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Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms

Shigella and enterotoxigenic Escherichia coli (ETEC) are major bacterial pathogens of diarrheal disease that is the second leading cause of childhood mortality globally. Currently, it is well known that Shigella spp., and E. coli are very closely related with many common characteristics. Evolutionar...

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Autores principales: Liu, Wei, Tang, Jia-Wei, Mou, Jing-Yi, Lyu, Jing-Wen, Di, Yu-Wei, Liao, Ya-Long, Luo, Yan-Fei, Li, Zheng-Kang, Wu, Xiang, Wang, Liang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10030586/
https://www.ncbi.nlm.nih.gov/pubmed/36970678
http://dx.doi.org/10.3389/fmicb.2023.1101357
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author Liu, Wei
Tang, Jia-Wei
Mou, Jing-Yi
Lyu, Jing-Wen
Di, Yu-Wei
Liao, Ya-Long
Luo, Yan-Fei
Li, Zheng-Kang
Wu, Xiang
Wang, Liang
author_facet Liu, Wei
Tang, Jia-Wei
Mou, Jing-Yi
Lyu, Jing-Wen
Di, Yu-Wei
Liao, Ya-Long
Luo, Yan-Fei
Li, Zheng-Kang
Wu, Xiang
Wang, Liang
author_sort Liu, Wei
collection PubMed
description Shigella and enterotoxigenic Escherichia coli (ETEC) are major bacterial pathogens of diarrheal disease that is the second leading cause of childhood mortality globally. Currently, it is well known that Shigella spp., and E. coli are very closely related with many common characteristics. Evolutionarily speaking, Shigella spp., are positioned within the phylogenetic tree of E. coli. Therefore, discrimination of Shigella spp., from E. coli is very difficult. Many methods have been developed with the aim of differentiating the two species, which include but not limited to biochemical tests, nucleic acids amplification, and mass spectrometry, etc. However, these methods suffer from high false positive rates and complicated operation procedures, which requires the development of novel methods for accurate and rapid identification of Shigella spp., and E. coli. As a low-cost and non-invasive method, surface enhanced Raman spectroscopy (SERS) is currently under intensive study for its diagnostic potential in bacterial pathogens, which is worthy of further investigation for its application in bacterial discrimination. In this study, we focused on clinically isolated E. coli strains and Shigella species (spp.), that is, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, based on which SERS spectra were generated and characteristic peaks for Shigella spp., and E. coli were identified, revealing unique molecular components in the two bacterial groups. Further comparative analysis of machine learning algorithms showed that, the Convolutional Neural Network (CNN) achieved the best performance and robustness in bacterial discrimination capacity when compared with Random Forest (RF) and Support Vector Machine (SVM) algorithms. Taken together, this study confirmed that SERS paired with machine learning could achieve high accuracy in discriminating Shigella spp., from E. coli, which facilitated its application potential for diarrheal prevention and control in clinical settings.
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spelling pubmed-100305862023-03-23 Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms Liu, Wei Tang, Jia-Wei Mou, Jing-Yi Lyu, Jing-Wen Di, Yu-Wei Liao, Ya-Long Luo, Yan-Fei Li, Zheng-Kang Wu, Xiang Wang, Liang Front Microbiol Microbiology Shigella and enterotoxigenic Escherichia coli (ETEC) are major bacterial pathogens of diarrheal disease that is the second leading cause of childhood mortality globally. Currently, it is well known that Shigella spp., and E. coli are very closely related with many common characteristics. Evolutionarily speaking, Shigella spp., are positioned within the phylogenetic tree of E. coli. Therefore, discrimination of Shigella spp., from E. coli is very difficult. Many methods have been developed with the aim of differentiating the two species, which include but not limited to biochemical tests, nucleic acids amplification, and mass spectrometry, etc. However, these methods suffer from high false positive rates and complicated operation procedures, which requires the development of novel methods for accurate and rapid identification of Shigella spp., and E. coli. As a low-cost and non-invasive method, surface enhanced Raman spectroscopy (SERS) is currently under intensive study for its diagnostic potential in bacterial pathogens, which is worthy of further investigation for its application in bacterial discrimination. In this study, we focused on clinically isolated E. coli strains and Shigella species (spp.), that is, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, based on which SERS spectra were generated and characteristic peaks for Shigella spp., and E. coli were identified, revealing unique molecular components in the two bacterial groups. Further comparative analysis of machine learning algorithms showed that, the Convolutional Neural Network (CNN) achieved the best performance and robustness in bacterial discrimination capacity when compared with Random Forest (RF) and Support Vector Machine (SVM) algorithms. Taken together, this study confirmed that SERS paired with machine learning could achieve high accuracy in discriminating Shigella spp., from E. coli, which facilitated its application potential for diarrheal prevention and control in clinical settings. Frontiers Media S.A. 2023-03-08 /pmc/articles/PMC10030586/ /pubmed/36970678 http://dx.doi.org/10.3389/fmicb.2023.1101357 Text en Copyright © 2023 Liu, Tang, Mou, Lyu, Di, Liao, Luo, Li, Wu and Wang. 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
Liu, Wei
Tang, Jia-Wei
Mou, Jing-Yi
Lyu, Jing-Wen
Di, Yu-Wei
Liao, Ya-Long
Luo, Yan-Fei
Li, Zheng-Kang
Wu, Xiang
Wang, Liang
Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title_full Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title_fullStr Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title_full_unstemmed Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title_short Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms
title_sort rapid discrimination of shigella spp. and escherichia coli via label-free surface enhanced raman spectroscopy coupled with machine learning algorithms
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10030586/
https://www.ncbi.nlm.nih.gov/pubmed/36970678
http://dx.doi.org/10.3389/fmicb.2023.1101357
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