Dynamic energy budget approach to evaluate antibiotic effects on biofilms

•Hybrid dynamic energy budget models describe antibiotic effects on biofilms.•Experimentally measured death rates are reproduced numerically.•Spatial variations observed in the distribution of cell types are recreated.•Qualitative predictions in agreement with experimental observations follow.•Antibiotic resistance mechanisms may be incorporated. Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix. Coupling a dynamic energy budget based description of cell metabolism to surrounding concentration fields, we are able to approximate survival curves measured for different antibiotics. We reproduce numerically stratified distributions of cell types within the biofilm and introduce ways to incorporate different resistance mechanisms. Qualitative predictions follow that are in agreement with experimental observations, such as higher survival rates of cells close to the substratum when employing antibiotics targeting active cells or enhanced polymer production when antibiotics are administered. The current computational model enables validation and hypothesis testing when developing therapies.