A digital droplet microarray for measuring tolerance to antibiotics

Antibiotic tolerance enables populations of microbes to survive normally lethal antibiotic concentrations, increasing the likelihood of reinfection and facilitating the evolution of resistance. Tolerance measurements typically involve quantifying viable cells after antibiotic exposure. Existing methods range from accessible but low-throughput approaches, such as plate counting, to higher-throughput but semi-quantitative techniques, such as the TDtest. Here, we develop a new system for rapid, precise and high-throughput tolerance measurements. We utilize Surface Patterned Omniphobic Tiles (SPOTs) to discretize cell suspensions into nano-to microliter droplets and estimate the viable cell concentrations following antibiotic exposure from the proportion of empty droplets using Poissonian statistics. We apply the platform to monitor Klebsiella pneumoniae tolerance to meropenem over time as a proof of concept. The resulting assay is accessible, compatible with multiple media, and boasts a large dynamic range, sufficient resolution, and rapid handling.