Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

ABSTRACT Machine learning has proven to be a powerful method to predict antimicrobial resistance (AMR) without using prior knowledge for selected bacterial species-antimicrobial combinations. To date, only species-specific machine learning models have been developed, and to the best of our knowledge, the inclusion of information from multiple species has not been attempted. The aim of this study was to determine the feasibility of including information from multiple bacterial species to predict AMR for an individual species, since this may make it easier to train and update resistance predictions for multiple species and may lead to improved predictions. Whole-genome sequence data and susceptibility profiles from 3,528 Mycobacterium tuberculosis, 1,694 Escherichia coli, 658 Salmonella enterica, and 1,236 Staphylococcus aureus isolates were included. We developed machine learning models trained by the features of the PointFinder and ResFinder programs detected to predict binary (susceptible/resistant) AMR profiles. We tested four feature representation methods to determine the most efficient way for introducing features into the models. When training the model only on the Mycobacterium tuberculosis isolates, high prediction performances were obtained for the six AMR profiles included. By adding information on ciprofloxacin from the additional 3,588 isolates, there was no reduction in performance for the other antimicrobials but an increased performance for ciprofloxacin AMR profile prediction for Mycobacterium tuberculosis and Escherichia coli. In conclusion, the species-independent models can predict multi-AMR profiles for multiple species without losing any robustness. IMPORTANCE Machine learning is a proven method to predict AMR; however, the performance of any machine learning model depends on the quality of the input data. Therefore, we evaluated different methods of representing information about mutations as well as mobilizable genes, so that the information can serve as input for a robust model. We combined data from multiple bacterial species in order to develop species-independent machine learning models that can predict resistance profiles for multiple antimicrobials and species with high performance.