# Machine Learning for Pre-Culture ESBL Risk Stratification to Guide Empiric Antibiotic Selection: A 12-Hospital Study of Enterobacteriaceae Cultures

arXiv: https://arxiv.org/abs/2609.05970 · HTML: https://mlsanity.com/paper/2609.05970/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 40 references that are in the map.
- First posted on arXiv 5 Sep 2026.

## Builds on (most cited first, 4 of 4)

- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [The harm of class imbalance corrections for risk prediction models: illustration and simulation using logistic regression](https://mlsanity.com/paper/2202.09101/) (2022)

## Abstract (arXiv)

Empiric antibiotic therapy for suspected ESBL-producing Enterobacteriaceae must be selected 48-72 hours before culture results, forcing clinicians to choose between undertreating resistant infections and overusing carbapenems that drive further resistance. We developed a cost-sensitive XGBoost model predicting an ESBL phenotype (resistance to ceftriaxone, ceftazidime, cefepime or piperacillin-tazobactam) at culture ordering using 45 pre-culture EHR features across 132,955 cultures from 72,217 patients at 12 hospitals (14.41% with the ESBL phenotype). Cultures were partitioned at the patient level. At 90% sensitivity, the model achieved 95.8% NPV, reducing post-test ESBL probability to 4.2%, a threshold that may support safe carbapenem-sparing in non-ICU settings, while sparing 307 of every 1,000 cultures an unnecessary broad-spectrum course at the cost of 14 missed ESBL cases per 1,000. SHAP analysis identified prior ESBL colonization as the dominant predictor, ahead of prior organism burden and neighborhood deprivation; removing deprivation features caused minimal performance loss (DeltaAUROC = -0.020), enabling equitable bedside deployment. Discrimination was unchanged under a strict IDSA ESBL-E definition (AUROC 0.766), with specimen type added as a predictor (0.764) and without any class-imbalance correction (0.762), and ranged from 0.71 to 0.78 across organism strata.