Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa

Antibiotics are a cornerstone of modern medicine, targeting pathogen cells by disrupting essential cellular processes. However, standard antibiotic susceptibility metrics (e.g., MIC) and textbook models neglect transient dynamics and density-dependent effects, despite their ubiquity in nature. In clinical infections, where bacterial populations are the units we treat, this can increase the risk of under treatment. To address this gap, we generate high resolution optical density time series data for Pseudomonas aeruginosa (3 antibiotics, 12 doses, 7 inoculum sizes, 4x replication), enabling gradient estimation and gradient-based model parameterization. We develop a dynamics-led computational pipeline that (1) evaluates population scale ordinary differential equation models in the context of estimated time derivative data, and (2) classifies transient dynamics in dose-inoculum space using unsupervised clustering. Applied to our data, the pipeline identifies an ordinary differential equation model with a saturating antibiotic-loss term and a threshold-dependent weak Allee term that recapitulates and quantifies classic rate, yield, and inoculum effects of antibiotics. In addition, our model and clustering approach suggest a set of novel metrics, defining thresholds separating distinct dynamical regimes. Beyond antibiotic data sets, our approach utilizing a derivative-based fitting algorithm and clustering of derivative trajectories is applicable to any biological time series with controlled perturbations and variable initial conditions.