A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Scientific Reports
Claudia WylezichDirk Höper

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.

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Citations

Nov 9, 2018·Transboundary and Emerging Diseases·Dennis RubbenstrothLydia Teske
Mar 26, 2019·Emerging Infectious Diseases·Jan H ForthMartin Beer
May 6, 2019·Genes·Arthur W D EdridgeLia van der Hoek
Oct 18, 2019·BioTechniques·Leonie F Forth, Dirk Höper
Mar 31, 2020·Transboundary and Emerging Diseases·Vanessa SchulzeDennis Rubbenstroth
Apr 21, 2020·Environmental Microbiology·Jun-Seob KimChoong-Min Ryu
Jun 28, 2020·Parasitology Research·Claudia WylezichDirk Höper
Apr 25, 2020·Virus Genes·Florian BinderRainer G Ulrich
Sep 5, 2020·BMC Infectious Diseases·Jacqueline KingAnne Pohlmann
Nov 5, 2019·Frontiers in Microbiology·Sofia StrubbiaFrançoise S Le Guyader
Aug 27, 2019·Frontiers in Microbiology·Josephine GrützkeCarlus Deneke
Jan 19, 2020·Virology Journal·Silvia BlahakKore Schlottau
Nov 21, 2019·Indian Journal of Medical Microbiology·Jobin John JacobKarthick Vasudevan
May 23, 2020·Viruses·Joyce Odeke AkelloChristian Beuret
Oct 9, 2020·Nature·Andrew J BennettTony L Goldberg
Dec 2, 2020·Microorganisms·Claudia SalaAlessandra De Cesare
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Apr 1, 2019·Indian Journal of Medical Microbiology·Jobin John JacobKarthick Vasudevan
Feb 9, 2021·Computational and Structural Biotechnology Journal·Arnt EbingerDirk Höper
Jul 6, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Ibrahim MoharamChristian Grund
Mar 4, 2021·Transboundary and Emerging Diseases·Pauline Dianne SantosUte Ziegler
Mar 14, 2021·Molecular Ecology Resources·Patricia GilSerafin Gutierrez
Apr 9, 2021·One Health Outlook·Marion DesdouitsMarion P G Koopmans
Oct 22, 2020·Transboundary and Emerging Diseases·Carola Sauter-LouisSandra Blome
Jul 20, 2021·Frontiers in Microbiology·Frits F J FranssenMark W J van Passel

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Datasets Mentioned

BETA
KF478765

Methods Mentioned

BETA
PCR
Chip
nucleic acid extraction

Software Mentioned

RIEMS

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