Coupling between spatial structure and heterogeneous antibiotic responses through self-generated nutrient gradients in microbial populations

In confined colonies, bacterial metabolism and environmental transport lead to self-generated nutrient gradients and emergent phenotypic structure with spatially heterogeneous cell growth and gene expression. Such structure strongly modulates the response to antibiotics, which, even in single cells, depends on a dynamic interplay between the drug’s effect and regulation of resistance gene expression. Here, we observe the response of spatially extended microcolonies of tetracycline-resistant E. coli to precisely defined dynamic drug regimens in a custom microfluidic device. We find complex and counter-intuitive responses, such as local growth rate increases upon antibiotic exposure and enhanced population-level resistance to subsequent exposures. A mathematical model incorporating direct regulation of resistance genes, metabolism-induced changes in expression, as well as nutrient diffusion across the colony captures these phenomena and thereby uncovers an intricate coupling between drug-induced growth modulation, resistance, and reorganization of the growth pattern through nutrient redistribution. Our results highlight the role of physical mechanisms such as nutrient transport for spatial structure and may inform the design of drug regimens that account for this heterogeneity.