Published in:
01-05-2021 | Original Article
Deep learning model for prediction of extended-spectrum beta-lactamase (ESBL) production in community-onset Enterobacteriaceae bacteraemia from a high ESBL prevalence multi-centre cohort
Authors:
Alfred Lok Hang Lee, Curtis Chun Kit To, Angus Lang Sun Lee, Ronald Cheong Kin Chan, Janus Siu Him Wong, Chun Wai Wong, Viola Chi Ying Chow, Raymond Wai Man Lai
Published in:
European Journal of Clinical Microbiology & Infectious Diseases
|
Issue 5/2021
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Abstract
Adequate empirical antimicrobial coverage is instrumental in clinical management of community-onset Enterobacteriaceae bacteraemia in areas with high ESBL prevalence, while balancing the risk of carbapenem overuse and emergence of carbapenem-resistant organisms. It is unknown whether machine learning offers additional advantages to conventional statistical methods in prediction of ESBL production. To develop a validated model to predict ESBL production in Enterobacteriaceae causing community-onset bacteraemia. 5625 patients with community-onset bacteraemia caused by Escherichia coli, Klebsiella species and Proteus mirabilis during 1 January 2015–31 December 2019 from three regional hospitals in Hong Kong were included in the analysis, after exclusion of blood cultures obtained beyond 48 h of admission. The prevalence of ESBL-producing Enterobacteriaceae was 23.7% (1335/5625). Deep neural network and other machine learning algorithms were compared against conventional statistical model via multivariable logistic regression. Primary outcomes compared consisted of predictive model area under curve of receiver-operator characteristic curve (AUC), and macro-averaged F1 score. Secondary outcomes included sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Deep neural network yielded an AUC of 0.761 (95% CI 0.725–0.797) and F1 score of 0.661 (95% CI 0.633–0.689), which was superior to logistic regression (AUC 0.667 (95% CI 0.627–0.707), F1 score 0.596 (95% CI 0.567–0.625)). Deep neural network had a specificity of 91.5%, sensitivity of 37.5%, NPV of 82.5%, and PPV of 57.9%. Deep neural network is superior to logistic regression in predicting ESBL production in Enterobacteriaceae causing community-onset bacteraemia in high-ESBL prevalence area. Machine learning offers clinical utility in guiding judicious empirical antibiotics use.