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

Abstract

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. Author summaryWe show that standard math models and antibiotic susceptibility metrics fail to capture the regimes of dynamical behavior that result from combined antibiotic and inoculum effects when Pseudomonas aeruginosa (PAO1) is exposed to antibiotics. Using iterations of forward and data-driven modeling, we highlight the importance of transient dynamics, derivative-based model fitting, and higher-order nonlinearities in quantifying bacterial dynamics under perturbation. We identify an ordinary differential equation-based model that describes the observed inoculum effect as a type of weak Allee effect (positive density-dependence) and also captures antibiotic effects on population growth rate and yield governed by a saturating loss function. We show that these results generalize across antibiotic mechanisms of action and highlight the importance of fitting models using dynamics-based algorithms. Finally, we explore a clustering method for bacterial dynamics that, in combination with our mathematical model, advises a set of novel metrics for measuring antibiotic susceptibility.