Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset
Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detectio...
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Format: | Article |
Language: | English |
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Frontiers Media S.A.
2020-11-01
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Series: | Frontiers in Microbiology |
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Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2020.575377/full |
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doaj-164e01e2d411478786f4f6ee00210833 |
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Article |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dirk Höper Josephine Grützke Annika Brinkmann Joël Mossong Sébastien Matamoros Richard J. Ellis Carlus Deneke Simon H. Tausch Isabel Cuesta Sara Monzón Miguel Juliá Thomas Nordahl Petersen Rene S. Hendriksen Sünje J. Pamp Mikael Leijon Mikhayil Hakhverdyan Aaron M. Walsh Paul D. Cotter Lakshmi Chandrasekaran Moon Y. F. Tay Joergen Schlundt Claudia Sala Alessandra De Cesare Andreas Nitsche Martin Beer Claudia Wylezich |
spellingShingle |
Dirk Höper Josephine Grützke Annika Brinkmann Joël Mossong Sébastien Matamoros Richard J. Ellis Carlus Deneke Simon H. Tausch Isabel Cuesta Sara Monzón Miguel Juliá Thomas Nordahl Petersen Rene S. Hendriksen Sünje J. Pamp Mikael Leijon Mikhayil Hakhverdyan Aaron M. Walsh Paul D. Cotter Lakshmi Chandrasekaran Moon Y. F. Tay Joergen Schlundt Claudia Sala Alessandra De Cesare Andreas Nitsche Martin Beer Claudia Wylezich Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset Frontiers in Microbiology background contamination diagnostic assessment high-throughput sequencing metagenomics pathogen proficiency test |
author_facet |
Dirk Höper Josephine Grützke Annika Brinkmann Joël Mossong Sébastien Matamoros Richard J. Ellis Carlus Deneke Simon H. Tausch Isabel Cuesta Sara Monzón Miguel Juliá Thomas Nordahl Petersen Rene S. Hendriksen Sünje J. Pamp Mikael Leijon Mikhayil Hakhverdyan Aaron M. Walsh Paul D. Cotter Lakshmi Chandrasekaran Moon Y. F. Tay Joergen Schlundt Claudia Sala Alessandra De Cesare Andreas Nitsche Martin Beer Claudia Wylezich |
author_sort |
Dirk Höper |
title |
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset |
title_short |
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset |
title_full |
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset |
title_fullStr |
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset |
title_full_unstemmed |
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset |
title_sort |
proficiency testing of metagenomics-based detection of food-borne pathogens using a complex artificial sequencing dataset |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2020-11-01 |
description |
Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants’ reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary. |
topic |
background contamination diagnostic assessment high-throughput sequencing metagenomics pathogen proficiency test |
url |
https://www.frontiersin.org/articles/10.3389/fmicb.2020.575377/full |
work_keys_str_mv |
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doaj-164e01e2d411478786f4f6ee002108332020-11-25T04:08:08ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-11-011110.3389/fmicb.2020.575377575377Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing DatasetDirk Höper0Josephine Grützke1Annika Brinkmann2Joël Mossong3Sébastien Matamoros4Richard J. Ellis5Carlus Deneke6Simon H. Tausch7Isabel Cuesta8Sara Monzón9Miguel Juliá10Thomas Nordahl Petersen11Rene S. Hendriksen12Sünje J. Pamp13Mikael Leijon14Mikhayil Hakhverdyan15Aaron M. Walsh16Paul D. Cotter17Lakshmi Chandrasekaran18Moon Y. F. Tay19Joergen Schlundt20Claudia Sala21Alessandra De Cesare22Andreas Nitsche23Martin Beer24Claudia Wylezich25Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyCentre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, GermanyDépartement de Microbiologie, Laboratoire National de Santé, Dudelange, LuxembourgDepartment of Medical Microbiology, Amsterdam UMC University of Amsterdam, Amsterdam, NetherlandsAnimal and Plant Health Agency, Addlestone, United KingdomDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyBioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, SpainBioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, SpainBioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, SpainResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkDepartment of Microbiology, National Veterinary Institute (SVA), Uppsala, SwedenDepartment of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden0Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland0Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland1Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore1Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore1Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore2Department of Physics and Astronomy, University of Bologna, Bologna, Italy3Department of Veterinary Medical Sciences, University of Bologna, Bologna, ItalyCentre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyMetagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants’ reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary.https://www.frontiersin.org/articles/10.3389/fmicb.2020.575377/fullbackground contaminationdiagnostic assessmenthigh-throughput sequencingmetagenomicspathogenproficiency test |