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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Published in:Scientific reports Vol. 8; no. 1; pp. 13108 - 12
Main Authors: Wylezich, Claudia, Papa, Anna, Beer, Martin, Höper, Dirk
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 30.08.2018
Nature Publishing Group
Subjects:
45/90
45/91
692/699/255/1318
692/699/255/1715
692/699/255/2514
Animal human relations
Humanities and Social Sciences
multidisciplinary
Pathogens
RNA viruses
Science
Science (multidisciplinary)
ISSN:2045-2322, 2045-2322
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Abstract 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.
AbstractList 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.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.
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.
ArticleNumber 13108
Author Wylezich, Claudia
Beer, Martin
Höper, Dirk
Papa, Anna
Author_xml – sequence: 1
  givenname: Claudia
  surname: Wylezich
  fullname: Wylezich, Claudia
  email: Claudia.Wylezich@fli.de
  organization: Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI)
– sequence: 2
  givenname: Anna
  surname: Papa
  fullname: Papa, Anna
  organization: Department of Microbiology, Medical School, Aristotle University of Thessaloniki
– sequence: 3
  givenname: Martin
  surname: Beer
  fullname: Beer, Martin
  organization: Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI)
– sequence: 4
  givenname: Dirk
  orcidid: 0000-0001-8408-2274
  surname: Höper
  fullname: Höper, Dirk
  email: Dirk.Hoeper@fli.de
  organization: Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI)
BackLink https://www.ncbi.nlm.nih.gov/pubmed/30166611$$D View this record in MEDLINE/PubMed
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Snippet Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA...
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692/699/255/1318
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Animal human relations
Humanities and Social Sciences
multidisciplinary
Pathogens
RNA viruses
Science
Science (multidisciplinary)
Title A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
URI https://link.springer.com/article/10.1038/s41598-018-31496-1
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Volume 8
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