High resolution melting analysis of a COI mini-barcode as a new approach for Penaeidae shrimp species discrimination

Filling Analytical Gaps in Allergen Detection─Real-Time PCR for the Detection of Commercially Relevant Cephalopods and Gastropods in Food

Mollusks belong to the group of shellfish, which are considered to be among the elicitors of severe food allergies worldwide. In recent years, numerous PCR detection methods have been developed for other shellfish such as crustaceans. However, cephalopods and gastropods were not considered in the development of these shellfish detection systems. In this study, we have developed highly specific real-time PCR methods for the comprehensive detection of all commercially relevant cephalopod species and the gastropod families Helicidae, Buccinidae, and Muricidae in food matrices. In total, we cross-tested over 100 animal and plant species to show the specificity of our systems. The limit of detection (LOD12) was set at 1 pg of cephalopod and gastropod DNA or 10 ppm (mg/kg) spiked in a vegetarian food product. The robustness of the protocol was confirmed by testing multiple parameters while cooking and autoclaving of samples ensured the practical applicability of the systems.

An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System

Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.

Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art

Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.

A new real-time PCR assay to specifically detect crustaceans in vegan raw materials and vegan shrimps

Contamination of vegan products and vegan shrimps with real shrimps and crustaceans must be avoided to comply with vegan claims, even more for preventing strong allergenic reactions. Therefore, the detection of crustaceans must be reliable and sensitive enough for authenticity, traceability, and food safety purposes. A new real-time PCR assay was developed targeting the mitochondrial 16S rRNA gene of crustaceans and was optimised to avoid critical mismatches with primers and probe. By testing several crustacean species and common food ingredients, the method was demonstrated to be specific to crustaceans only. To comply with the limit of non-vegan contamination established at 0.1% (w/w) by the European Vegetarian Union, dedicated cut-off C_T values were determined on vegan raw materials and on vegan shrimps spiked with crustacean materials. The method reached a sensitivity ≤ 0.0005% (w/w), which was further confirmed on reference materials containing a similar amount of crustacean.

The development of genus-specific and species-specific real-time PCR assays for the authentication of Patagonian toothfish and Antarctic toothfish in commercial seafood products

BACKGROUND

The substitution or mislabeling of toothfish is an issue of significant concern for seafood authorities; it also reduces the effectiveness of marine conservation and management programs for its over-exploitation and illegal trafficking, boosting the need for identification methods.

RESULTS

Two species-specific real-time polymerase chain reaction (PCR) assays for the identification of Patagonian toothfish (Dissostichus eleginoides) and Antarctic toothfish (Dissostichus mawsoni) and a genus-specific real-time PCR assay for Dissostichus spp. identification were developed based on fragments of the 16S rRNA and COI (cytochrome c oxidase subunit I) genes. These methods were confirmed to be rapid, simple, and sensitive (absolute sensitivity of 0.0002 ng μL^-1 and relative sensitivity of 0.1 g kg^-1 with good specificity). These methods can be applied to processed and commercial fish products.

CONCLUSIONS

These approaches can be beneficial for protecting both consumers and producers from economic fraud and might also help protect toothfish from over-exploitation as well as combat illegal, unreported, and unregulated (IUU) fisheries. © 2021 Society of Chemical Industry.

Detection of Species Substitution in the Meat Value Chain by High-Resolution Melting Analysis of Mitochondrial PCR Products

Substituting high commercial-value meats with similar cheaper or undesirable species is a common form of food fraud that raises ethical, religious, and dietary concerns. Measures to monitor meat substitution are being put in place in many developed countries. However, information about similar efforts in sub-Saharan Africa is sparse. We used PCR coupled with high-resolution melting (PCR-HRM) analysis targeting three mitochondrial genes—cytochrome oxidase 1 (CO1), cytochrome b (cyt b), and 16S rRNA—to detect species substitution in meat sold to consumers in Nairobi, Kenya. Out of 107 meat samples representing seven livestock animals, 11 (10.3%) had been substituted, with the highest rate being observed in samples sold as goat. Our results indicate that PCR-HRM analysis is a cost- and time-effective technique that can be employed to detect species substitution. The combined use of the three mitochondrial markers produced PCR-HRM profiles that successfully allowed for the consistent distinction of species in the analysis of raw, cooked, dried, and rotten meat samples, as well as of meat admixtures. We propose that this approach has broad applications in the protection of consumers against food fraud in the meat industry in low- and middle-income countries such as Kenya, as well as in developed countries.

The use of molecular markers in the verification of fish and seafood authenticity and the detection of adulteration

The verification of authenticity and detection of food mislabeling are elements that have been of high importance for centuries. During the last few decades there has been an increasing consumer demand for the verification of food identity and the implementation of stricter controls around these matters. Fish and seafood are among the most easily adulterated foodstuffs mainly due to the significant alterations of the species' morphological characteristics that occur during the different types of processing, which render the visual identification of the animals impossible. Even simple processes, such as filleting remove very important morphological elements and suffice to prevent the visual identification of species in marketed products. Novel techniques have therefore been developed that allow identification of species, the differentiation between species and also the differentiation of individuals that belong to the same species but grow in different populations and regions. Molecular markers have been used during the last few decades to fulfill this purpose and several improvements have been implemented rendering their use applicable to a commercial scale. The reliability, accuracy, reproducibility, and time-and cost-effectiveness of these techniques allowed them to be established as routine methods in the industry and research institutes. This review article aims at presenting the most important molecular markers used for the authentication of fish and seafood. The most important techniques are described, and the results of numerous studies are outlined and discussed, allowing interested parties to easily access and compare information about several techniques and fish/seafood species.

High-Resolution Melting Analysis of COI Sequences Distinguishes Pufferfish Species (Takifugu spp.) in China

Pufferfish is a traditional, delicious dish in Asia. However, eating wild or improperly processed pufferfish causes serious poisoning. This study aimed to exploit the high-resolution melting (HRM) method for authenticating four species of Takifugu pufferfish (Takifugu xanthopterus, T. fasciatus, T. flavidus, and T. rubripes). Candidate DNA barcodes, including the cytochrome c oxidase subunit I (COI), cytochrome oxidase b (Cytb), and the control region (D-loop), were analyzed, with COI selected as the optimal DNA barcode. An HRM method was developed to identify 57 commercial fish samples in China, including 33 commercial pufferfish products and 24 unlabeled fish products. The findings revealed that the pufferfish products were T. rubripes or T. fasciatus, and four T. xanthopterus samples were detected in unlabeled fish products. These results showed that DNA barcode coupled with HRM analysis was a rapid and efficient tool to identify pufferfish, which might aid in the prevention of consumer fraud or mislabeling of fish products.

DNA-based techniques for seafood species authentication

Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.

The trnL (UAA)-trnF (GAA) intergenic spacer is a robust marker of green pea (Pisum sativum L.) adulteration in economically valuable pistachio nuts (Pistacia vera L.)

BACKGROUND

Pistachio (Pistacia vera L.) is an expensive culinary nut species; it is therefore susceptible to adulteration for economic profit. Green pea (Pisum sativum L.) kernels constitute the most common material used for adulterating chopped / ground pistachio nuts and pistachio paste. Food genomics enables the species composition of a food sample to be ascertained through DNA analysis. Accordingly, a barcode DNA genotyping approach was used to standardize a test method to identify green pea adulteration in pistachio nuts.

RESULTS

The trnL (UAA)-trnF (GAA) intergenic spacer in the plastid genome was the target analyte in the present study. The barcode locus displayed a significant, discriminatory size difference between pistachio and pea, with amplicon sizes of 449 and 179 bp, respectively. Polymerase chain reaction-capillary electrophoresis (PCR-CE) analysis of the intergenic spacer resulted in the successful identification of species composition in the in-house admixtures, which contained 5% to 30% of green pea.

CONCLUSION

The present work describes a fast and straightforward DNA test that identifies green pea adulteration in pistachio nuts without requiring a statistical data interpretation process. The plastid trnL (UAA)-trnF (GAA) intergenic spacer length widely varies among plant taxa, so the PCR-CE protocol that operates on the intergenic spacer holds the potential to reveal adulteration with a plethora of adulterants. The PCR-CE assay described in the present work can be adopted readily by food-quality laboratories in the public sector or the food industry as an easy and reliable method to analyze pistachio authenticity. © 2020 Society of Chemical Industry.

Review of Recent DNA-Based Methods for Main Food-Authentication Topics

Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all along the distribution chain, thereby avoiding food fraud and adulteration. Accordingly, there is a growing need for new analytical methods able to verify that all the ingredients included in a foodstuff match the qualities claimed by the manufacturer or distributor. In this sense, the improved performance of most recent DNA-based tools in term of sensitivity, multiplexing ability, high-throughput, and relatively low-cost give them a game-changing role in food-authenticity-related topics. Here, we provide a thorough and updated vision on the recently reported approaches that are applying these DNA-based tools to assess the authenticity of food components and products.

Identification of Peptide Biomarkers for Discrimination of Shrimp Species through SWATH-MS-Based Proteomics and Chemometrics

Incorrect labeling and adulteration of shrimp occurs due to interspecies similarities and carapace removal during processing. This study attempted to identify three related commercial shrimp species of the order Decapoda: Marsupenaeus japonicus, Fenneropenaeus chinensis, and Litopenaeus vannamei. All measurable trypsin-digested peptides in the individual shrimp were detected using ultrahigh-performance liquid chromatography quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition. Further analysis of peptide biomarkers was carried out with an orthogonal partial least-squares discriminant analysis (OPLS-DA) model. BLAST was used for species-specific analysis. Subsequently, multiple reaction monitoring (MRM) methods were developed for sensitivity and selectivity screening of the selected peptides, and 27 were identified as biomarkers allowing rapid and accurate discrimination of shrimp species without high-resolution mass spectrometry or statistical model building. These strategies could be applied in authentication of other products containing highly homologous proteomes.