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.
