Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput, and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done.
In the current study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF), and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin (CIP), cefotaxime (CTX), ceftazidime (CTZ), and gentamicin (GEN) based on WGS data with label encoding and FCGR encoding.
