Deep learning model for personalized prediction of positive MRSA culture using time-series electronic health records

Methicillin-resistant Staphylococcus aureus (MRSA) poses significant morbidity and mortality in hospitals. Rapid, accurate risk stratification of MRSA is crucial for optimizing antibiotic therapy. Our study introduced a deep learning model, PyTorch_EHR, which leverages electronic health record (EHR) time-series data, including wide-variety patient specific data, to predict MRSA culture positivity within two weeks. 8,164 MRSA and 22,393 non-MRSA patient events from Memorial Hermann Hospital System, Houston, Texas are used for model development. PyTorch_EHR outperforms logistic regression (LR) and light gradient boost machine (LGBM) models in accuracy (AUROC PyTorch_EHR = 0.911, AUROC LR = 0.857, AUROC LGBM = 0.892). External validation with 393,713 patient events from the Medical Information Mart for Intensive Care (MIMIC)-IV dataset in Boston confirms its superior accuracy (AUROC PyTorch_EHR = 0.859, AUROC LR = 0.816, AUROC LGBM = 0.838). Our model effectively stratifies patients into high-, medium-, and low-risk categories, potentially optimizing antimicrobial therapy and reducing unnecessary MRSA-specific antimicrobials. This highlights the advantage of deep learning models in predicting MRSA positive cultures, surpassing traditional machine learning models and supporting clinicians’ judgments.