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Singh M, Young RG, Hellberg RS, Hanner RH, Corradini MG, Farber JM. Twenty-three years of PCR-based seafood authentication assay development: What have we learned? Compr Rev Food Sci Food Saf 2024; 23:e13401. [PMID: 39073284 DOI: 10.1111/1541-4337.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay-based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA-based method was real-time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species-specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA-based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.
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Affiliation(s)
- Maleeka Singh
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, Orange, California, USA
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Maria G Corradini
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Arrell Food Institute, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Wax N, Pförtner LS, Holz N, Sterzl S, Melnik M, Kappel K, Bade P, Schröder U, Haase I, Fritsche J, Fischer M. Fast and User-Friendly Detection of Flatfish Species ( Pleuronectes platessa and Solea solea) via Loop-Mediated Isothermal Amplification (LAMP). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14795-14805. [PMID: 37751470 DOI: 10.1021/acs.jafc.3c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
The detection of a Cytochrome b gene (cytb) for species differentiation in fish is intensively used. A fast alternative to expensive and time-consuming DNA barcoding is loop-mediated isothermal amplification (LAMP) in combination with efficient readout systems. For this reason, we developed LAMP assays for rapid species detection of Pleuronectes platessa and Solea solea, two economically important flatfish species in Europe that are prone to mislabeling. Species-specific primer sets targeting cytb were designed, and LAMP assays were optimized. With the optimized LAMP assays, we were able to detect up to 0.1 and 0.01 ng of target DNA of P. platessa and S. solea, respectively, and in each case up to 1% (w/w) of target species in mixtures with nontarget species. For future on-site detection, a lateral flow assay and a pocket-sized lab-on-phone assay were used as readout systems. The lab-on-phone assay with the S. solea specific primer set revealed cross-reactivity to Solea senegalensis. The assay targeting P. platessa proved to be highly specific. Both assays could be performed within 45 min and provided rapid and easy detection of fish species.
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Affiliation(s)
- Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Laura Sophie Pförtner
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nathalie Holz
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Svenja Sterzl
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Melina Melnik
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Kristina Kappel
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Patrizia Bade
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Ute Schröder
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Ilka Haase
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Jan Fritsche
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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Deconinck D, Robbens J, Volckaert FA, Derycke S. Rapid and low-cost identification of common sole (Solea solea) in the field using a fast DNA isolation protocol and loop-mediated isothermal amplification (LAMP). J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Hong Y, Kim JJ, Yu YC, Kim HS, Moon G, Park EM. Ultra-fast PCR method for the distinguishing between Miichthys miiuy and Sciaenops ocellatus. Food Sci Biotechnol 2021; 30:1225-1231. [PMID: 34603821 DOI: 10.1007/s10068-021-00954-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022] Open
Abstract
The mi-iuy croaker Miichthys miiuy has immense commercial value in the Republic of Korea. The red drum Sciaenops ocellatus is widely produced by aquaculture, although its price is approximately 25% that of M. miiuy. S. ocellatus has black spots on its tail, enabling it to be distinguished from M. miiuy based on appearance. However, identifying S. ocellatus after simple processing steps, such as skin removal and dicing, is difficult. Certain traders misrepresent and sell S. ocellatus as M. miiuy or cultured M. miiuy for illegal economical gain. Therefore, an accurate and rapid identification method is required to distinguish between M. miiuy and S. ocellatus in the field. Here, a method for rapid field identification was developed based on species-specific primers using a portable ultra-fast PCR instrument. The ultra-fast real-time PCR method can complete the entire analytical procedure, including DNA isolation, amplification, and detection, within 30 min, thus maintaining the accuracy of identifying M. miiuy and S. ocellatus products on site. Forty-nine commercial products were tested, and all samples were successfully identified. Thus, the developed method is rapid, efficient tool for ensuring consumer protection. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00954-4.
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Affiliation(s)
- Yewon Hong
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Jung Ju Kim
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Yeon-Cheol Yu
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Hyung Soo Kim
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Guiim Moon
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Eun Mi Park
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
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Fernandes TJR, Amaral JS, Mafra I. DNA barcode markers applied to seafood authentication: an updated review. Crit Rev Food Sci Nutr 2020; 61:3904-3935. [DOI: 10.1080/10408398.2020.1811200] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain. Food Chem Toxicol 2020; 141:111417. [PMID: 32437897 DOI: 10.1016/j.fct.2020.111417] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/28/2020] [Accepted: 05/04/2020] [Indexed: 01/24/2023]
Abstract
Seafood is an important component of the human diet. With depleting fish stocks and increasing prices, seafood is prone to fraudulent substitution. DNA barcoding has illustrated fraudulent substitution of fishes in retail and restaurants. Whether substitution also occurs in other steps of the supply chain remains largely unknown. DNA barcoding relies on public reference databases for species identification, but these can contain incorrect identifications. The creation of a high quality genetic reference database for 42 European commercially important fishes was initiated containing 145 Cytochrome c oxidase subunit I (COI) and 152 Cytochrome b (cytB) sequences. This database was used to identify substitution rates of Atlantic cod (Gadus morhua) and common sole (Solea solea) along the fish supply chain in Belgium using DNA barcoding. Three out of 132 cod samples were substituted, in catering (6%), import (5%) and fishmongers (3%). Seven out of the 41 processed sole samples were substituted, in wholesale (100%), food services (50%), retailers (20%) and catering (8%). Results show that substitution of G. morhua and S. solea is not restricted to restaurants, but occurs in other parts of the supply chain, warranting for more stringent controls along the supply chain to increase transparency and trust among consumers.
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Verrez-Bagnis V, Sotelo CG, Mendes R, Silva H, Kappel K, Schröder U. Methods for Seafood Authenticity Testing in Europe. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-78030-6_69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Paracchini V, Petrillo M, Lievens A, Puertas Gallardo A, Martinsohn JT, Hofherr J, Maquet A, Silva APB, Kagkli DM, Querci M, Patak A, Angers-Loustau A. Novel nuclear barcode regions for the identification of flatfish species. Food Control 2017; 79:297-308. [PMID: 28867876 PMCID: PMC5446357 DOI: 10.1016/j.foodcont.2017.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 01/30/2023]
Abstract
The development of an efficient seafood traceability framework is crucial for the management of sustainable fisheries and the monitoring of potential substitution fraud across the food chain. Recent studies have shown the potential of DNA barcoding methods in this framework, with most of the efforts focusing on using mitochondrial targets such as the cytochrome oxidase 1 and cytochrome b genes. In this article, we show the identification of novel targets in the nuclear genome, and their associated primers, to be used for the efficient identification of flatfishes of the Pleuronectidae family. In addition, different in silico methods are described to generate a dataset of barcode reference sequences from the ever-growing wealth of publicly available sequence information, replacing, where possible, labour-intensive laboratory work. The short amplicon lengths render the analysis of these new barcode target regions ideally suited to next-generation sequencing techniques, allowing characterisation of multiple fish species in mixed and processed samples. Their location in the nucleus also improves currently used methods by allowing the identification of hybrid individuals.
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Affiliation(s)
- Valentina Paracchini
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Antoon Lievens
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | | | | | - Johann Hofherr
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Alain Maquet
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | | | - Dafni Maria Kagkli
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Maddalena Querci
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Alex Patak
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
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Espiñeira M, Vieites JM. FAST Real Time PCR for control of intra-species recycling in aquaculture feed, focused to the most relevant fish species farmed in Europe. Food Chem 2016; 204:352-357. [DOI: 10.1016/j.foodchem.2016.02.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/10/2015] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
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10
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The detection of Atlantic cod (Gadus morhua) using loop mediated isothermal amplification in conjunction with a simplified DNA extraction process. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.05.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Kappel K, Schröder U. Substitution of high-priced fish with low-priced species: Adulteration of common sole in German restaurants. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.06.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Genetic system for an integral traceability of European eel (Anguilla anguilla) in aquaculture and seafood products: authentication by fast real-time PCR. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2514-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Detection of dog and cat traces in food, pet food and farm animal feed by real-time PCR. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2448-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Genetic system for traceability of goatfishes by FINS methodology and authentication of mullets (Mullus barbatus and Mullus surmuletus) by RT-PCR. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2341-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Espiñeira M, Vieites JM. Rapid method for controlling the correct labeling of products containing common octopus (Octopus vulgaris) and main substitute species (Eledone cirrhosa and Dosidicus gigas) by fast real-time PCR. Food Chem 2012; 135:2439-44. [DOI: 10.1016/j.foodchem.2012.07.056] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/04/2012] [Accepted: 07/07/2012] [Indexed: 11/30/2022]
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