High resolution real-time PCR melting curve assay for identification of top five Penaeidae shrimp species

Rapid PCR-lateral flow assay for the onsite detection of Atlantic white shrimp

The Atlantic white shrimp (Litopenaeus setiferus) is of great economic importance to the United States and risk being substituted with imported species due to a shortage in domestic production. To improve the current methods used for the identification of the Atlantic white shrimp species, we designed and validated a robust multiplex PCR-lateral flow assay for the onsite identification of L. setiferus. The standardized assay was validated using a miniaturized, low-cost PCR instrument with 68 shrimp, prawn, and fish samples, spread over fourteen seafood species. L. setiferus was simultaneously amplified by the multiplex assay to give three visual bands, which distinguished it from other species having either one or two bands on the dipstick. The standardized assay showed 100% inclusivity for target L. setiferus samples, 100% exclusivity for non-target samples and can be completed in less than two hours. The assay standardized in this study can be used for onsite testing of L. setiferus samples at processing facilities, restaurants, and wholesalers' facilities.

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.

Real-Time PCR High-Resolution Melting Assays for the Detection of Foodborne Pathogens

Real-time PCR high-resolution melting assays are a method for the identification of single nucleotide polymorphisms (SNPs). The assay is performed by amplifying a short DNA fragment using a specific primer pair flanking a target SNP in the presence of a high-resolution melting dye. The HRM analysis of amplicons groups the samples based on the differences in the melting temperature and the shape of the melt curves, facilitating a convenient genotyping of samples. This chapter describes the steps and considerations of real-time PCR HRM assay standardization.

Study on the physicochemical indexes, nutritional quality, and flavor compounds of Trichiurus lepturus from three representative origins for geographical traceability

Trichiurus lepturus (hairtail) is an important economic component of China's marine fishing industry. However, due to the difficulty in identifying the appearance of hairtail from different geographical distributions, hairtails with geographical indication trademarks were imitated by general varieties. In this study, the texture characteristics, color, basic nutrients, amino acids, mineral, fatty acids, and volatile flavor substances were used as indicators for multivariate statistical analysis to determine whether three origins of hairtails from the habitats of Zhoushan (East China Sea, T.Z), Hainan (South China Sea, T.N), and Qingdao (Yellow Sea, T.Q) in the market could be distinguished. The findings revealed that there were significant differences in amino acids composition, mineral composition, fatty acid composition in lipids, and volatile flavor substances among the hairtails of three origins (P < 0.05), but no differences in color, texture, protein content. T.Z had moisture, crude fat, essential amino acids (EAA), flavor amino acids (FAA), unsaturated fatty acids (UFA), and docosahexaenoic acids and dicosapentaenoic acids (ΣEPA + DHA) contents of 74.33, 5.4%, 58.25 mg⋅g-1, 46.20 mg⋅g-1, 66.84 and 19.38%, respectively, and the contents of volatile alcohols, aldehydes and ketones were 7.44, 5.30, and 5.38%, respectively. T.N contains moisture, crude fat, EAA, FAA, UFA and ΣEPA + DHA as 77.69, 2.38%, 64.76 mg⋅g-1, 52.44 mg⋅g-1, 65.52 and 29.45%, respectively, and the contents of volatile alcohols, aldehydes and ketones as 3.21, 8.92, and 10.98%, respectively. T.Q had the contents of moisture, crude fat, EAA, FAA, UFA, and ΣEPA + DHA 79.69, 1.43%, 60.9 mg⋅g-1, and 49.42 mg⋅g-1, respectively. The contents of unsaturated fatty acid and ΣEPA + DHA were 63.75 and 26.12%, respectively, while the volatile alcohols, aldehydes, and ketones were 5.14, 5.99, and 7.85%, respectively. Partial least squares-discriminant analysis (PLS-DA) multivariate statistical analysis showed that volatile flavor compounds could be used as the most ideal indicators for tracing the source of hairtail. In conclusion, the findings of this study can distinguish the three hairtail origins using some basic indicators, providing ideas for hairtail geographical identification.

Real-time authentication of minced shrimp by rapid evaporative ionization mass spectrometry

Minced shrimp is popular seafood due to its delicious flavor and nutritional value. However, the biological species of raw material of minced shrimp are not distinguished by naked eyes after processing. Thus, an in situ and real-time minced shrimp authentication method was established using iKnife rapid evaporative ionization mass spectrometry (REIMS) based lipidomics. The samples were analyzed under ambient ionization without any tedious preparation step. Seven economic shrimp samples were tested, whose phenotypes were used to develop a real-time recognition model. A total of 19 fatty acids and 45 phospholipid molecular species were efficiently identified and statistically analyzed by multivariate statistical analysis. The results showed that the seven shrimp species were well distinguished, and the most contributing ions at m/z 255.2, 279.2, 301.2, 327.2, 699.5, 742.5, etc., were revealed by variable importance in projection. The proposed iKnife REIMS showed excellent performance in minced shrimp authentication.

Molecular tools for assuring human health and environment-friendly frozen shellfish products in the United Arab Emirates markets

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Frozen UAE shellfish samples were identified using 16S rDNA barcoding.

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Significant substitutions were identified for calamari by peanut worm, cattle, and rat.

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Although labelled as UAE in origin most shrimps were non-native species.

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Analyzed shellfish barcodes showed most species belong to low diversity populations.

Shellfish consumption in the United Arab Emirates (UAE) exceeds local supply and frozen fish and seafood products are imported to fill the gap. To determine the species in frozen shellfish brands on the UAE markets, 95 frozen samples were subjected to PCR amplification and sequencing of the hypervariable region of the 16S rDNA. This identified 11 different shrimp species and two squid species in the frozen shellfish packs. About 40% of calamari brands contained peanut worm, cattle, and rat 16S rDNA. Also, most shellfish species analyzed had low nucleotide diversity, including two shrimp species (Litopenaeus vannamei and Metapenopsis barbata), which had very limited genetic diversity, low raggedness, and an absence of population expansion. Species misnaming, substitution, overexploitation, origin misreporting, and low genetic diversity were found across frozen UAE shellfish samples analyzed, suggesting inspection and monitoring of frozen seafood sold in UAE markets would be appropriate.

A Bioinspired Peptide in TIR Protein as Recognition Molecule on Electrochemical Biosensors for the Detection of E. coli O157:H7 in an Aqueous Matrix

Currently, the detection of pathogens such as Escherichia coli through instrumental alternatives with fast response and excellent sensitivity and selectivity are being studied. Biosensors are systems consisting of nanomaterials and biomolecules that exhibit remarkable properties such as simplicity, portable, affordable, user‑friendly, and deliverable to end‑users. For this, in this work we report for the first time, to our knowledge, the bioinformatic design of a new peptide based on TIR protein, a receptor of Intimin membrane protein which is characteristic of E. coli. This peptide (named PEPTIR‑1.0) was used as recognition element in a biosensor based on AuNPs‑modified screen‑printed electrodes for the detection of E. coli. The morphological and electrochemical characteristics of the biosensor obtained were studied. Results show that the biosensor can detect the bacteria with limits of detection and quantification of 2 and 6 CFU/mL, respectively. Moreover, the selectivity of the system is statistically significant towards the detection of the pathogen in the presence of other microorganisms such as P. aeruginosa and S. aureus. This makes this new PEPTIR‑1.0 based biosensor can be used in the rapid, sensitive, and selective detection of E. coli in aqueous matrices.