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Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS
Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid p...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8290857/ https://www.ncbi.nlm.nih.gov/pubmed/34295837 http://dx.doi.org/10.3389/fcimb.2021.687240 |
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author | Ning, Ya-Ting Yang, Wen-Hang Zhang, Wei Xiao, Meng Wang, Yao Zhang, Jing-Jia Zhang, Ge Duan, Si-Meng Dong, Ai-Ying Guo, Da-Wen Zou, Gui-Ling Wen, Hai-Nan Guo, Yan-Yan Chen, Li-Ping Chai, Miao He, Jing-Dong Duan, Qiong Zhang, Li-Xia Zhang, Li Xu, Ying-Chun |
author_facet | Ning, Ya-Ting Yang, Wen-Hang Zhang, Wei Xiao, Meng Wang, Yao Zhang, Jing-Jia Zhang, Ge Duan, Si-Meng Dong, Ai-Ying Guo, Da-Wen Zou, Gui-Ling Wen, Hai-Nan Guo, Yan-Yan Chen, Li-Ping Chai, Miao He, Jing-Dong Duan, Qiong Zhang, Li-Xia Zhang, Li Xu, Ying-Chun |
author_sort | Ning, Ya-Ting |
collection | PubMed |
description | Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. The better method was applied to build a filamentous fungi in-house spectra library for the M-Discover 100 MS, and then another one and routine method were performed in parallel to verify the accuracy and commonality of the in-house library. Using the two optimized methods, the dedicated operating time before MALDI-TOF MS analysis was reduced from 30 min to 7 (ZSB) or 5 (FUS) min per sample, with only a few seconds added for each additional strain. And both two methods identified isolates from most mold types equal to or better than the routine method, and the total correct identification rate using VITEK MS was 79.67, 76.42, and 76.42%, respectively. On the other hand, the two rapid methods generally achieved higher maximum and minimum S/N ratios with these isolates tested as compared to the routine method. Besides, the ZSB method produced overall mean of maximum and minimum S/N ratio higher than that by FUS. An in-house library of M-Discover MS was successfully built from 135 isolates from 42 species belonging to 18 genera using the ZSB method. Analysis of 467 isolates resulted in 97.22% correctly identified isolates to the species level by the ZSB method versus 95.50% by the routine method. The two novel methods are time- and cost-effective and allow efficient identification of filamentous fungi while providing a simplified procedure to build an in-house library. Thus, more clinical laboratories may consider adopting MALDI-TOF MS for filamentous fungi identification in the future. |
format | Online Article Text |
id | pubmed-8290857 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-82908572021-07-21 Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS Ning, Ya-Ting Yang, Wen-Hang Zhang, Wei Xiao, Meng Wang, Yao Zhang, Jing-Jia Zhang, Ge Duan, Si-Meng Dong, Ai-Ying Guo, Da-Wen Zou, Gui-Ling Wen, Hai-Nan Guo, Yan-Yan Chen, Li-Ping Chai, Miao He, Jing-Dong Duan, Qiong Zhang, Li-Xia Zhang, Li Xu, Ying-Chun Front Cell Infect Microbiol Cellular and Infection Microbiology Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. The better method was applied to build a filamentous fungi in-house spectra library for the M-Discover 100 MS, and then another one and routine method were performed in parallel to verify the accuracy and commonality of the in-house library. Using the two optimized methods, the dedicated operating time before MALDI-TOF MS analysis was reduced from 30 min to 7 (ZSB) or 5 (FUS) min per sample, with only a few seconds added for each additional strain. And both two methods identified isolates from most mold types equal to or better than the routine method, and the total correct identification rate using VITEK MS was 79.67, 76.42, and 76.42%, respectively. On the other hand, the two rapid methods generally achieved higher maximum and minimum S/N ratios with these isolates tested as compared to the routine method. Besides, the ZSB method produced overall mean of maximum and minimum S/N ratio higher than that by FUS. An in-house library of M-Discover MS was successfully built from 135 isolates from 42 species belonging to 18 genera using the ZSB method. Analysis of 467 isolates resulted in 97.22% correctly identified isolates to the species level by the ZSB method versus 95.50% by the routine method. The two novel methods are time- and cost-effective and allow efficient identification of filamentous fungi while providing a simplified procedure to build an in-house library. Thus, more clinical laboratories may consider adopting MALDI-TOF MS for filamentous fungi identification in the future. Frontiers Media S.A. 2021-07-06 /pmc/articles/PMC8290857/ /pubmed/34295837 http://dx.doi.org/10.3389/fcimb.2021.687240 Text en Copyright © 2021 Ning, Yang, Zhang, Xiao, Wang, Zhang, Zhang, Duan, Dong, Guo, Zou, Wen, Guo, Chen, Chai, He, Duan, Zhang, Zhang and Xu 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 | Cellular and Infection Microbiology Ning, Ya-Ting Yang, Wen-Hang Zhang, Wei Xiao, Meng Wang, Yao Zhang, Jing-Jia Zhang, Ge Duan, Si-Meng Dong, Ai-Ying Guo, Da-Wen Zou, Gui-Ling Wen, Hai-Nan Guo, Yan-Yan Chen, Li-Ping Chai, Miao He, Jing-Dong Duan, Qiong Zhang, Li-Xia Zhang, Li Xu, Ying-Chun Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title | Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title_full | Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title_fullStr | Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title_full_unstemmed | Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title_short | Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS |
title_sort | developing two rapid protein extraction methods using focused-ultrasonication and zirconia-silica beads for filamentous fungi identification by maldi-tof ms |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8290857/ https://www.ncbi.nlm.nih.gov/pubmed/34295837 http://dx.doi.org/10.3389/fcimb.2021.687240 |
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