Abstract
Rapid and accurate diagnostics of bacterial infections are necessary for efficient treatment of antibiotic-resistant pathogens. Cultivation-based methods, such as antibiotic susceptibility testing (AST), are limited by bacterial growth rates and seldom yield results before treatment needs to start, increasing patient risk and contributing to antibiotic overprescription. Here, we present a deep-learning method that leverages patient data and available AST results to predict antibiotic susceptibilities that have not yet been measured. After training on three million AST results from 30 European countries, the method achieved an average accuracy of 93% across bacterial species and antibiotics. It predicted susceptibility with an average major error rate below 5% for quinolones, cephalosporins, and carbapenems, and below 8% and 14% for aminoglycosides and penicillins, respectively. Furthermore, the model predicted resistance with an average very major error rate below 10% for cephalosporins, carbapenems, and aminoglycosides, but with higher very major error rates for penicillins and quinolones. We combined the method with conformal prediction and demonstrated accurate estimation of the predictive uncertainty at the patient level. Our results suggest that artificial intelligence-based decision support may offer new means to meet the growing burden of antibiotic resistance.