Background: Carbapenemase-Producing Enterobacteriace (CPE) poses a critical concern for infection prevention and control in hospitals. However, predictive modeling of previously highlighted CPE-associated risks such as readmission, mortality, and extended length of stay (LOS) remains underexplored, particularly with modern deep learning approaches. This study introduces an eXplainable AI (XAI) modeling framework to investigate CPE impact on patient outcomes from Electronic Medical Records (EMR) data of an Irish hospital. Methods We analyzed an inpatient dataset from an Irish acute hospital (2018–2022), incorporating diagnostic codes, ward transitions, patient demographics, infection-related variables and contact network features. Several Transformerbased architectures (e.g., TabTransformer, TabNet) were benchmarked alongside traditional machine learning models. Clinical outcomes were predicted, and XAI techniques were applied to interpret model decisions. Results Our framework successfully demonstrated the utility of Transformer-based models, with TabTransformer consistently outperforming baselines across multiple clinical prediction tasks, especially for CPE acquisition (Area Under Receiver Operating Characteristic and sensitivity). We found infection-related features, including historical hospital exposure, admission context, and network centrality measures, to be highly influential in predicting patient outcomes and CPE acquisition risk. Explainability analyses revealed that features like ”Area of Residence”, ”Admission Ward” and prior admissions are key risk factors. Network variables like ”Ward PageRank” also ranked highly, reflecting the potential value of structural exposure information. Conclusion: This study presents a robust and explainable AI framework for analyzing complex EMR data to identify key risk factors and predict CPE-related outcomes. Our findings underscore the superior performance of the Transformer models and highlight the importance of diverse clinical and network features. The transparent interpretability offered by our XAI approach provides actionable insights for infection prevention and control, paving the way for more targeted interventions and ultimately enhancing patient safety within acute healthcare settings.