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Fraiture MA, Gobbo A, Guillitte C, Marchesi U, Verginelli D, De Greve J, D'aes J, Vanneste K, Papazova N, Roosens NH. Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GM Bacillus licheniformis producing alpha-amylase. Food Chem (Oxf) 2024; 8:100186. [PMID: 38179151 PMCID: PMC10762378 DOI: 10.1016/j.fochms.2023.100186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/16/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024]
Abstract
Using high-throughput metagenomics on commercial microbial fermentation products, DNA from a new unauthorized genetically modified microorganism (GMM), namely the GM B. licheniformis strain producing alpha-amylase (GMM alpha-amylase2), was recently discovered and characterized. On this basis, a new qPCR method targeting an unnatural association of sequences specific to the GMM alpha-amylase2 strain was designed and developed in this study, allowing to strengthen the current GMM detection strategy. The performance of the newly developed qPCR method was assessed for its specificity and sensitivity to comply with the minimum performance requirements established by the European Network of GMO Laboratories for GMO analysis. Moreover, the transferability of the in house validated qPCR method was demonstrated. Finally, its applicability was confirmed by a pilot market surveillance of GMM contaminations conducted for the first time on 40 alpha-amylase food enzyme products labelled as containing alpha-amylase. This pilot market surveillance allowed also to highlight numerous contaminations with GMM alpha-amylase2, including frequent cross-contaminations with other GMM strains previously characterized. In addition, the presence of full-length AMR genes, raising health concerns, was also reported.
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Affiliation(s)
- Marie-Alice Fraiture
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Chloé Guillitte
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Ugo Marchesi
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M.Aleandri”, Unità Operativa Semplice a valenza Direzionale – Ricerca e controllo degli organismi geneticamente modificati, via Appia Nuova 1411, 00178 Roma, Italia
| | - Daniela Verginelli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M.Aleandri”, Unità Operativa Semplice a valenza Direzionale – Ricerca e controllo degli organismi geneticamente modificati, via Appia Nuova 1411, 00178 Roma, Italia
| | - Joke De Greve
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Jolien D'aes
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Kevin Vanneste
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Nina Papazova
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Nancy H.C. Roosens
- Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium
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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. Water Environ Res 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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3
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Bogaerts B, Fraiture MA, Huwaert A, Van Nieuwenhuysen T, Jacobs B, Van Hoorde K, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B 2 products sold on the Belgian market using whole-genome sequencing. Front Microbiol 2023; 14:1173594. [PMID: 37415815 PMCID: PMC10321352 DOI: 10.3389/fmicb.2023.1173594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Bacillus cereus is a spore-forming bacterium that occurs as a contaminant in food and feed, occasionally resulting in food poisoning through the production of various toxins. In this study, we retrospectively characterized viable B. cereus sensu lato (s.l.) isolates originating from commercial vitamin B2 feed and food additives collected between 2016 and 2022 by the Belgian Federal Agency for the Safety of the Food Chain from products sold on the Belgian market. In total, 75 collected product samples were cultured on a general medium and, in case of bacterial growth, two isolates per product sample were collected and characterized using whole-genome sequencing (WGS) and subsequently characterized in terms of sequence type (ST), virulence gene profile, antimicrobial resistance (AMR) gene profile, plasmid content, and phylogenomic relationships. Viable B. cereus was identified in 18 of the 75 (24%) tested products, resulting in 36 WGS datasets, which were classified into eleven different STs, with ST165 (n = 10) and ST32 (n = 8) being the most common. All isolates carried multiple genes encoding virulence factors, including cytotoxin K-2 (52.78%) and cereulide (22.22%). Most isolates were predicted to be resistant to beta-lactam antibiotics (100%) and fosfomycin (88.89%), and a subset was predicted to be resistant to streptothricin (30.56%). Phylogenomic analysis revealed that some isolates obtained from different products were closely related or even identical indicating a likely common origin, whereas for some products the two isolates obtained did not show any close relationship to each other or other isolates found in other products. This study reveals that potentially pathogenic and drug-resistant B. cereus s.l. can be present in food and feed vitamin B2 additives that are commercially available, and that more research is warranted to assess whether their presence in these types of products poses a threat to consumers.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Bram Jacobs
- Foodborne Pathogens, Sciensano, Brussels, Belgium
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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D’aes J, Fraiture MA, Bogaerts B, De Keersmaecker SCJ, Roosens NHCJ, Vanneste K. Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products. Life (Basel) 2022; 12:life12121971. [PMID: 36556336 PMCID: PMC9781105 DOI: 10.3390/life12121971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.
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Fraiture MA, Guiderdoni E, Meunier AC, Papazova N, Roosens NH. ddPCR strategy to detect a gene-edited plant carrying a single variation point: Technical feasibility and interpretation issues. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Deckers M, De Loose M, Papazova N, Deforce D, Fraiture MA, Roosens NH. First monitoring for unauthorized genetically modified bacteria in food enzymes from the food market. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Deckers M, Braekel JV, Vanneste K, Deforce D, Fraiture MA, Roosens NHC. Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market. Database (Oxford) 2022; 2022:6551021. [PMID: 35311900 PMCID: PMC9216514 DOI: 10.1093/database/baac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2022] [Indexed: 11/20/2022]
Affiliation(s)
- Marie Deckers
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ghent B-9000, Ghent, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ghent B-9000, Ghent, Belgium
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Van Poelvoorde LAE, Gand M, Fraiture MA, De Keersmaecker SCJ, Verhaegen B, Van Hoorde K, Cay AB, Balmelle N, Herman P, Roosens N. Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution. Curr Issues Mol Biol 2021; 43:1937-1949. [PMID: 34889894 PMCID: PMC8928932 DOI: 10.3390/cimb43030134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Bavo Verhaegen
- Food Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (K.V.H.)
| | | | - Ann Brigitte Cay
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Nadège Balmelle
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, 1050 Brussels, Belgium;
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
- Correspondence:
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D’aes J, Fraiture MA, Bogaerts B, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products. Foods 2021; 10:2637. [PMID: 34828918 PMCID: PMC8624754 DOI: 10.3390/foods10112637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/02/2022] Open
Abstract
Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.
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Affiliation(s)
- Jolien D’aes
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Ghent, Belgium
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics (TAG), Department Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (J.D.); (M.-A.F.); (B.B.); (S.C.J.D.K.); (N.H.C.R.)
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Deckers M, Van Braeckel J, Vanneste K, Deforce D, Fraiture MA, Roosens NHC. Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market. Database (Oxford) 2021; 2021:6385791. [PMID: 34626475 PMCID: PMC8502015 DOI: 10.1093/database/baab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/14/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
Following the European Commission No. 1332/2008 regulation and the consequent necessity of a scientific evaluation of food enzymes (FEs) for their approval for sale on the European Union market, many FE dossiers have been submitted to the European Commission and various documents currently co-exist. In order to centralize all relevant information in one structured location that is easily accessible to support enforcement laboratories and the competent authorities, we developed a web application, called Food Enzyme Database (FEDA). FEDA allows searching and collection of information originating from many different sources in one centralized portal. Queries can be performed using key information types, which include information on the producing company, production source (strain type, genetically modified microorganism status), type of enzyme protein and evaluation status with employed evaluation criteria. The database contains all current publicly available information. Centralizing all information coupled with intuitive searching functionality also allows the generation of general statistics regarding the current market situation. FEDA is open access and is freely available at the following location: https://feda.sciensano.be. Database URL:https://feda.sciensano.be
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Affiliation(s)
- Marie Deckers
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium.,Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ghent B-9000, Belgium
| | - Julien Van Braeckel
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ghent B-9000, Belgium
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels 1050, Belgium
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Buytaers FE, Fraiture MA, Berbers B, Vandermassen E, Hoffman S, Papazova N, Vanneste K, Marchal K, Roosens NH, De Keersmaecker SC. A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products. Food Chemistry: Molecular Sciences 2021; 2:100023. [PMID: 35415629 PMCID: PMC8991599 DOI: 10.1016/j.fochms.2021.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 10/27/2022]
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Fraiture MA, Coucke W, Pol M, Rousset D, Gourinat AC, Biron A, Broeders S, Vandermassen E, Dupont-Rouzeyrol M, Roosens NHC. Non-Invasive versus Invasive Samples for Zika Virus Surveillance: A Comparative Study in New Caledonia and French Guiana in 2015-2016. Microorganisms 2021; 9:microorganisms9061312. [PMID: 34208593 PMCID: PMC8235784 DOI: 10.3390/microorganisms9061312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
Zika virus, an arbovirus responsible for major outbreaks, can cause serious health issues, such as neurological diseases. In the present study, different types of samples (serum, saliva, and urine), collected in 2015–2016 in New Caledonia and French Guiana from 53 patients presenting symptoms and clinical signs triggered by arbovirus infections, were analyzed using a recently developed, and in-house validated, 4-plex RT-qPCR TaqMan method for simultaneous detection and discrimination of the Zika and Chikungunya viruses. Subsequently, statistical analyses were performed in order to potentially establish recommendations regarding the choice of samples type to use for an efficient and early stage Zika infection diagnosis. On this basis, the use of only urine samples presented the highest probability to detect viral RNA from Zika virus. Moreover, such a probability was improved using both urine and saliva samples. Consequently, the added value of non-invasive samples, associated with a higher acceptance level for collection among patients, instead of serum samples, for the detection of Zika infections was illustrated.
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Affiliation(s)
- Marie-Alice Fraiture
- Transversal & Applied Genomics (TAG), Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium; (M.-A.F.); (S.B.); (E.V.)
| | - Wim Coucke
- Quality of Laboratories, Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium;
| | - Morgane Pol
- URE Dengue et Arboviroses, Institut Pasteur of New Caledonia, 11 avenue Paul Doumer, BP 61, CEDEX, 98845 Noumea, New Caledonia; (M.P.); (A.-C.G.); (A.B.); (M.D.-R.)
| | - Dominique Rousset
- Laboratoire de Virologie CNR Arbovirus, Institut Pasteur de la Guyane, 23 avenue Pasteur, BP 6010, CEDEX, 97306 Cayenne, French Guiana;
| | - Ann-Claire Gourinat
- URE Dengue et Arboviroses, Institut Pasteur of New Caledonia, 11 avenue Paul Doumer, BP 61, CEDEX, 98845 Noumea, New Caledonia; (M.P.); (A.-C.G.); (A.B.); (M.D.-R.)
| | - Antoine Biron
- URE Dengue et Arboviroses, Institut Pasteur of New Caledonia, 11 avenue Paul Doumer, BP 61, CEDEX, 98845 Noumea, New Caledonia; (M.P.); (A.-C.G.); (A.B.); (M.D.-R.)
| | - Sylvia Broeders
- Transversal & Applied Genomics (TAG), Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium; (M.-A.F.); (S.B.); (E.V.)
- Quality of Laboratories, Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium;
| | - Els Vandermassen
- Transversal & Applied Genomics (TAG), Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium; (M.-A.F.); (S.B.); (E.V.)
| | - Myrielle Dupont-Rouzeyrol
- URE Dengue et Arboviroses, Institut Pasteur of New Caledonia, 11 avenue Paul Doumer, BP 61, CEDEX, 98845 Noumea, New Caledonia; (M.P.); (A.-C.G.); (A.B.); (M.D.-R.)
| | - Nancy H. C. Roosens
- Transversal & Applied Genomics (TAG), Sciensano, rue Juliette Wytsman 14, 1050 Brussels, Belgium; (M.-A.F.); (S.B.); (E.V.)
- Correspondence: ; Tel.: +32-(0)-2-642-52-58
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Fraiture MA, Joly L, Vandermassen E, Delvoye M, Van Geel D, Michelet JY, Van Hoeck E, De Jaeger N, Papazova N, Roosens NH. Retrospective survey of unauthorized genetically modified bacteria harbouring antimicrobial resistance genes in feed additive vitamin B2 commercialized in Belgium: Challenges and solutions. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fraiture MA, Papazova N, Roosens NHC. DNA walking strategy to identify unauthorized genetically modified bacteria in microbial fermentation products. Int J Food Microbiol 2020; 337:108913. [PMID: 33126077 DOI: 10.1016/j.ijfoodmicro.2020.108913] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 01/07/2023]
Abstract
Recently, unexpected contaminations of unauthorized genetically modified microorganisms (GMM) carrying antimicrobial resistance (AMR) genes were reported in microbial fermentation products commercialized on the food and feed chain. To guarantee the traceability and safety of the food and feed chain, whole-genome sequencing (WGS) has played a key role to prove GMM contaminations via the characterization of unnatural associations of sequences. However, WGS requires a prior microbial isolation of the GMM strain, which can be difficult to successfully achieve. Therefore, in order to avoid such bottleneck, a culture-independent approach was proposed in this study. First, the screening for the aadD gene, an AMR gene conferring a resistance to kanamycin, and for the pUB110 shuttle vector, carrying the aadD gene and commonly used to produce GMM, is performed. In case of a positive signal, DNA walking methods anchored on the two borders of the detected pUB110 shuttle vector are applied to characterize unknown flanking regions. Following to the sequencing of the generated amplicons, unnatural associations of sequences can be identified, allowing to demonstrate the presence of unauthorized GMM. The developed culture-independent strategy was successfully applied on commercialized microbial fermentation products, allowing to prove the presence of GMM contaminations in the food and feed chain.
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Affiliation(s)
- Marie-Alice Fraiture
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nina Papazova
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Fraiture MA, Deckers M, Papazova N, Roosens NHC. Strategy to Detect Genetically Modified Bacteria Carrying Tetracycline Resistance Gene in Fermentation Products. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01803-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fraiture MA, Bogaerts B, Winand R, Deckers M, Papazova N, Vanneste K, De Keersmaecker SCJ, Roosens NHC. Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing. Sci Rep 2020; 10:7094. [PMID: 32341433 PMCID: PMC7184583 DOI: 10.1038/s41598-020-63987-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Recently, the unexpected presence of a viable unauthorized genetically modified bacterium in a commercialized food enzyme (protease) product originating from a microbial fermentation process has been notified at the European level (RASFF 2019.3332). This finding was made possible thanks to the use of the next-generation sequencing technology, as reported in this study. Whole-genome sequencing was used to characterize the genetic modification comprising a sequence from the pUB110 shuttle vector (GenBank: M19465.1), harbouring antimicrobial resistance genes conferring a resistance to kanamycine, neomycin and bleomycin, flanked on each side by a sequence coding for a protease (GenBank: WP_032874795.1). In addition, based on these data, two real-time PCR methods, that can be used by enforcement laboratories, specific to this unauthorized genetically modified bacterium were developed and validated. The present study emphasizes the key role that whole-genome sequencing can take for detection of unknown and unauthorized genetically modified microorganisms in commercialized microbial fermentation products intended for the food and feed chain. Moreover, current issues encountered by the Competent Authorities and enforcement laboratories with such unexpected contaminations and the importance of performing official controls were highlighted.
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Affiliation(s)
- Marie-Alice Fraiture
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Bert Bogaerts
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Marie Deckers
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nina Papazova
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Deckers M, Deforce D, Fraiture MA, Roosens NHC. Genetically Modified Micro-Organisms for Industrial Food Enzyme Production: An Overview. Foods 2020; 9:E326. [PMID: 32168815 PMCID: PMC7143438 DOI: 10.3390/foods9030326] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
The use of food enzymes (FE) by the industrial food industry is continuously increasing. These FE are mainly obtained by microbial fermentation, for which both wild-type (WT) and genetically modified (GM) strains are used. The FE production yield can be increased by optimizing the fermentation process, either by using genetically modified micro-organism (GMM) strains or by producing recombinant enzymes. This review provides a general overview of the different methods used to produce FE preparations and how the use of GMM can increase the production yield. Additionally, information regarding the construction of these GMM strains is provided. Thereafter, an overview of the different European regulations concerning the authorization of FE preparations on the European market and the use of GMM strains is given. Potential issues related to the authorization and control of FE preparations sold on the European market are then identified and illustrated by a case study. This process highlighted the importance for control of FE preparations and the consequent need for appropriate detection methods targeting the presence of GMM, which is used in fermentation products.
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Affiliation(s)
- Marie Deckers
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
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Broeders S, Garlant L, Fraiture MA, Vandermassen E, Suin V, Vanhomwegen J, Dupont-Rouzeyrol M, Rousset D, Van Gucht S, Roosens N. A new multiplex RT-qPCR method for the simultaneous detection and discrimination of Zika and chikungunya viruses. Int J Infect Dis 2020; 92:160-170. [PMID: 31884173 PMCID: PMC7129992 DOI: 10.1016/j.ijid.2019.12.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/11/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE The re-emergence and spread of tropical viruses to new areas has raised a wave of concern worldwide. In order to treat patients at an early stage and prevent the diffusion of an outbreak, early diagnosis, and therefore fast and adequate detection, is needed. To this end, a multiplex reverse transcription real-time polymerase chain reaction TaqMan method was designed to detect Zika (ZIKV) and chikungunya (CHIKV) viruses simultaneously. METHODS Two methods targeting different genome segments were selected from the literature for each virus. These were adapted for high genome coverage and combined in a four-plex assay that was thoroughly validated in-house. The SCREENED tool was used to evaluate the sequence coverage of the method. RESULTS The full validation approach showed that the new four-plex method allows the specific and sensitive identification and discrimination of ZIKV and CHIKV in routine samples. The combination of two targets per virus allowing almost 100% coverage of about 500 genomes is shown for the first time. CONCLUSIONS PCR is a reliable user-friendly technique that can be applied in remote areas. Such multiplex methods enable early and efficient diagnosis, leading to rapid treatment and effective confinement in outbreak cases. They may also serve as an aid for surveillance, and the full validation permits easy method-transfer allowing worldwide harmonization.
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Affiliation(s)
- Sylvia Broeders
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Linda Garlant
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Marie-Alice Fraiture
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Els Vandermassen
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Vanessa Suin
- Sciensano, Viral Diseases, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Jessica Vanhomwegen
- Institut Pasteur France, Cellule d'Intervention Biologique d'Urgence (CIBU), 25-28 rue du docteur Roux, 75724 Paris Cedex 15, France.
| | - Myrielle Dupont-Rouzeyrol
- Institut Pasteur de Nouvelle-Calédonie, URE Dengue et Arboviroses, 11 ave P. Doumer, BP 61, 98845 Nouméa Cedex, New Caledonia.
| | - Dominique Rousset
- Institut Pasteur de la Guyane, Laboratoire de Virologie, 23 avenue Pasteur - BP 6010, 97306 Cayenne Cedex, Guyana.
| | - Steven Van Gucht
- Sciensano, Viral Diseases, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nancy Roosens
- Sciensano, Transversal Activities in Applied Genomics, J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Deckers M, Vanneste K, Winand R, Keersmaecker SCD, Denayer S, Heyndrickx M, Deforce D, Fraiture MA, Roosens NH. Strategy for the identification of micro-organisms producing food and feed products: Bacteria producing food enzymes as study case. Food Chem 2020; 305:125431. [DOI: 10.1016/j.foodchem.2019.125431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/30/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
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Fraiture MA, Vandamme J, Herman P, Roosens NHC. Development and validation of an integrated DNA walking strategy to detect GMO expressing cry genes. BMC Biotechnol 2018; 18:40. [PMID: 29945581 PMCID: PMC6020286 DOI: 10.1186/s12896-018-0446-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/15/2018] [Indexed: 01/09/2023] Open
Abstract
Background Recently, an integrated DNA walking strategy has been proposed to prove the presence of GMO via the characterisation of sequences of interest, including their transgene flanking regions and the unnatural associations of elements in their transgenic cassettes. To this end, the p35S, tNOS and t35S pCAMBIA elements have been selected as key targets, allowing the coverage of most of GMO, EU authorized or not. In the present study, a bidirectional DNA walking method anchored on the CryAb/c genes is proposed with the aim to cover additional GMO and additional sequences of interest. Results The performance of the proposed bidirectional DNA walking method anchored on the CryAb/c genes has been evaluated in a first time for its feasibility using several GM events possessing these CryAb/c genes. Afterwards, its sensitivity has been investigated through low concentrations of targets (as low as 20 HGE). In addition, to illustrate its applicability, the entire workflow has been tested on a sample mimicking food/feed matrices analysed in GMO routine analysis. Conclusion Given the successful assessment of its performance, the present bidirectional DNA walking method anchored on the CryAb/c genes can easily be implemented in GMO routine analysis by the enforcement laboratories and allows completing the entire DNA walking strategy in targeting an additional transgenic element frequently found in GMO. Electronic supplementary material The online version of this article (10.1186/s12896-018-0446-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Julie Vandamme
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Operational Direction Expertise, Service provisions & Customer relations by: Sciensano, Scientific Direction Expertise, Service provisions & Customer relations, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Fraiture MA, Saltykova A, Hoffman S, Winand R, Deforce D, Vanneste K, De Keersmaecker SCJ, Roosens NHC. Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO. Sci Rep 2018; 8:7903. [PMID: 29785005 PMCID: PMC5962636 DOI: 10.1038/s41598-018-26259-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Assia Saltykova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Ghent University (UGent), Department of Information Technology, IMEC, Internet Technology and Data Science Lab (IDLab), Technologiepark-Zwijnaarde 15, 9052, Ghent, Belgium
| | - Stefan Hoffman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Kevin Vanneste
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Fraiture MA, Herman P, De Loose M, Debode F, Roosens NH. How Can We Better Detect Unauthorized GMOs in Food and Feed Chains? Trends Biotechnol 2017; 35:508-517. [DOI: 10.1016/j.tibtech.2017.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022]
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Fraiture MA, Herman P, Papazova N, De Loose M, Deforce D, Ruttink T, Roosens NH. An integrated strategy combining DNA walking and NGS to detect GMOs. Food Chem 2017; 232:351-358. [PMID: 28490084 DOI: 10.1016/j.foodchem.2017.03.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 10/17/2016] [Accepted: 03/11/2017] [Indexed: 12/21/2022]
Abstract
Recently, we developed a DNA walking system for the detection and characterization of a broad spectrum of GMOs in routine analysis of food/feed matrices. Here, we present a new version with improved throughput and sensitivity by coupling the DNA walking system to Pacific Bioscience® Next-generation sequencing technology. The performance of the new strategy was thoroughly assessed through several assays. First, we tested its detection and identification capability on grains with high or low GMO content. Second, the potential impacts of food processing were investigated using rice noodle samples. Finally, GMO mixtures and a real-life sample were analyzed to illustrate the applicability of the proposed strategy in routine GMO analysis. In all tested samples, the presence of multiple GMOs was unambiguously proven by the characterization of transgene flanking regions and the combinations of elements that are typical for transgene constructs.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural, Fisheries and Food Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820 Merelbeke, Belgium; Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nina Papazova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Marc De Loose
- Institute for Agricultural, Fisheries and Food Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820 Merelbeke, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium.
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Tom Ruttink
- Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium.
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Fraiture MA, Roosens NH, Taverniers I, De Loose M, Deforce D, Herman P. Biotech rice: Current developments and future detection challenges in food and feed chain. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. Current and new approaches in GMO detection: challenges and solutions. Biomed Res Int 2015; 2015:392872. [PMID: 26550567 PMCID: PMC4624882 DOI: 10.1155/2015/392872] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 11/17/2022]
Abstract
In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.
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Affiliation(s)
- Marie-Alice Fraiture
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Philippe Herman
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Nancy H. Roosens
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
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Fraiture MA, Herman P, Lefèvre L, Taverniers I, De Loose M, Deforce D, Roosens NH. Integrated DNA walking system to characterize a broad spectrum of GMOs in food/feed matrices. BMC Biotechnol 2015; 15:76. [PMID: 26272331 PMCID: PMC4535744 DOI: 10.1186/s12896-015-0191-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/29/2015] [Indexed: 01/28/2023] Open
Abstract
Background In order to provide a system fully integrated with qPCR screening, usually used in GMO routine analysis, as well as being able to detect, characterize and identify a broad spectrum of GMOs in food/feed matrices, two bidirectional DNA walking methods targeting p35S or tNOS, the most common transgenic elements found in GM crops, were developed. These newly developed DNA walking methods are completing the previously implemented DNA walking method targeting the t35S pCAMBIA element. Methods Food/feed matrices containing transgenic crops (Bt rice or MON863 maize) were analysed using the integrated DNA walking system. Results First, the newly developed DNA walking methods, anchored on the sequences used for the p35S or tNOS qPCR screening, were tested on Bt rice that contains these two transgenic elements. Second, the methods were assessed on a maize sample containing a low amount of the GM MON863 event, representing a more complex matrix in terms of genome size and sensitivity. Finally, to illustrate its applicability in GMO routine analysis by enforcement laboratories, the entire workflow of the integrated strategy, including qPCR screening to detect the potential presence of GMOs and the subsequent DNA walking methods to characterize and identify the detected GMOs, was applied on a GeMMA Scheme Proficiency Test matrix. Via the characterization of the transgene flanking region between the transgenic cassette and the plant genome as well as of a part of the transgenic cassette, the presence of GMOs was properly confirmed or infirmed in all tested samples. Conclusion Due to their simple procedure and their short time-frame to get results, the developed DNA walking methods proposed here can be easily implemented in GMO routine analysis by the enforcement laboratories. In providing crucial information about the transgene flanking regions and/or the transgenic cassettes, this DNA walking strategy is a key molecular tool to prove the presence of GMOs in any given food/feed matrix. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0191-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium. .,Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium. .,Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
| | - Loic Lefèvre
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
| | - Isabel Taverniers
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium.
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium. .,Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052, Ghent, Belgium.
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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27
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Willems S, Fraiture MA, Deforce D, De Keersmaecker SCJ, De Loose M, Ruttink T, Herman P, Van Nieuwerburgh F, Roosens N. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing. Food Chem 2015; 192:788-98. [PMID: 26304412 DOI: 10.1016/j.foodchem.2015.07.074] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/26/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
Abstract
Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove their integration into the host genome and to identify the specific transgene event in a sample with known composition. This framework was validated by applying it to experimental data from food matrices composed of pure GM rice, processed GM rice (noodles) or a 10% GM/non-GM rice mixture, revealing some influential factors. Finally, feasibility of NGS for routine analysis of GM crops was investigated by applying the framework to samples commonly encountered in routine analysis of GM crops.
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Affiliation(s)
- Sander Willems
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium
| | - Dieter Deforce
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium
| | - Tom Ruttink
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Caritasstraat 21, 9090 Melle, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Filip Van Nieuwerburgh
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Nancy Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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28
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Fraiture MA, Herman P, Taverniers I, De Loose M, Van Nieuwerburgh F, Deforce D, Roosens NH. Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products. Food Chem 2014; 173:1259-65. [PMID: 25466152 DOI: 10.1016/j.foodchem.2014.09.148] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 08/14/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Dieter Deforce
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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29
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Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. An innovative and integrated approach based on DNA walking to identify unauthorised GMOs. Food Chem 2013; 147:60-9. [PMID: 24206686 DOI: 10.1016/j.foodchem.2013.09.112] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/12/2013] [Accepted: 09/19/2013] [Indexed: 01/23/2023]
Abstract
In the coming years, the frequency of unauthorised genetically modified organisms (GMOs) being present in the European food and feed chain will increase significantly. Therefore, we have developed a strategy to identify unauthorised GMOs containing a pCAMBIA family vector, frequently present in transgenic plants. This integrated approach is performed in two successive steps on Bt rice grains. First, the potential presence of unauthorised GMOs is assessed by the qPCR SYBR®Green technology targeting the terminator 35S pCAMBIA element. Second, its presence is confirmed via the characterisation of the junction between the transgenic cassette and the rice genome. To this end, a DNA walking strategy is applied using a first reverse primer followed by two semi-nested PCR rounds using primers that are each time nested to the previous reverse primer. This approach allows to rapidly identify the transgene flanking region and can easily be implemented by the enforcement laboratories.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
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