amR: an R package suite to predict antimicrobial resistance in bacterial pathogens

Identifying bacterial antimicrobial resistance (AMR) is critical for diagnostics and treatment, but resistance is a complex trait arising from myriad mechanisms spanning multiple molecular scales. Existing computational approaches often function as black boxes and rarely explore cross-species or multi-drug patterns. We developed amR, an integrated R package suite that provides a complete framework from bacterial genome data curation to interpretable AMR predictions, enabling identification of resistance mechanisms across species and drugs.

The amR R package suite contains three modular packages. amRdata downloads genomes and paired antimicrobial susceptibility testing data from BV-BRC and processes them, constructs pangenomes, and extracts features at gene/protein cluster, protein domain, annotated Clusters of Orthologous Groups and ResFinder AMR-associated features, and structural variant scales; data are stored in memory-efficient formats (Parquet, DuckDB). amRml trains interpretable machine learning models per species-drug combination, calculates feature importance and performance metrics, and provides rich ground for hypothesis generation and mechanism discovery. amRviz provides an interactive Shiny dashboard to explore metadata distributions and model performance across species and drugs, visualize top predictive AMR features, and analyze cross-model patterns across geographic/temporal strata. We apply the suite to Shigella sonnei, achieving a median Matthews Correlation Coefficient of 0.89 across 23 drugs and drug classes. With thousands of genomes, multi-scale features, and interpretable models, amR provides an accessible, comprehensive framework for AMR research. The amR package suite is installable via GitHub (https://github.com/JRaviLab/amR; BSD-3-Clause license).