PARGT: a software tool for predicting antimicrobial resistance in bacteria

Sci Rep. 2020 Jul 3;10(1):11033. doi: 10.1038/s41598-020-67949-9.

Abstract

With the ever-increasing availability of whole-genome sequences, machine-learning approaches can be used as an alternative to traditional alignment-based methods for identifying new antimicrobial-resistance genes. Such approaches are especially helpful when pathogens cannot be cultured in the lab. In previous work, we proposed a game-theory-based feature evaluation algorithm. When using the protein characteristics identified by this algorithm, called 'features' in machine learning, our model accurately identified antimicrobial resistance (AMR) genes in Gram-negative bacteria. Here we extend our study to Gram-positive bacteria showing that coupling game-theory-identified features with machine learning achieved classification accuracies between 87% and 90% for genes encoding resistance to the antibiotics bacitracin and vancomycin. Importantly, we present a standalone software tool that implements the game-theory algorithm and machine-learning model used in these studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacitracin / pharmacology
  • Bacteria / drug effects
  • Bacteria / genetics*
  • Computational Biology / methods*
  • Drug Resistance, Bacterial*
  • Game Theory
  • Machine Learning
  • Microbial Sensitivity Tests
  • Software
  • Vancomycin / pharmacology
  • Whole Genome Sequencing

Substances

  • Anti-Bacterial Agents
  • Bacitracin
  • Vancomycin