Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

Type Article
Date 2020-12
Language English
Author(s) Sala Claudia1, Mordhorst Hanne2, Grützke Joesphine3, Brinkmann Annika4, Petersen Thomas N2, Poulsen Casper2, Cotter Paul D5, Crispie Fiona5, Ellis Richard J6, Castellani Gastone7, Amid Clara8, Hakhverdyan Mikhayil9, Le Guyader Soizick10, Manfreda Gerardo11, Mossong Joël12, Nitsche Andreas4, Ragimbeau Catherine12, Schaeffer Julien10, Schlundt Joergen13, Tay Moon Y. F.13, Aarestrup Frank M.2, Hendriksen Rene S.2, Pamp Sünje Johanna2, de Cesare Alessandra14
Affiliation(s) 1 : Department of Physics and Astronomy, University of Bologna, 40127 Bologna, Italy
2 : Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark
3 : German Federal Institute for Risk Assessment, Department of Biological Safety, 12277 Berlin, Germany
4 : Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany
5 : Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and Vistamilk, T12 YN60 Co. Cork, Ireland
6 : Surveillance and Laboratory Services Department, Animal and Plant Health Agency, APHA Weybridge, Addlestone, Surrey, KT15 3NB, UK
7 : Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40127 Bologna, Italy
8 : European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
9 : National Veterinary Institute, Ulls väg 2B, 75189 Uppsala, Sweden
10 : Laboratoire de Microbiologie, CEDEX 03, 44311 Nantes, France
11 : Department of Agricultural and Food Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
12 : Epidemiology and Microbial Genomics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
13 : Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), 62 Nanyang Dr, Singapore 637459, Singapore
14 : Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell’Emilia, Italy * Author to whom correspondence should be addressed.
Source Microorganisms (2076-2607) (Multidisciplinary Digital Publishing Institute), 2020-12 , Vol. 8 , N. 12 , P. 1861 (16p.)
DOI 10.3390/microorganisms8121861
WOS© Times Cited 1
Note This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods
Keyword(s) shotgun metagenomics, smoked salmon, proficiency test, experimentally spiked samples, wet-lab protocols
Abstract

An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.

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Sala Claudia, Mordhorst Hanne, Grützke Joesphine, Brinkmann Annika, Petersen Thomas N, Poulsen Casper, Cotter Paul D, Crispie Fiona, Ellis Richard J, Castellani Gastone, Amid Clara, Hakhverdyan Mikhayil, Le Guyader Soizick, Manfreda Gerardo, Mossong Joël, Nitsche Andreas, Ragimbeau Catherine, Schaeffer Julien, Schlundt Joergen, Tay Moon Y. F., Aarestrup Frank M., Hendriksen Rene S., Pamp Sünje Johanna, de Cesare Alessandra (2020). Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms, 8(12), 1861 (16p.). Publisher's official version : https://doi.org/10.3390/microorganisms8121861 , Open Access version : https://archimer.ifremer.fr/doc/00664/77615/