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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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2
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Chen H, Wei C, Lin Z, Pei J, Pan H, Li H. Protocol to retrieve unknown flanking DNA sequences using semi-site-specific PCR-based genome walking. STAR Protoc 2024; 5:102864. [PMID: 38308839 PMCID: PMC10850853 DOI: 10.1016/j.xpro.2024.102864] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/21/2023] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Here, we describe a protocol based on semi-site-specific primer PCR (3SP-PCR) to access unknown flanking DNA sequences. We specify the guidelines for designing primers for 3SP-PCR. We also describe experimental procedures for the 3SP-PCR, along with PCR product purification and subsequent sequencing and analysis. For complete details on the use and execution of this protocol, please refer to Wei et al.1.
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Affiliation(s)
- Hong Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Cheng Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China; School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, P.R. China
| | - Jinfen Pei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China
| | - Hao Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China; School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, P.R. China
| | - Haixing Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China.
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3
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Li H, Lin Z, Guo X, Pan Z, Pan H, Wang D. Primer extension refractory PCR: an efficient and reliable genome walking method. Mol Genet Genomics 2024; 299:27. [PMID: 38466442 DOI: 10.1007/s00438-024-02126-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 02/10/2024] [Indexed: 03/13/2024]
Abstract
Genome walking, a molecular technique for obtaining unknown flanking genomic sequences from a known genomic sequence, has been broadly applied to determine transgenic sites, mine new genetic resources, and fill in chromosomal gaps. This technique has advanced genomics, genetics, and related disciplines. Here, an efficient and reliable genome walking technique, called primer extension refractory PCR (PER-PCR), is presented. PER-PCR uses a set of primary, secondary, and tertiary walking primers. The middle 15 nt of the primary walking primer overlaps with the 3' parts of the secondary and tertiary primers. The 5' parts of the three primers are heterologous to each other. The short overlap allows the walking primer to anneal to its predecessor only in a relaxed-stringency PCR cycle, resulting in a series of single-stranded DNAs; however, the heterologous 5' part prevents the creation of a perfect binding site for the walking primer. In the next stringent cycle, the target single strand can be extended into a double-stranded DNA molecule by the sequence-specific primer and thus can be exponentially amplified by the remaining stringent cycles. The nontarget single strand fails to be enriched due to the lack of a perfect binding site for any primer. PER-PCR was validated by extension into unknown flanking regions of the hyg gene in rice and the gadR gene in Levilactobacillus brevis CD0817. In summary, in this study, a new practical PER-PCR method was constructed as a potential alternative to existing genome walking methods.
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Affiliation(s)
- Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Boya Bio-Pharmaceutical Group Co., Ltd, High-Tech Industrial Development Zone, Fuzhou, 344100, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Hao Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Dongying Wang
- Physical Education Department, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China.
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Lin Z, Wei C, Pei J, Li H. Bridging PCR: An Efficient and Reliable Scheme Implemented for Genome-Walking. Curr Issues Mol Biol 2023; 45:501-11. [PMID: 36661519 DOI: 10.3390/cimb45010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
The efficacy of the available genome-walking methods is restricted by low specificity, high background, or composite operations. We herein conceived bridging PCR, an efficient genome-walking approach. Three primers with random sequences, inner walker primer (IWP), bridging primer (BP), and outer walker primer (OWP), are involved in bridging PCR. The BP is fabricated by splicing OWP to the 5'-end of IWP's 5'-part. A bridging PCR set is constituted by three rounds of amplification reactions, sequentially performed by IWP, BP plus OWP, and OWP, respectively pairing with three nested sequence-specific primers (SSP). A non-target product arising from IWP alone undergoes end-lengthening mediated by BP. This modified non-target product is a preferentially formed hairpin between the lengthened ends, instead of binding with shorter OWP. Meanwhile, a non-target product, triggered by SSP alone or SSP plus IWP, is removed by nested SSP. As a result, only the target DNA is accumulated. The efficacy of bridging PCR was validated by walking the gadA/R genes of Levilactobacillus brevis CD0817 and the hyg gene of rice.
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Wei C, Lin Z, Pei J, Pan H, Li H. Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool. Curr Issues Mol Biol 2023; 45:512-523. [PMID: 36661520 PMCID: PMC9857434 DOI: 10.3390/cimb45010034] [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: 12/16/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Genome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overlaps its corresponding primary site-specific primer. A 3SP-PCR set comprises two rounds of nested amplification reactions. In each round of reaction, any primer is allowed to partially anneal to the DNA template once only in the single relaxed-stringency cycle, creating a pool of single-stranded DNAs. The target single-stranded DNA can be converted into a double-stranded molecule directed by the site-specific primer, and thus can be exponentially amplified by the subsequent high-stringency cycles. The non-target one cannot be converted into a double-strand due to the lack of a perfect binding site to any primer, and thus fails to be amplified. We validated the 3SP-PCR method by using it to probe the unknown DNA regions of rice hygromycin genes and Levilactobacillus brevis CD0817 glutamic acid decarboxylase genes.
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Affiliation(s)
- Cheng Wei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Jinfeng Pei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Hao Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
- Correspondence:
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Lensch A, Duwenig E, Dederer HG, Kärenlampi SO, Custers R, Borg A, Wyss M. Recombinant DNA in fermentation products is of no regulatory relevance. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109170] [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: 11/29/2022]
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7
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Pei J, Sun T, Wang L, Pan Z, Guo X, Li H. Fusion primer driven racket PCR: A novel tool for genome walking. Front Genet 2022; 13:969840. [PMID: 36330444 PMCID: PMC9623105 DOI: 10.3389/fgene.2022.969840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/16/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The limitations of the current genome-walking strategies include strong background and cumbersome experimental processes. Herein, we report a genome-walking method, fusion primer-driven racket PCR (FPR-PCR), for the reliable retrieval of unknown flanking DNA sequences. Four sequence-specific primers (SSP1, SSP2, SSP3, and SSP4) were sequentially selected from known DNA (5'→3′) to perform FPR-PCR. SSP3 is the fragment that mediates intra-strand annealing (FISA). The FISA fragment is attached to the 5′ end of SSP1, generating a fusion primer. FPR-PCR comprises two rounds of amplification reactions. The single-fusion primary FPR-PCR begins with the selective synthesis of the target first strand, then allows the primer to partially anneal to some place(s) on the unknown region of this strand, producing the target second strand. Afterward, a new first strand is synthesized using the second strand as the template. The 3′ end of this new first strand undergoes intra-strand annealing to the FISA site, followed by the formation of a racket-like DNA by a loop-back extension. This racket-like DNA is exponentially amplified in the secondary FPR-PCR performed using SSP2 and SSP4. We validated this FPR-PCR method by identifying the unknown flanks of Lactobacillus brevis CD0817 glutamic acid decarboxylase genes and the rice hygromycin gene.
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Affiliation(s)
- Jinfeng Pei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Tianyi Sun
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, China
| | - Lingqin Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- *Correspondence: Haixing Li,
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Fraiture M, Gobbo A, Papazova N, Roosens NHC. Development of a Taxon-Specific Real-Time PCR Method Targeting the Bacillus subtilis Group to Strengthen the Control of Genetically Modified Bacteria in Fermentation Products. Fermentation 2022; 8:78. [DOI: 10.3390/fermentation8020078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Most of the bacteria that are used to produce fermentation products, such as enzymes, additives and flavorings, belong to the Bacillus subtilis group. Recently, unexpected contaminations with unauthorized genetically modified (GM) bacteria (viable cells and associated DNA) that were carrying antimicrobial resistance (AMR) genes was noticed in several microbial fermentation products that have been commercialized on the food and feed market. These contaminations consisted of GM Bacillus species belonging to the B. subtilis group. In order to screen for the potential presence of such contaminations, in this study we have developed a new real-time PCR method targeting the B. subtilis group, including B. subtilis, B. licheniformis, B. amyloliquefaciens and B. velezensis. The method’s performance was successfully assessed as specific and sensitive, complying with the Minimum Performance Requirements for Analytical Methods of GMO Testing that is used as a standard by the GMO enforcement laboratories. The method’s applicability was also tested on 25 commercial microbial fermentation products. In addition, this method was developed to be compatible with the PCR-based strategy that was recently developed for the detection of unauthorized GM bacteria. This taxon-specific method allows the strengthening of the set of screening markers that are targeting key sequences that are frequently found in GM bacteria (AMR genes and shuttle vector), reinforcing control over the food and feed chain in order to guarantee its safety and traceability.
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Druml B, Uhlig S, Simon K, Frost K, Hettwer K, Cichna-Markl M, Hochegger R. Real-Time PCR Assay for the Detection and Quantification of Roe Deer to Detect Food Adulteration-Interlaboratory Validation Involving Laboratories in Austria, Germany, and Switzerland. Foods 2021; 10:foods10112645. [PMID: 34828926 PMCID: PMC8623729 DOI: 10.3390/foods10112645] [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: 09/18/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Game meat products are particularly prone to be adulterated by replacing game meat with cheaper meat species. Recently, we have presented a real-time polymerase chain reaction (PCR) assay for the identification and quantification of roe deer in food. Quantification of the roe deer content in % (w/w) was achieved relatively by subjecting the DNA isolates to a reference real-time PCR assay in addition to the real-time PCR assay for roe deer. Aiming at harmonizing analytical methods for food authentication across EU Member States, the real-time PCR assay for roe deer has been tested in an interlaboratory ring trial including 14 laboratories from Austria, Germany, and Switzerland. Participating laboratories obtained aliquots of DNA isolates from a meat mixture containing 24.8% (w/w) roe deer in pork, roe deer meat, and 12 meat samples whose roe deer content was not disclosed. Performance characteristics included amplification efficiency, level of detection (LOD95%), repeatability, reproducibility, and accuracy of quantitative results. With a relative reproducibility standard deviation ranging from 13.35 to 25.08% (after outlier removal) and recoveries ranging from 84.4 to 114.3%, the real-time PCR assay was found to be applicable for the detection and quantification of roe deer in raw meat samples to detect food adulteration.
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Affiliation(s)
- Barbara Druml
- Department of Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220 Vienna, Austria;
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Steffen Uhlig
- QuoData GmbH, Prellerstraße 14, 01309 Dresden, Germany; (S.U.); (K.S.); (K.F.); (K.H.)
| | - Kirsten Simon
- QuoData GmbH, Prellerstraße 14, 01309 Dresden, Germany; (S.U.); (K.S.); (K.F.); (K.H.)
| | - Kirstin Frost
- QuoData GmbH, Prellerstraße 14, 01309 Dresden, Germany; (S.U.); (K.S.); (K.F.); (K.H.)
| | - Karina Hettwer
- QuoData GmbH, Prellerstraße 14, 01309 Dresden, Germany; (S.U.); (K.S.); (K.F.); (K.H.)
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
- Correspondence: (M.C.-M.); (R.H.)
| | - Rupert Hochegger
- Department of Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220 Vienna, Austria;
- Correspondence: (M.C.-M.); (R.H.)
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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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Fraiture MA, Gobbo A, Marchesi U, Verginelli D, Papazova N, Roosens NHC. Development of a real-time PCR marker targeting a new unauthorized genetically modified microorganism producing protease identified by DNA walking. Int J Food Microbiol 2021; 354:109330. [PMID: 34303961 DOI: 10.1016/j.ijfoodmicro.2021.109330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/22/2022]
Abstract
A PCR-based DNA walking analysis was performed on a protease product suspected to contain a new unauthorized genetically modified microorganism (GMM). Though the characterization of unnatural associations of sequences between the pUB110 shuttle vector and a Bacillus amyloliquefaciens gene coding for a protease, the presence of the GMM was shown. Based on these sequences of interest, a real-time PCR marker was developed to target specifically the newly discovered GMM, namely GMM protease2. The performance of the real-time PCR marker was assessed in terms of specificity and sensitivity. The applicability of the real-time PCR GMM protease2 marker was also demonstrated on microbial fermentation products. To confirm its use by other GMO enforcement laboratories, the transferability of the in-house validated real-time PCR marker was demonstrated by assays performed by an external laboratory.
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12
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Kalendar R, Shustov AV, Schulman AH. Palindromic Sequence-Targeted (PST) PCR, Version 2: An Advanced Method for High-Throughput Targeted Gene Characterization and Transposon Display. Front Plant Sci 2021; 12:691940. [PMID: 34239528 PMCID: PMC8258406 DOI: 10.3389/fpls.2021.691940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 05/28/2023]
Abstract
Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that are in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for combining of sequence-specific primers with designed capturing primers capable of annealing to unknown DNA targets, thereby offering the rapidity and effectiveness of PCR. This study presents a methodological improvement to the previously described GW technique known as palindromic sequence-targeted PCR (PST-PCR). Like PST-PCR, this new method (called PST-PCR v.2) relies on targeting of capturing primers to palindromic sequences arbitrarily present in natural DNA templates. PST-PCR v.2 consists of two rounds of PCR. The first round uses a combination of one sequence-specific primer with one capturing (PST) primer. The second round uses a combination of a single (preferred) or two universal primers; one anneals to a 5' tail attached to the sequence-specific primer and the other anneals to a different 5' tail attached to the PST primer. The key advantage of PST-PCR v.2 is the convenience of using a single universal primer with invariable sequences in GW processes involving various templates. The entire procedure takes approximately 2-3 h to produce the amplified PCR fragment, which contains a portion of a template flanked by the sequence-specific and capturing primers. PST-PCR v.2 is highly suitable for simultaneous work with multiple samples. For this reason, PST-PCR v.2 can be applied beyond the classical task of GW for studies in population genetics, in which PST-PCR v.2 is a preferred alternative to amplified fragment length polymorphism (AFLP) or next-generation sequencing. Furthermore, the conditions for PST-PCR v.2 are easier to optimize, as only one sequence-specific primer is used. This reduces non-specific random amplified polymorphic DNA (RAPD)-like amplification and formation of non-templated amplification. Importantly, akin to the previous version, PST-PCR v.2 is not sensitive to template DNA sequence complexity or quality. This study illustrates the utility of PST-PCR v.2 for transposon display (TD), which is a method to characterize inter- or intra-specific variability related to transposon integration sites. The Ac transposon sequence in the maize (Zea mays) genome was used as a sequence tag during the TD procedure to characterize the Ac integration sites.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Alan H. Schulman
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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Fraiture M, Marchesi U, Verginelli D, Papazova N, Roosens NHC. Development of a Real-time PCR Method Targeting an Unauthorized Genetically Modified Microorganism Producing Alpha-Amylase. FOOD ANAL METHOD 2021; 14:2211-20. [DOI: 10.1007/s12161-021-02044-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractUsing a recently developed genetically modified microorganisms (GMM) detection strategy, unexpected contaminations of unauthorized GMM in commercialized microbial fermentation products have been reported. A first-line real-time PCR screening analysis was initially performed to determine the presence of key targets frequently found in genetically modified (GM) bacteria. A second-line real-time PCR analysis was subsequently applied to identify specific GMM, including to date a GM Bacillus velezensis producing protease and a GM B. subtilis producing vitamin B2. In this study, an additional real-time PCR method specific to a newly identified GMM producing alpha-amylase was developed to be integrated in such second-line real-time PCR analysis, allowing to strengthen the GMM detection strategy. This method was successfully validated based on the assessment of its specificity and sensitivity performance. In addition, its applicability was confirmed using several food enzyme products commercialized on the market. Finally, via its transfer to an external laboratory, the transferability of the in-house validated method was positively evaluated, allowing its easy implementation in enforcement laboratories.
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