The Physics of Bacteriophage-coated Antimicrobial Surfaces
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Physics and Astronomy
Abstract
Bacteriophages (phages) are viruses that prey on bacteria. In the early 20th century they were widely used to treat dangerous bacterial infections, e.g., cholera, but their popularity was eclipsed by the rise of conventional molecular antibiotics like penicillin. However, the growth of antimicrobial resistance (the rapid evolution in bacteria of resistance to conventional antibiotics) is now driving a resurgence of interest in phages as effective antibacterial agents, with approximately 40 phage-based companies set up so far worldwide. Many of the antibacterial applications rely on binding phages to surfaces, e.g., food packaging, seed coatings, animal feed, catheters and wound dressings, and companies, including the project partner Fixed Phage Ltd, are actively researching how to do this in a way that retains maximum antibacterial activity. The aim of this proposal is to understand the basic science underlying this problem, and to apply this understanding to design and optimize these phage-coated surfaces.
For human infections, we have the benefit of detailed mathematical models that help us to stop these infections spreading. I want to be able to use these mathematical models to enhance the spreading of phage infections among bacteria, but there are several basic science questions that must be answered before this can be done. This proposal addresses three of these questions, which are also of direct relevance to understanding how bacteriophage-coated surfaces work:
1) How does phage infection affect bacterial swimming and vice versa? Many bacteria swim, and this can spread the phage infection further. This is analogous to the way human infections can be spread by long-distance air travel, but for bacteria, very little is known; even the simple question of whether bacteria stop swimming immediately after infection, or just before they die some minutes later, remains open. Understanding this difference is important for mathematically modeling phage infections, including on antibacterial surfaces, and will help to determine important design parameters such as the density of phage coverage needed to ensure the infection spreads through the whole bacterial population.
2) How are the phages distributed and oriented on the surface? Phages inject DNA into bacteria through tube-like tail fibres. To be effective these fibres must contact the bacteria, but phages probably bind in random orientations, which will limit their activity. Similarly, the most effective phage-coated surfaces will have a uniform distribution of phages across the surface, but a widespread phenomenon in drying droplets, called the 'coffee-ring effect' may cause the bacteriophages to clump together. This is particularly significant because bacteria attached to surfaces can grow and aggregate into highly resistant colonies known as biofilms; a phage-poor region of the surface presents an ideal opportunity to do this. This leads to:
3) How does bacterial aggregation affect infection dynamics? Dense bacterial aggregates present a physical challenge for bacteriophage treatment (the phages can't get in), but they can also act as phage reservoirs. Understanding the competitive dynamics between bacterial aggregation and phage infection is a key challenge, and modelling this will be important for a wide range of applications. This includes using phages to treat human infections, where resistant biofilms pose a huge challenge.
I will address these questions with experiments and mathematical modelling, looking for fundamental physical principles that can be applied to optimize antimicrobial surfaces, and design new devices for novel applications. With the aim of developing clinical applications, I will also test how these principles carry over into a system containing bacteriophages, bacteria and cultured human cells, which is a model for bacterial infections.
For human infections, we have the benefit of detailed mathematical models that help us to stop these infections spreading. I want to be able to use these mathematical models to enhance the spreading of phage infections among bacteria, but there are several basic science questions that must be answered before this can be done. This proposal addresses three of these questions, which are also of direct relevance to understanding how bacteriophage-coated surfaces work:
1) How does phage infection affect bacterial swimming and vice versa? Many bacteria swim, and this can spread the phage infection further. This is analogous to the way human infections can be spread by long-distance air travel, but for bacteria, very little is known; even the simple question of whether bacteria stop swimming immediately after infection, or just before they die some minutes later, remains open. Understanding this difference is important for mathematically modeling phage infections, including on antibacterial surfaces, and will help to determine important design parameters such as the density of phage coverage needed to ensure the infection spreads through the whole bacterial population.
2) How are the phages distributed and oriented on the surface? Phages inject DNA into bacteria through tube-like tail fibres. To be effective these fibres must contact the bacteria, but phages probably bind in random orientations, which will limit their activity. Similarly, the most effective phage-coated surfaces will have a uniform distribution of phages across the surface, but a widespread phenomenon in drying droplets, called the 'coffee-ring effect' may cause the bacteriophages to clump together. This is particularly significant because bacteria attached to surfaces can grow and aggregate into highly resistant colonies known as biofilms; a phage-poor region of the surface presents an ideal opportunity to do this. This leads to:
3) How does bacterial aggregation affect infection dynamics? Dense bacterial aggregates present a physical challenge for bacteriophage treatment (the phages can't get in), but they can also act as phage reservoirs. Understanding the competitive dynamics between bacterial aggregation and phage infection is a key challenge, and modelling this will be important for a wide range of applications. This includes using phages to treat human infections, where resistant biofilms pose a huge challenge.
I will address these questions with experiments and mathematical modelling, looking for fundamental physical principles that can be applied to optimize antimicrobial surfaces, and design new devices for novel applications. With the aim of developing clinical applications, I will also test how these principles carry over into a system containing bacteriophages, bacteria and cultured human cells, which is a model for bacterial infections.
Planned Impact
Industrial Impact - The main industrial beneficiaries of this work will be companies that exploit bacteriophage technologies for antibacterial applications, principally my industrial partner Fixed Phage. Bacteriophage-based technologies are one strand of attack in our battle against antimicrobial resistance (AMR), which is a global challenge with huge social and economic implications (see Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a crisis for the Health and Wealth of Nations. 2014). Basic science knowledge about how bacteriophages and bacteria interact on surfaces like food packaging or catheters will assist in optimizing existing bacteriophage-based technology, and developing it for novel applications. With Fixed Phage I also expect to adapt the techniques and models developed through this research to serve as quality control and research and development tools, e.g., to determine the distribution of bacteriophages through a phage coating.
Training - The simultaneous challenges (or opportunities) of AMR and the 'big data' revolution call for a new generation of researchers skilled in both microbiology and physical sciences, with the ability to look beyond academia and envisage or exploit the practical implications of their research. This combination of skills is rare, and this research proposal will help to meet this need.
From Fixed Phage the Edinburgh PDRA and PhD student, as well as other undergraduate and graduate students associated with the project, will receive comprehensive training in phage and microbiology research in a rigorous industrial environment; this insight into industry will also give these researchers a stepping stone to forging their own industrial links later in their career.
Scientific Impact Across Disciplines - This work will reveal the basic science underlying bacteriophage-bacterial interactions in complex model environments. The immediate beneficiaries will be phage biologists, microbiologists, and biophysicists. The work on drying bacteriophage droplets will also contribute to general research into the drying of other complex droplets, e.g., blood drying for forensic science applications, or pesticides on crops.
Outreach - I will run 3 workshops on bacteriophages at venues such as the Edinburgh Science Festival. These workshops will introduce bacteriophages to the general public as objects of scientific and general interest, helping to overcome some of the barriers in public perception of phages, associated with viruses and genetic modification.
Training - The simultaneous challenges (or opportunities) of AMR and the 'big data' revolution call for a new generation of researchers skilled in both microbiology and physical sciences, with the ability to look beyond academia and envisage or exploit the practical implications of their research. This combination of skills is rare, and this research proposal will help to meet this need.
From Fixed Phage the Edinburgh PDRA and PhD student, as well as other undergraduate and graduate students associated with the project, will receive comprehensive training in phage and microbiology research in a rigorous industrial environment; this insight into industry will also give these researchers a stepping stone to forging their own industrial links later in their career.
Scientific Impact Across Disciplines - This work will reveal the basic science underlying bacteriophage-bacterial interactions in complex model environments. The immediate beneficiaries will be phage biologists, microbiologists, and biophysicists. The work on drying bacteriophage droplets will also contribute to general research into the drying of other complex droplets, e.g., blood drying for forensic science applications, or pesticides on crops.
Outreach - I will run 3 workshops on bacteriophages at venues such as the Edinburgh Science Festival. These workshops will introduce bacteriophages to the general public as objects of scientific and general interest, helping to overcome some of the barriers in public perception of phages, associated with viruses and genetic modification.
Publications
Attrill EL
(2021)
Individual bacteria in structured environments rely on phenotypic resistance to phage.
in PLoS biology
Huisman M
(2023)
Evaporation of Concentrated Polymer Solutions Is Insensitive to Relative Humidity.
in Physical review letters
Koumakis N
(2019)
Dynamic optical rectification and delivery of active particles.
in Soft matter
Le Nagard L
(2022)
Encapsulated bacteria deform lipid vesicles into flagellated swimmers
in Proceedings of the National Academy of Sciences
Marton HL
(2024)
Screening of Hydrophilic Polymers Reveals Broad Activity in Protecting Phages during Cryopreservation.
in Biomacromolecules
Marton HL
(2021)
Polymer-Mediated Cryopreservation of Bacteriophages.
in Biomacromolecules
Marton HL
(2023)
Anionic Synthetic Polymers Prevent Bacteriophage Infection.
in Journal of the American Chemical Society
Poon WCK
(2020)
Soft matter science and the COVID-19 pandemic.
in Soft matter
Styles KM
(2022)
Transposable Element Insertions into the Escherichia coli Polysialic Acid Gene Cluster Result in Resistance to the K1F Bacteriophage.
in Microbiology spectrum
Styles KM
(2021)
A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions.
in Frontiers in microbiology
Vissers T
(2019)
Dynamical analysis of bacteria in microscopy movies.
in PloS one
Description | So far, research performed in this award has led to: 1) Improvements in our ability to automatically track and analyse the motion of bacteria in microscopy videos. This can be applied to any research question where the motion of bacteria is important, e.g., in studies of the infection of bacteria by bacterial viruses (bacteriophages), which is the field of this grant. The related publication is available at: https://doi.org/10.1371/journal.pone.0217823 2) A theoretical model for the behaviour of light-sensitive bacteria when exposed to moving patterns of light. This model can be adapted to investigate, e.g., bacterial behaviours such as chemotaxis (the directed motion towards favourable chemical signals, e.g., sources of food); or the spread of a bacteriophage infection through a bacterial population. The light-sensitive bacteria developed for this work will also be helpful in such studies, e.g., by investigating the role of bacterial swimming speed (which can be controlled by the light patterns) on the spread of bacteriophage infections. The related publication is available at https://doi.org/10.1039/c9sm00799g 3) Various computational and mathematical models for the spread of bacteriophage infections through bacterial populations which will make it possible to predict better the speed and nature of such infections in a range of contexts, e.g., in phage therapy, or in the use of phage-coated antimicrobial surfaces. A manuscript is being prepared for publication. This research together with staff and student training have made it possible to routinely investigate bacteriophage-bacterial interactions within the School of Physics and Astronomy at Edinburgh University. This has led to several successful undergraduate projects, including on electron microscopy of bacteriophages, and mathematical modeling of infections, which I expect to be able to develop into research outputs, and use in collaboration with my industral partner. I now have active and productive collaborations with the academic (Warwick) and industrial (Fixed Phage) partners. |
Exploitation Route | The outcomes 1-3 represent fundamental research outputs, so I expect these to be taken up by other researchers in the fields of e.g., biophysics, active matter, antimicrobial resistance, infectious diseases, and bacteriophage research. I expect to develop the industrial and academic collaborations by opening up new joint investigations, probably focusing on direct applications to phage-coated antimicrobial surfaces, and to experimental models of infection. |
Sectors | Agriculture Food and Drink Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology Other |
Description | APEX Award |
Amount | £98,706 (GBP) |
Funding ID | APX\R1\191020 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2019 |
End | 01/2021 |
Description | Impact Acceleration Account: Optimization of the biocidal efficacy of an electrolytically generated fog by modifying its physico-chemical properties. |
Amount | £14,801 (GBP) |
Funding ID | EPSRC IAA PIV078 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2022 |
End | 06/2022 |
Description | Institutional Strategic Support Fund |
Amount | £30,000 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2023 |
End | 09/2023 |
Description | Institutional Strategic Support Fund |
Amount | £30,000 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2021 |
End | 10/2021 |
Description | Wellcome Trust Institutional Strategic Support Fund |
Amount | £30,000 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2021 |
End | 08/2021 |
Description | Whole-room and workplace disinfection by means of electrogenerated oxidants delivered in the form of a fog, mist or spray. |
Amount | £550,000 (GBP) |
Funding ID | 83701 |
Organisation | Innovate UK |
Sector | Public |
Country | United Kingdom |
Start | 12/2020 |
End | 02/2022 |
Title | Automated analysis of bacteria in microscopy videos |
Description | Code written by Teun Vissers to automatically identify and analyze the trajectories of bacteria in microscopy videos. Code is available from: https://git.ecdf.ed.ac.uk/tvissers/findRods2Dt https://git.ecdf.ed.ac.uk/tvissers/trackRods2Dt https://git.ecdf.ed.ac.uk/tvissers/filterTracks2Dt https://git.ecdf.ed.ac.uk/tvissers/analyzeBugTracks2Dt and is described and used in: https://doi.org/10.1371/journal.pone.0217823 |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | None known |
Description | General interest seminar for Physics students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | Lecture about `The Physics of Bacteria' given to a general audience from the School of Physics and Astronomy. |
Year(s) Of Engagement Activity | 2023 |
Description | Interview with children from a local primary school |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | I was interviewed about my research on viruses by two school children from a local primary school. The children later wrote up this interview, which was disseminated in the primary school and on my departmental website. |
Year(s) Of Engagement Activity | 2020 |
URL | https://blogs.ed.ac.uk/physics-astronomy/2020/09/23/interview-with-dr-aidan-brown/ |
Description | Physics Teacher Training Session |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | 30 physics teachers from across Scotland attended the School of Physics and Astronomy for a Scottish Schools Education Research Centre training day. A colleague, Dr Vincent Martinez, and I spoke to the teachers about 'The Physics of Bacteria' for 30 minutes and gave a practical demonstration of measuring bacterial swimming speed. |
Year(s) Of Engagement Activity | 2019 |
Description | Presentation at Academic/Industrial Workshop 'The Physics of Cleaning and Disinfection' |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | I gave a 15-minute talk on the physics of using bacteriophages to kill bacteria to an audience of academics and industrialists. |
Year(s) Of Engagement Activity | 2019 |
URL | https://cleaninganddisinfection.meeting-mojo.com/ |
Description | Presentation of Talk at Living Materials Interdisciplinary Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I presented a 15 minute talk giving a historical overview of Bacteriophage therapy research in 'Material Imagination - Symposium: Living innovation: interdisciplinary approaches to research on living materials' at Durham Univeristy on 22-23 January. The aim was to present the approximately 100-year history of bacteriophage research and usage in clinical therapy as a case study in Responsible Innovation. The participants included academics, policymakers, public engagement professionals, artists, entrepreneurs. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.dur.ac.uk/ias/1920projects/morieraandstaykova/ |