A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food...

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Autores principales: Wylezich, Claudia, Papa, Anna, Beer, Martin, Höper, Dirk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117295/
https://www.ncbi.nlm.nih.gov/pubmed/30166611
http://dx.doi.org/10.1038/s41598-018-31496-1
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author Wylezich, Claudia
Papa, Anna
Beer, Martin
Höper, Dirk
author_facet Wylezich, Claudia
Papa, Anna
Beer, Martin
Höper, Dirk
author_sort Wylezich, Claudia
collection PubMed
description Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.
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spelling pubmed-61172952018-09-05 A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection Wylezich, Claudia Papa, Anna Beer, Martin Höper, Dirk Sci Rep Article Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework. Nature Publishing Group UK 2018-08-30 /pmc/articles/PMC6117295/ /pubmed/30166611 http://dx.doi.org/10.1038/s41598-018-31496-1 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Wylezich, Claudia
Papa, Anna
Beer, Martin
Höper, Dirk
A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title_full A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title_fullStr A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title_full_unstemmed A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title_short A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
title_sort versatile sample processing workflow for metagenomic pathogen detection
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117295/
https://www.ncbi.nlm.nih.gov/pubmed/30166611
http://dx.doi.org/10.1038/s41598-018-31496-1
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