Prediction of antimicrobial minimum inhibitory concentration from bacterial genomes using a scalable and interpretable machine learning approach

Abstract

Although machine learning models can predict antimicrobial susceptibility from bacterial whole genome sequencing (WGS), state-of-the-art approaches are computationally demanding or dependent on knowledge of genetic resistance determinants. Here, we describe an efficient data-driven approach to predicting minimum inhibitory concentration (MIC) by progressively extending and refining predictive genome segments, independent of prior knowledge of resistance determinants. Resultant models had high interpretability — known and potentially novel resistance determinants were captured. Using 762 clinical E. coli strains, 71.6% of predictions were within one dilution of the measured MIC. Models trained with this algorithm generalised better onto external data (F1 score = 0.85) compared with alternative models trained on annotated resistance determinants (F1 = 0.82) or k -mer counts (F1 = 0.74). Computational demands were low (RAM usage 23.6GB vs 38.8GB for k -mer model). These advantages represent an important advance in predicting antimicrobial susceptibility from WGS, with potential applications for clinical diagnostics, drug development, and surveillance.