Periodic Reporting for period 4 - EvoStruc (The physics of antibiotic resistance evolution in spatially-structured multicellular assemblies)
Okres sprawozdawczy: 2020-12-01 do 2022-05-31
Antimicrobial resistance (AMR) is a huge and growing challenge to modern healthcare. Combating AMR is a challenge for physicists as well as for biologists and clinicians. This is because we need mathematical and computational models to understand how bacterial infections develop and grow, and to predict the effects of antibiotics. Improving our understanding of how antibiotics work and how resistance evolves is essential if we are to design better treatment regimes for bacterial infections, that can use less antibiotics, and prevent resistance from happening.
One of the reasons that we need physics to understand bacterial infections is that they can be spatially structured: often, bacteria in an infection grow in densely packed communities, known as biofilms. Statistical and soft matter physics can help us understand how these spatial structures form and their response to antibiotics.
The EVOSTRUC project aims to uncover the two-way link between the emergence of spatial structure in bacterial populations, such as infections, and the evolution of antibiotic resistance. We will do this using a combination of experiments, computer simulations and mathematical models.
One of the reasons that we need physics to understand bacterial infections is that they can be spatially structured: often, bacteria in an infection grow in densely packed communities, known as biofilms. Statistical and soft matter physics can help us understand how these spatial structures form and their response to antibiotics.
The EVOSTRUC project aims to uncover the two-way link between the emergence of spatial structure in bacterial populations, such as infections, and the evolution of antibiotic resistance. We will do this using a combination of experiments, computer simulations and mathematical models.
In the first part of our project (WP1), we aimed to understand from a fundamental point of view how antibiotics inhibit bacteria and how spatially structured bacterial populations respond differently to antibiotics. To this end, we developed new models, combining theory and experiment, for the action of a DNA-targeting antibiotic, ciprofloxacin, and for the action of the cell-wall targeting antibiotic, mecillinam. We also performed computer simulations to investigate the interplay between spatial gradients of antibiotic and of nutrient for expanding bacterial populations. Moving from mechanism of action to the evolution of antibiotic resistance, we investigated in detail how a time-delay between the emergence of an antibiotic-resistance mutation and its phenotypic effect could change the evolutionary outcome.
The second part of our project (WP2), focused on antibiotic effects in dense, spatially structured, bacterial populations. Biofilms that form on solid surfaces are one example of such populations; bacterial aggregates suspended in liquid are a second example and bacterial colonies on gel-plates are a third example. In the case of biofilms, we used computer simulations to gain new insights into the mechanisms controlling spatial structure formation in growing biofilms, and to understand the spatial patterning of genetic diversity in growing biofilms. In both cases we showed that the active layer of growing cells at the biofilm interface plays a crucial role. In the case of suspended aggregates, we investigated the mechanism of aggregate formation in the bacterium Pseudomonas aeruginosa, finding that it depends on the growth state of the bacterial culture, and we discovered that a very low dose of antibiotic can actually cause aggregation in another bacterium, Escherichia coli. In the case of bacterial colonies, we discovered a new phenomenon, where individual cells that pump out antibiotic as part of their resistance mechanism (efflux) can inhibit surrounding cells, leading to large-scale spatial structure in colonies. This is now being investigated further with experiments and models.
The third part of our project (WP3) aimed to explore the clinical and industrial implications of our findings. Here we have developed a collaboration with the international surface coatings manufacturer Akzo Nobel, leading to a joint publication on the formation of multi species biofilms on ship hulls coated in antifouling paint, and a further project on biofilm removal from topologically modified (riblet) surfaces. We have also developed a second collaboration with medical devices manufacturer Kimal Plc, in which we investigated the factors contributing to biofilm formation on intravenous catheters, and explored methods for early stage biofilm detection via pH changes.
Overall, our project has led to new, physics-based models for the mechanism of action of several classes of antibiotics, new understanding of the basic mechanisms underlying antibiotic resistance evolution, new understanding of how biofilm spatial structure is established and its implications for evolution, and translation of these insights into the industrial and clinical field. Some of these findings have already been published but others are still being prepared for publication and will emerge in the coming months.
The second part of our project (WP2), focused on antibiotic effects in dense, spatially structured, bacterial populations. Biofilms that form on solid surfaces are one example of such populations; bacterial aggregates suspended in liquid are a second example and bacterial colonies on gel-plates are a third example. In the case of biofilms, we used computer simulations to gain new insights into the mechanisms controlling spatial structure formation in growing biofilms, and to understand the spatial patterning of genetic diversity in growing biofilms. In both cases we showed that the active layer of growing cells at the biofilm interface plays a crucial role. In the case of suspended aggregates, we investigated the mechanism of aggregate formation in the bacterium Pseudomonas aeruginosa, finding that it depends on the growth state of the bacterial culture, and we discovered that a very low dose of antibiotic can actually cause aggregation in another bacterium, Escherichia coli. In the case of bacterial colonies, we discovered a new phenomenon, where individual cells that pump out antibiotic as part of their resistance mechanism (efflux) can inhibit surrounding cells, leading to large-scale spatial structure in colonies. This is now being investigated further with experiments and models.
The third part of our project (WP3) aimed to explore the clinical and industrial implications of our findings. Here we have developed a collaboration with the international surface coatings manufacturer Akzo Nobel, leading to a joint publication on the formation of multi species biofilms on ship hulls coated in antifouling paint, and a further project on biofilm removal from topologically modified (riblet) surfaces. We have also developed a second collaboration with medical devices manufacturer Kimal Plc, in which we investigated the factors contributing to biofilm formation on intravenous catheters, and explored methods for early stage biofilm detection via pH changes.
Overall, our project has led to new, physics-based models for the mechanism of action of several classes of antibiotics, new understanding of the basic mechanisms underlying antibiotic resistance evolution, new understanding of how biofilm spatial structure is established and its implications for evolution, and translation of these insights into the industrial and clinical field. Some of these findings have already been published but others are still being prepared for publication and will emerge in the coming months.
Prior to this project, there were few quantitative, mechanistic models that could predict how antibiotics affect growing bacterial cells. Our project has contributed two such models, for DNA-targeting and cell-wall targeting antibiotics. Furthermore, there were few predictive models for antibiotic resistance evolution. Our project has provided new insight by highlighting the importance of phenotypic delay before the emergence of resistance. Moreover in work that is still underway, we are testing whether simple models, accepted in the literature, can really predict qualitatively the outcome of simple evolution experiments. The results of this study should emerge over the coming year.
Concerning the role of spatial structure, our project has led to new understanding of the importance of the active layer of growing cells at the edge of a growing biofilm, for both spatial structure formation and evolution. We now plan to build on these computer simulation results to construct simple theoretical models for biofilm growth. This process has already started with a paper submitted to PRL on biofilm initiation. We have also discovered several new phenomena relating to bacterial aggregates in liquid suspension, and we now plan to follow this up by investigating in detail the ecological and evolutionary role of these aggregates. For example, is aggregation of bacteria within the human gut affected by antibiotic treatment and/or secretion of surfactants by the liver, and if so, how does this affect the gut microbiome? For bacterial colonies, we have discovered a new interplay between antibiotic resistance via efflux pumps, and spatial structure, since efflux can poison neighbouring bacteria. We plan to investigate this further with microfluidic experiments to measure the pair-wise efflux-mediated interactions, together with mathematical modelling.
Finally, we have developed significant and productive links with two industrial partners: Akzo Nobel and Kimal, both supported by PhD studentships funded externally to the ERC grant. We plan to build on both of these collaborations with further grant applications.
Concerning the role of spatial structure, our project has led to new understanding of the importance of the active layer of growing cells at the edge of a growing biofilm, for both spatial structure formation and evolution. We now plan to build on these computer simulation results to construct simple theoretical models for biofilm growth. This process has already started with a paper submitted to PRL on biofilm initiation. We have also discovered several new phenomena relating to bacterial aggregates in liquid suspension, and we now plan to follow this up by investigating in detail the ecological and evolutionary role of these aggregates. For example, is aggregation of bacteria within the human gut affected by antibiotic treatment and/or secretion of surfactants by the liver, and if so, how does this affect the gut microbiome? For bacterial colonies, we have discovered a new interplay between antibiotic resistance via efflux pumps, and spatial structure, since efflux can poison neighbouring bacteria. We plan to investigate this further with microfluidic experiments to measure the pair-wise efflux-mediated interactions, together with mathematical modelling.
Finally, we have developed significant and productive links with two industrial partners: Akzo Nobel and Kimal, both supported by PhD studentships funded externally to the ERC grant. We plan to build on both of these collaborations with further grant applications.