A Microfluidic Chip for Studies of the Dynamics of Antibiotic Resistance Selection in Bacterial Biofilms

Biofilms are arguably the most important mode of growth of bacteria, but how antibiotic resistance emerges and is selected in biofilms remains poorly understood. Several models to study evolution of antibiotic resistance have been developed, however, their usability varies depending on the nature of the biological question. Here, we developed and validated a microfluidic chip (Brimor) for studying the dynamics of enrichment of antibiotic-resistant bacteria in biofilms using real-time monitoring with confocal microscopy. In situ extracellular cellulose staining and physical disruption of the biomass confirmed Escherichia coli growth as biofilms in the chip. We showed that seven generations of growth occur in 16 h when biofilms were established in the growth chambers of Brimor, and that bacterial death and growth rates could be estimated under these conditions using a plasmid with a conditional replication origin. Additionally, competition experiments between antibiotic-susceptible and -resistant bacteria at sub-inhibitory concentrations demonstrated that the antibiotic ciprofloxacin selected for antibiotic resistance in bacterial biofilms at concentrations 17-fold below the minimal inhibitory concentration of susceptible planktonic bacteria. Overall, the microfluidic chip is easy to use and a relevant model for studying the dynamics of selection of antibiotic resistance in bacterial biofilms and we anticipate that the Brimor chip will facilitate basic research in this area.