Precision single cell analysis to characterize host dependent antimicrobial response heterogeneity in physiological medium

Antimicrobial stewardship plays an essential role in combating the global health threat posed by multidrug-resistant pathogens. Phenotypic antimicrobial susceptibility testing (AST) is the gold standard for analyzing bacterial responses to antimicrobials. However, current AST techniques, which rely on end-point bulk measurements of bacterial growth under antimicrobial treatment in a broth solution, have limitations in resembling the physiological working environment and resolving heterogeneity in response kinetics within the population. In this study, we investigate the responses of uropathogenic bacteria under antimicrobial treatment in individual urine. Our results demonstrate substantial heterogeneity in time-kill kinetics in response to antimicrobials in a host-dependent manner. We also establish a microfluidic gel encapsulation platform for single cell imaging to rapidly resolve heterogeneous subpopulations in response to antimicrobials. The platform captures both bacterial growth and killing within the gel and enables medium exchange to assess the ability of surviving cells to resume growth after antimicrobial removal. Our study lays the foundation for a new generation of precision single cell analysis for personalizing antimicrobial treatment.