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Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We te...

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Autores principales: Buytaers, Florence E., Verhaegen, Bavo, Gand, Mathieu, D’aes, Jolien, Vanneste, Kevin, Roosens, Nancy H. C., Marchal, Kathleen, Denayer, Sarah, De Keersmaecker, Sigrid C. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654790/
https://www.ncbi.nlm.nih.gov/pubmed/36359961
http://dx.doi.org/10.3390/foods11213348
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author Buytaers, Florence E.
Verhaegen, Bavo
Gand, Mathieu
D’aes, Jolien
Vanneste, Kevin
Roosens, Nancy H. C.
Marchal, Kathleen
Denayer, Sarah
De Keersmaecker, Sigrid C. J.
author_facet Buytaers, Florence E.
Verhaegen, Bavo
Gand, Mathieu
D’aes, Jolien
Vanneste, Kevin
Roosens, Nancy H. C.
Marchal, Kathleen
Denayer, Sarah
De Keersmaecker, Sigrid C. J.
author_sort Buytaers, Florence E.
collection PubMed
description In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field.
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spelling pubmed-96547902022-11-15 Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study Buytaers, Florence E. Verhaegen, Bavo Gand, Mathieu D’aes, Jolien Vanneste, Kevin Roosens, Nancy H. C. Marchal, Kathleen Denayer, Sarah De Keersmaecker, Sigrid C. J. Foods Article In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field. MDPI 2022-10-25 /pmc/articles/PMC9654790/ /pubmed/36359961 http://dx.doi.org/10.3390/foods11213348 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Buytaers, Florence E.
Verhaegen, Bavo
Gand, Mathieu
D’aes, Jolien
Vanneste, Kevin
Roosens, Nancy H. C.
Marchal, Kathleen
Denayer, Sarah
De Keersmaecker, Sigrid C. J.
Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title_full Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title_fullStr Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title_full_unstemmed Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title_short Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
title_sort metagenomics to detect and characterize viruses in food samples at genome level? lessons learnt from a norovirus study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654790/
https://www.ncbi.nlm.nih.gov/pubmed/36359961
http://dx.doi.org/10.3390/foods11213348
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