expression of the phage receptor is a key determinant of bacterial survival. This survival strategy is in contrast with the emergence of genetic resistance in the absence of ephemeral refuges in well-mixed environments. Predictions generated via a mathematical modelling framework to track bacterial response to phages reveal that the presence of spatial refuges leads to fundamentally different population dynamics that should be considered in order to predict and manipulate the evolutionary and ecological dynamics of bacteria–phage interactions in naturally structured environments. Bacteriophages represent a promising avenue to overcome the current antibiotic resistance crisis, but evolution of phage resistance remains a concern. This study shows that in the presence of spatial refuges, genetic resistance to phage is less of a problem than commonly assumed, but the persistence of genetically susceptible bacteria suggests that eradicating bacterial pathogens from structured environments may require combined phage-antibiotic therapies.
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Affiliation(s)
- Erin L. Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rory Claydon
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Sean Meaden
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Aidan T. Brown
- SUPA, School of Physics and Astronomy, The University of Edinburgh, United Kingdom
| | - Edze R. Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, United Kingdom
| | - Sarah V. Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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Grabowski Ł, Łepek K, Stasiłojć M, Kosznik-Kwaśnicka K, Zdrojewska K, Maciąg-Dorszyńska M, Węgrzyn G, Węgrzyn A. Bacteriophage-encoded enzymes destroying bacterial cell membranes and walls, and their potential use as antimicrobial agents. Microbiol Res 2021; 248:126746. [PMID: 33773329 DOI: 10.1016/j.micres.2021.126746] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Appearance of pathogenic bacteria resistant to most, if not all, known antibiotics is currently one of the most significant medical problems. Therefore, development of novel antibacterial therapies is crucial for efficient treatment of bacterial infections in the near future. One possible option is to employ enzymes, encoded by bacteriophages, which cause destruction of bacterial cell membranes and walls. Bacteriophages use such enzymes to destroy bacterial host cells at the final stage of their lytic development, in order to ensure effective liberation of progeny virions. Nevertheless, to use such bacteriophage-encoded proteins in medicine and/or biotechnology, it is crucial to understand details of their biological functions and biochemical properties. Therefore, in this review article, we will present and discuss our current knowledge on the processes of bacteriophage-mediated bacterial cell lysis, with special emphasis on enzymes involved in them. Regulation of timing of the lysis is also discussed. Finally, possibilities of the practical use of these enzymes as antibacterial agents will be underlined and perspectives of this aspect will be presented.
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Affiliation(s)
- Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Krzysztof Łepek
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Monika Maciąg-Dorszyńska
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
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