Development, Evaluation, and Multisite Deployment of a Machine Learning Decision Tree Algorithm To Optimize Urinalysis Parameters for Predicting Urine Culture Positivity

• Published in: Journal of clinical microbiology Vol. 61; no. 6; p. e0029123
• Main Authors: Seheult, Jansen N, Stram, Michelle N, Contis, Lydia, Pontzer, Raymond E, Hardy, Stephanie, Wertz, William, Baxter, Carla M, Ondras, Michael, Kip, Paula L, Snyder, Graham M, Pasculle, A William
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 20-06-2023
• Subjects: Bacteriology; Clinical Microbiology; Decision Trees; Humans; Machine Learning; Middle Aged; Retrospective Studies; ROC Curve; Urinalysis - methods; Urinary Tract Infections - diagnosis; Urinary Tract Infections - microbiology; Urine - microbiology; reflex protocol; PittUDT algorithm; machine learning; receiver operating characteristic; urine culture
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/jcm.00291-23

PittUDT, a recursive partitioning decision tree algorithm for predicting urine culture (UC) positivity based on macroscopic and microscopic urinalysis (UA) parameters, was developed in support of a broader system-wide diagnostic stewardship initiative to increase appropriateness of UC testing. Reflex algorithm training utilized results from 19,511 paired UA and UC cases (26.8% UC positive); the average patient age was 57.4 years, and 70% of samples were from female patients. Receiver operating characteristic (ROC) analysis identified urine white blood cells (WBCs), leukocyte esterase, and bacteria as the best predictors of UC positivity, with areas under the ROC curve of 0.79, 0.78, and 0.77, respectively. Using the held-out test data set (9,773 cases; 26.3% UC positive), the PittUDT algorithm met the prespecified target of a negative predictive value above 90% and resulted in a 30 to 60% total negative proportion (true-negative plus false-negative predictions). These data show that a supervised rule-based machine learning algorithm trained on paired UA and UC data has adequate predictive ability for triaging urine specimens by identifying low-risk urine specimens, which are unlikely to grow pathogenic organisms, with a false-negative proportion under 5%. The decision tree approach also generates human-readable rules that can be easily implemented across multiple hospital sites and settings. Our work demonstrates how a data-driven approach can be used to optimize UA parameters for predicting UC positivity in a reflex protocol, with the intent of improving antimicrobial stewardship and UC utilization, a potential avenue for cost savings.