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Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has recently become a useful analytical approach for microbial identification. The presence and absence of specific peaks on MS spectra are commonly used to identify the bacterial species and predict antibi...

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Autores principales: Wang, Hsin-Yao, Hsieh, Tsung-Ting, Chung, Chia-Ru, Chang, Hung-Ching, Horng, Jorng-Tzong, Lu, Jang-Jih, Huang, Jia-Hsin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9231590/
https://www.ncbi.nlm.nih.gov/pubmed/35756017
http://dx.doi.org/10.3389/fmicb.2022.821233
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author Wang, Hsin-Yao
Hsieh, Tsung-Ting
Chung, Chia-Ru
Chang, Hung-Ching
Horng, Jorng-Tzong
Lu, Jang-Jih
Huang, Jia-Hsin
author_facet Wang, Hsin-Yao
Hsieh, Tsung-Ting
Chung, Chia-Ru
Chang, Hung-Ching
Horng, Jorng-Tzong
Lu, Jang-Jih
Huang, Jia-Hsin
author_sort Wang, Hsin-Yao
collection PubMed
description Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has recently become a useful analytical approach for microbial identification. The presence and absence of specific peaks on MS spectra are commonly used to identify the bacterial species and predict antibiotic-resistant strains. However, the conventional approach using few single peaks would result in insufficient prediction power without using complete information of whole MS spectra. In the past few years, machine learning algorithms have been successfully applied to analyze the MALDI-TOF MS peaks pattern for rapid strain typing. In this study, we developed a convolutional neural network (CNN) method to deal with the complete information of MALDI-TOF MS spectra for detecting Enterococcus faecium, which is one of the leading pathogens in the world. We developed a CNN model to rapidly and accurately predict vancomycin-resistant Enterococcus faecium (VREfm) samples from the whole mass spectra profiles of clinical samples. The CNN models demonstrated good classification performances with the average area under the receiver operating characteristic curve (AUROC) of 0.887 when using external validation data independently. Additionally, we employed the score-class activation mapping (CAM) method to identify the important features of our CNN models and found some discriminative signals that can substantially contribute to detecting the ion of resistance. This study not only utilized the complete information of MALTI-TOF MS data directly but also provided a practical means for rapid detection of VREfm using a deep learning algorithm.
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spelling pubmed-92315902022-06-25 Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach Wang, Hsin-Yao Hsieh, Tsung-Ting Chung, Chia-Ru Chang, Hung-Ching Horng, Jorng-Tzong Lu, Jang-Jih Huang, Jia-Hsin Front Microbiol Microbiology Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has recently become a useful analytical approach for microbial identification. The presence and absence of specific peaks on MS spectra are commonly used to identify the bacterial species and predict antibiotic-resistant strains. However, the conventional approach using few single peaks would result in insufficient prediction power without using complete information of whole MS spectra. In the past few years, machine learning algorithms have been successfully applied to analyze the MALDI-TOF MS peaks pattern for rapid strain typing. In this study, we developed a convolutional neural network (CNN) method to deal with the complete information of MALDI-TOF MS spectra for detecting Enterococcus faecium, which is one of the leading pathogens in the world. We developed a CNN model to rapidly and accurately predict vancomycin-resistant Enterococcus faecium (VREfm) samples from the whole mass spectra profiles of clinical samples. The CNN models demonstrated good classification performances with the average area under the receiver operating characteristic curve (AUROC) of 0.887 when using external validation data independently. Additionally, we employed the score-class activation mapping (CAM) method to identify the important features of our CNN models and found some discriminative signals that can substantially contribute to detecting the ion of resistance. This study not only utilized the complete information of MALTI-TOF MS data directly but also provided a practical means for rapid detection of VREfm using a deep learning algorithm. Frontiers Media S.A. 2022-06-06 /pmc/articles/PMC9231590/ /pubmed/35756017 http://dx.doi.org/10.3389/fmicb.2022.821233 Text en Copyright © 2022 Wang, Hsieh, Chung, Chang, Horng, Lu and Huang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Wang, Hsin-Yao
Hsieh, Tsung-Ting
Chung, Chia-Ru
Chang, Hung-Ching
Horng, Jorng-Tzong
Lu, Jang-Jih
Huang, Jia-Hsin
Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title_full Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title_fullStr Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title_full_unstemmed Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title_short Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
title_sort efficiently predicting vancomycin resistance of enterococcus faecium from maldi-tof ms spectra using a deep learning-based approach
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9231590/
https://www.ncbi.nlm.nih.gov/pubmed/35756017
http://dx.doi.org/10.3389/fmicb.2022.821233
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