PARGT: a software tool for predicting antimicrobial resistance in bacteria
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 t...
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| Auteurs principaux: | , , |
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| Format: | article |
| Langue: | EN |
| Publié: |
Nature Portfolio
2020
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| Sujets: | |
| Accès en ligne: | https://doaj.org/article/fecbf25a3723448bb1b91406076c2eaf |
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| Résumé: | 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. |
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