English (United Kingdom)

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https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

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Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of  Klebsiella pneumoniae  to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ±1 two-fold dilution factor, is 92%. Individual accuracies are ≥90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a complete  in silico  MIC prediction panel for  K. pneumoniae  and provides a framework for building MIC prediction models for other pathogenic bacteria.

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae