Genome-Level Hierarchical Attention Transformer with Multi-Head Attention Weighted Sum for Broad-Spectrum Antimicrobial Resistance Prediction and Discovery of Resistance-Related Genomic Contexts

Abstract

Antimicrobial resistance is a growing global health concern, requiring reliable tools for predicting resistance across a wide range of bacteria and antibiotics. In this study, we introduce a genome-level hierarchical attention transformer (GL-HAT) that integrates a pretrained genomic foundation model with hierarchical attention mechanisms to analyze the full protein sequence context of bacterial genomes. GL-HAT is designed to deliver both accurate resistance predictions and interpretable insights into the genomic features associated with resistance using specialized modules. Trained and validated on a comprehensive dataset of bacterial genomes and antimicrobial susceptibility profiles, the model outperformed traditional machine learning method, with an F1-score of 0.845 and AUROC of 0.953. Moreover, GL-HAT could demonstrate the resistance-related contexts in the genome, such as vanA operon and nearby resolvase genes in vancomycin-resistant Enterococcus and tet(M) gene adjacent to conjugation proteins in tetracycline-resistant Streptococcus pneumoniae. By combining high accuracy with interpretability, GL-HAT offers a practical approach for advancing AMR diagnostics and research, supporting more informed clinical and public health decisions.