Next Generation Sequencing (NGS) approach applied to species identification in mixed processed seafood products

Piredda, Roberta; Mottola, Anna; Cipriano, Giulia; Carlucci, Roberto; Ciccarese, Giuseppina; Pinto, Angela Di

doi:10.1016/j.foodcont.2021.108590

Cited by 25 publications

(18 citation statements)

References 57 publications

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“…In this regard, the DNA based technologies have proven to be very effective as food fraud detection tools [ 13 , 14 ] and the methodology of DNA barcoding based on the cytochrome oxidase I sequences is the most used one [ 12 , 33 , 34 , 35 , 79 ]. In the last decade new techniques such as Real Time-PCR, Single Nucleotide Polymorphisms (SNPs), Forensically Informative Nucleotide Sequencing (FINS), Loop-mediated isothermal amplification (LAMP), Droplet Digital PCR (ddPCR), High Resolution Melting Analysis (HRMA), Next Generation Sequencing (NGS) metabarcoding, have been proposed by researchers with the aim of optimizing time, costs and effectiveness of species authentication in multi-species fish products [ 80 , 81 , 82 , 83 ]. Although these techniques have been also combined with COI barcoding by providing promising approaches for high throughput species discrimination in processed seafood [ 84 , 85 , 86 ], traditional mitochondrial DNA-based methods and the PCR-RFLP in particular is still employed due to the advantages offered such as relatively cheapness, lack of technical over-complication, suitability for routine analyses [ 85 ].…”

Section: Discussionmentioning

confidence: 99%

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

Pappalardo

Giuga

Raffa

et al. 2022

Foods

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The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as “bianchetto” and Aphia minuta sold as “rossetto”; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar–RFLP analysis. Cases of misdescription were detected: 3 samples labeled as “bianchetto” were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as “persico reale” (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.

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Section: Discussionmentioning

confidence: 99%

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

Pappalardo

Giuga

Raffa

et al. 2022

Foods

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“…The extraction and purification of genomic DNA were performed starting from aliquots of 25 mg of each sample, using the DNeasy Blood and Tissue Kit (QIAGEN, Hilden, Germany), as reported by Piredda et al (2022). In order to verify the purity of the extraction reagents, negative extraction control (no added tissue) (ENC) was included.…”

Section: Dna Extraction Purification and Sequencingmentioning

confidence: 99%

“…Then, molecular identifications of each sample were compared with the species declared in the ingredient list. Mislabelling was established if: a) labels did not report all mandatory information reported above; b) the scientific name and/or the commercial designation did not correspond to that detected by the molecular analysis (Piredda et al, 2022;Giusti et al, 2017). Furthermore, molecular identifications were cross-checked against the Annex I, Italian MiPAAF Decree dated 22 September 2017 in order to detect the presence of taxa unmarketable in Italy.…”

Section: Analysis Of Labels and Mislabelling Assessmentmentioning

confidence: 99%

“…As widely reported by several authors (D'Amico et al, 2016;Walker et al, 2017;Marchetti et al, 2020;Piredda et al, 2022), the absence of morphological identification characters, together with the complexity of the fish supply chain, as well as the price differential between lookalike species, and the multiplicity of species and their corresponding values, make processed fishery products very vulnerable to food fraud and mislabelling (Pardo et al, 2016;FAO, 2020b. To date, food labelling is the most important instrument for safeguarding consumer safety and should prevent fraud and provide consumers with sufficient information to perform conscious food choices in terms of ethical and sustainable production (Varunjikar et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Recent advances N o n -c o m m e r c i a l u s e o n l y in analysis tools came up with Next Generation Sequencing, an assay that simultaneously sequences many molecules of DNA of different targets contained in composite foods, as a promising tool for the authentication of mixed food matrices. In this sense, different studies have applied this technology to identifying ingredients in various types of food, including meat (Xing et al, 2019), honey (Milla et al, 2021), food supplements (Raclariu et al, 2018), vegetable products and herbal medicinals (Bruno et al, 2019;Seethapathy et al, 2019), processed seafood (Giusti et al, 2017;Noh et al, 2021;Piredda et al, 2022), and petfood (Preckel et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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DNA metabarcoding for identification of species used in fish burgers

et al. 2022

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The absence of morphological identification characters, together with the complexity of the fish supply chain make processed seafood vulnerable to cases of species substitution. Therefore, the authentication and the traceability of such products play a strategic role in ensuring quality and safety. The aim of the present study was to detect species used in the production of multi-species fish burgers and to evaluate mislabelling rates, using a DNA metabarcoding approach by sequencing a fragment of the 16S rRNA mitochondrial gene. The study highlighted the presence of 16 marine and 2 mammalian taxa with an overall mislabelling rate of 80%, including cases of species substitution, the undeclared presence of molluscs and of taxa whose use is not permitted by current Italian legislation. The presence of swine DNA as well as the inclusion of undeclared taxa potentially causing allergies raise concerns regarding consumer safety and protection regarding ethical or religious issues. Overall, the study shows that the application of DNA metabarcoding is a promising approach for successfully enforcing traceability systems targeting multi-species processed food and for supporting control activities, as a guarantee of an innovative food safety management system.

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Rapid detection of murine‐derived ingredients in meat products using real‐time enzymatic recombinase amplification

Xie,

Liu,

Liang

et al. 2024

J Sci Food Agric

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BACKGROUNDAccurate identification of meat species is critical to prevent economic fraud and safeguard public health. The use of inappropriate meat sources, such as murine, poses significant health risks because of potential contamination with pathogens and allergens, leading to foodborne illnesses. The present study aimed to develop a novel real‐time enzymatic recombinase amplification (ERA) method for the rapid and specific detection of murine DNA in meat products.RESULTSA novel ERA primer and probe set was designed, targeting a murine‐specific single‐copy nuclear gene identified through bioinformatics analysis. The assay demonstrates high specificity, showing no amplification in commonly consumed meats, other animals or major crops. Additionally, it exhibits remarkable sensitivity, detecting as few as five copies of murine genomic DNA. For practical application, the ERA method could effectively identify mouse DNA in laboratory‐prepared samples at concentrations as low as 0.5% and also quantify samples with mouse DNA content as low as 5%. It also accurately detects the presence of murine‐derived ingredients in commercially available meat products. The detection process is straightforward, utilizing a simple isothermal device for incubation, blue light excitation and a smartphone camera for result interpretation. This rapid analysis can be completed within 20 min.CONCLUSIONThe newly developed real‐time ERA method provides a valuable tool for standardizing meat trade practices, promoting food safety and enhancing consumer confidence in the authenticity of meat products. © 2024 Society of Chemical Industry.

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Next Generation Sequencing (NGS) approach applied to species identification in mixed processed seafood products

Cited by 25 publications

References 57 publications

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

DNA metabarcoding for identification of species used in fish burgers

Rapid detection of murine‐derived ingredients in meat products using real‐time enzymatic recombinase amplification

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