Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Academic Article uri icon

Overview

abstract

  • 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.

publication date

  • January 11, 2018

Research

keywords

  • Anti-Bacterial Agents
  • Klebsiella Infections
  • Klebsiella pneumoniae
  • Whole Genome Sequencing

Identity

PubMed Central ID

  • PMC5765115

Scopus Document Identifier

  • 85040465895

Digital Object Identifier (DOI)

  • 10.1093/nar/gkw290

PubMed ID

  • 29323230

Additional Document Info

volume

  • 8

issue

  • 1