Trends and advances in food analysis by real-time polymerase chain reaction

Rapid Detection of Salmonella and Listeria monocytogenes in Fresh Beef Using Loop-Mediated Isothermal Amplification

This study developed and optimized loop-mediated isothermal amplification (LAMP) assays for rapid detection of Salmonella and L. monocytogenes in fresh beef. LAMP primers targeting the invA gene of Salmonella and hly gene of L. monocytogenes were used. Reaction conditions including temperature, dNTP concentration, Mg2+ concentration, primer ratio, and Bst DNA polymerase amount were optimized for each pathogen. Differences were observed between the two pathogens in optimal temperature, Mg2+ concentration, and Bst DNA polymerase requirements, highlighting the importance of pathogen-specific optimization. The optimized assays demonstrated high sensitivity with detection limits of 120 fg/μL for Salmonella and 130 fg/μL for L. monocytogenes, achieving detection within 40 and 60 min, respectively. Specificity tests confirmed both assays were highly specific for their target pathogens in fresh beef samples with no cross-reactivity observed. Addition of hydroxynaphthol blue enabled simple visual detection of positive results, eliminating the need for specialized equipment. The developed LAMP assays offer rapid, sensitive, and specific detection of these important foodborne pathogens.

An integrated microfluidic platform for on-site qPCR analysis: food allergen detection from sample to result

Improving food safety is crucial in the context of a "One Health" approach. To guarantee product quality and safety, the food industry, which has a very high turnover rate, needs short time-to-result analyses. Therefore, user-friendly systems at the point-of-need are necessary, presenting relevant analytical information and fulfilling the current regulations. To answer these challenges, a microfluidic platform integrating sample preparation and subsequent multiplex qPCR detection has been developed for on-site testing. The system consists of a fully automated instrument driving a microfluidic cartridge dedicated to the detection of multiple allergens in complex food matrices. The first part of the microfluidic cartridge contains pumps, reservoirs, valves and a filter to achieve DNA extraction, concentration and purification. Multiplex qPCR detection is carried out in the second part of the cartridge including a negative control chamber and five chambers for target analyte detection. The in-house developed instrument contains all functions to autonomously drive the microfluidic cartridge: pneumatic control for fluid actuation, thermal control for qPCR amplification and an optical system using three fluorescent wavelengths for multiplex detection of the target analytes and controls. We demonstrate the simultaneous detection of four different allergens - gluten, sesame, soy and hazelnut - from various complex food matrices. The turn-around-time from sample to result is close to two hours and controls in place validate the obtained results. For gluten, a direct comparison with ELISA shows that the regulatory threshold of 20 ppm is comfortably fulfilled. Moreover, all results are in agreement with external laboratory analyses performed in parallel on the same samples. Our findings confirm that the system can be used safely on-site without the risk of cross contamination between the various samples being analysed. In conclusion, our microfluidic platform offers a robust method for on-site allergen management.

Application of real-time PCR for analysis canine meat (Canis lupus familiaris) in goat's satay for halal authentication study

Background

Canine meat (CM) is one of the non-halal meats prohibited for consumption by the Muslim community. Due to its low prices compared with beef, CM is typically used as meat adulterants in halal food-based products such as Satay and meatballs to get economic profits.

Aim

The objective of this study was to design a novel species-specific primer in combination with real-time polymerase chain reaction for analysis of Canine's DNA for halal authentication analysis.

Methods

A Primer targeting the D-loop region of mitochondrial DNA was designed and subjected to a validation procedure by assessing some performance characteristics including specificity, amplification efficiency (E), sensitivity, repeatability, and linearity describing the correlation between the concentration of Canine's DNA (x-axis) and quantification cycle (Cq) in y-axis. The designed primer was specific over other meat DNAs applying the annealing temperature (Tm) of 57.8°C.

Results

The Real-Time Polymerase Chain Reaction (RT-PCR) method produced an acceptable amplification efficiency (E) of 109.7% with the coefficient of determination (R 2) for the correlation between Cq and log DNA concentration of 0.999. The sensitivity of the developed method provides a limit of detection (LoD) value of 31.25 pg/µl. The precision of the analytical method is acceptable with a relative standard deviation value of 2%. The method with the designed D-loop primer was successfully applied for the detection and quantification of Canine's DNA in food products. There are no amplification profiles for Canine DNA in marketed goat's satay products.

Conclusion

RT-PCR combined with a novel primer targeting D-loop provides a specific and accurate analytical tool for the identification of CM for halal authentication studies.

Application of real-time PCR for analysis canine meat (Canis lupus familiaris) in goat's satay for halal authentication study

Background

Canine meat (CM) is one of the non-halal meats prohibited for consumption by the Muslim community. Due to its low prices compared with beef, CM is typically used as meat adulterants in halal food-based products such as Satay and meatballs to get economic profits.

Aim

The objective of this study was to design a novel species-specific primer in combination with real-time polymerase chain reaction for analysis of Canine's DNA for halal authentication analysis.

Methods

A Primer targeting the D-loop region of mitochondrial DNA was designed and subjected to a validation procedure by assessing some performance characteristics including specificity, amplification efficiency (E), sensitivity, repeatability, and linearity describing the correlation between the concentration of Canine's DNA (x-axis) and quantification cycle (Cq) in y-axis. The designed primer was specific over other meat DNAs applying the annealing temperature (Tm) of 57.8°C.

Results

The Real-Time Polymerase Chain Reaction (RT-PCR) method produced an acceptable amplification efficiency (E) of 109.7% with the coefficient of determination (R 2) for the correlation between Cq and log DNA concentration of 0.999. The sensitivity of the developed method provides a limit of detection (LoD) value of 31.25 pg/µl. The precision of the analytical method is acceptable with a relative standard deviation value of 2%. The method with the designed D-loop primer was successfully applied for the detection and quantification of Canine's DNA in food products. There are no amplification profiles for Canine DNA in marketed goat's satay products.

Conclusion

RT-PCR combined with a novel primer targeting D-loop provides a specific and accurate analytical tool for the identification of CM for halal authentication studies.

Towards Small Scale: Overview and Applications of Microfluidics in Biotechnology

Thanks to recent and continuing technological innovations, modern microfluidic systems are increasingly offering researchers working across all fields of biotechnology exciting new possibilities (especially with respect to facilitating high throughput analysis, portability, and parallelization). The advantages offered by microfluidic devices-namely, the substantially lowered chemical and sample consumption they require, the increased energy and mass transfer they offer, and their comparatively small size-can potentially be leveraged in every sub-field of biotechnology. However, to date, most of the reported devices have been deployed in furtherance of healthcare, pharmaceutical, and/or industrial applications. In this review, we consider examples of microfluidic and miniaturized systems across biotechnology sub-fields. In this context, we point out the advantages of microfluidics for various applications and highlight the common features of devices and the potential for transferability to other application areas. This will provide incentives for increased collaboration between researchers from different disciplines in the field of biotechnology.

Molecular Rapid Test for Identification of Tuna Species

Tuna is an excellent food product, relatively low in calories, that is recommended for a balanced diet. The continuously increasing demand, especially for bluefin-tuna-based food preparations, and its relatively high market price make adulteration by intentionally mixing with other lower-priced tunas more prospective. The development of rapid methods to detect tuna adulteration is a great challenge in food analytical science. We have thus developed a simple, fast, and low-cost molecular rapid test for the visual detection of tuna adulteration. It is the first sensor developed for tuna authenticity testing. The three species studied were Thunnus thynnus (BFT), Thunnus albacares, and Katsuwonus pelamis. DNA was isolated from fresh and heat-treated cooked fish samples followed by PCR. The PCR products were hybridized (10 min) to specific probes and applied to the rapid sensing device. The signal was observed visually in 10-15 min using gold nanoparticle reporters. The method was evaluated employing binary mixtures of PCR products from fresh tissues and mixtures of DNA isolates from heat-treated tissues (canned products) at adulteration percentages of 1-100%. The results showed that the method was reproducible and specific for each tuna species. As low as 1% of tuna adulteration was detected with the naked eye.

Paper-Based Microfluidic Chips for Food Hazard Factor Detection: Fabrication, Modification, and Application

Food safety and quality are paramount concerns for ensuring the preservation of human life and well-being. As the field of food processing continues to advance, there is a growing interest in the development of fast, instant, cost-effective, and convenient methods for detecting food safety issues. In this context, the utilization of paper-based microfluidic chips has emerged as a promising platform for enabling rapid detection, owing to their compact size, high throughput capabilities, affordability, and low resource consumption, among other advantages. To shed light on this topic, this review article focuses on the functionalization of paper-based microfluidic surfaces and provides an overview of the latest research and applications to colorimetric analysis, fluorescence analysis, surface-enhanced Raman spectroscopy, as well as their integration with paper-based microfluidic platforms for achieving swift and reliable food safety detection. Lastly, the article deliberates on the challenges these analytical methods and presents insights into their future development prospects in facilitating rapid food safety assessment.

Recent trends and developments of PCR-based methods for the detection of food-borne Salmonella bacteria and Norovirus

In recent years, rapid detection methods such as polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR) have been continuously developed to improve the detection of food-borne pathogens in food samples. The recent developments of PCR and qPCR in the detection and identification of these food-borne pathogens are described and elaborated throughout this review. Specifically, further developments and improvements of qPCR are discussed in detecting Salmonella and norovirus. Promising advances in these molecular detection methods have been widely used to prevent human food-borne illnesses and death caused by the food-borne pathogens. In addition, this review presents the limitations and challenges of the detection methods which include conventional culture method and conventional PCR method in detecting Salmonella and norovirus. Furthermore, several advances of qPCR such as viability PCR (vPCR) and digital PCR (dPCR) have been discussed in the detection of Salmonella and norovirus. Good practice of analysis of the food-borne pathogens and other contaminants in the food industry as well as the advancement of molecular detection methods will help improve and ensure food safety and food quality.

Optimization of quantitative reverse transcription PCR method for analysis of weakly expressed genes in crops based on rapeseed

Rapeseed (Brassica napus) is an allopolyploid hybrid (AACC genome) of turnip rape (B. rapa, genome: AA) and vegetable cabbage (B. oleraceae, genome: CC). Rapeseed oil is one of the main vegetable oils used worldwide for food and other technical purposes. Therefore, breeding companies worldwide are interested in developing rapeseed varieties with high yields and increased adaptation to harsh climatic conditions such as heat and prolonged drought. One approach to studying the mechanism of the epigenetically regulated stress response is to analyze the transcriptional changes it causes. In addition, comparing the expression of certain genes between stress- and non-stress-tolerant varieties will help guide breeding in the desired direction. Quantitative reverse transcription PCR (RT-qPCR) has been intensively used for gene expression analysis for several decades. However, the transfer of this method from model plants to crop species has several limitations due to the high accumulation of secondary metabolites, the higher water content in some tissues and therefore problems with their grinding and other factors. For allopolyploid rapeseed, the presence of two genomes, often with different levels of expression of homeologous genes, must also be considered. In this study, we describe the optimization of transcriptional RT-qPCR analysis of low-expression epigenetic genes in rapeseed, using Kinetochore Null2 (KNL2), a regulator of kinetochore complex assembly, as an example. We demonstrated that a combination of various factors, such as tissue homogenization and RNA extraction with TRIzol, synthesis of cDNA with gene-specific primers, and RT-qPCR in white plates, significantly increased the sensitivity of RT-qPCR for the detection of BnKNL2A and BnKNL2C gene expression.

Application of DNA barcoding for ensuring food safety and quality

With increasing international food trade, food quality and safety are high priority worldwide. The consumption of contaminated and adulterated food can cause serious health problems such as infectious diseases and allergies. Therefore, the authentication and traceability systems are needed to improve food safety. The mitochondrial DNA can be used for species authentication of food and food products. Effective DNA barcode markers have been developed to correctly identify species. The US FDA approved to the use of DNA barcoding for various food products. The DNA barcoding technology can be used as a regulatory tool for identification and authenticity. The application of DNA barcoding can reduce the microbiological and toxicological risks associated with the consumption of food and food products. DNA barcoding can be a gold-standard method in food authenticity and fraud detection. This review describes the DNA barcoding method for preventing food fraud and adulteration in meat, fish, and medicinal plants.

Infrared thermography can detect previsual bacterial growth in a laboratory setting via metabolic heat detection

Aims

Detection of bacterial contamination in healthcare and industry takes many hours if not days. Thermal imaging, the measurement of heat by an infrared camera, was investigated as a potential noninvasive method of detecting bacterial growth.

Methods and Results

Infrared thermography can detect the presence of Escherichia coli and Staphylococcus aureus on solid growth media by an increase in temperature before they are visually observable. A heat decrease is observed after treatment with ultraviolet light and heat increased after incubation with dinitrophenol.

Conclusions

Infrared thermography can detect early growth of bacteria before they are detectable by other microbiology‐based method. The heat observed is due to the cells being viable and metabolically active, as cells killed with ultraviolet light exhibit reduced increase in temperature and treatment with dinitrophenol increases heat detected.

Significance and Impact of the Study

Infrared thermography detects bacterial growth without the need for specialized temperature control facilities. The method is statistically robust and can be undertaken in situ, thus is highly versatile. These data support the application of infrared thermography in a laboratory, clinical and industrial setting for vegetative bacteria, thus may become into an important methodology for the timely and straightforward detection of early‐stage bacterial growth.

Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis

This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.

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.

Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms

Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one universal LNA probe is used for multiple DNA targets instead of using one to one TaqMan probe. The specificity, sensitivity, dynamic range, and accuracy of the ULNA-ddPCR method are determined by employing GM rice analysis as an example. Simplex and triplex ULNA-ddPCR assays for three GM rice events, T2A-1, T1C-19, and G6H1, are established and evaluated. All results indicate that the developed simplex and triplex ULNA-ddPCR assays are suitable for quantitative analysis of GM rice events with high sensitivity, accuracy, and low cost. The ULNA-ddPCR method also has the potential for multiple DNA target quantification in other research fields.

Electrowetting-on-dielectric (EWOD): Current perspectives and applications in ensuring food safety

Digital microfluidic (DMF) platforms have contributed immensely to the development of multifunctional lab-on-chip systems for performing complete sets of biological and analytical assays. Electrowetting-on-dielectric (EWOD) technology, due to its outstanding flexibility and integrability, has emerged as a promising candidate for such lab-on-chip applications. Triggered by an electrical stimulus, EWOD devices allow precise manipulation of single droplets along the designed electrode arrays without employing external pumps and valves, thereby enhancing the miniaturization and portability of the system towards transcending important laboratory assays in resource-limited settings. In recent years, the simple fabrication process and reprogrammable architecture of EWOD chips have led to their widespread applications in food safety analysis. Various EWOD devices have been developed for the quantitative monitoring of analytes such as food-borne pathogens, heavy metal ions, vitamins, and antioxidants, which are significant in food samples. In this paper, we reviewed the advances and developments in the design of EWOD systems for performing versatile functions starting from sample preparation to sample detection, enabling rapid and high-throughput food analysis.

Detection of DNA from undeclared animal species in commercial canine and feline raw meat diets using qPCR

The best diagnostic test for cutaneous adverse food reactions (CAFR) in companion animals is an elimination diet and subsequent provocation trials. Many commercial diets contain novel protein ingredients used in elimination diets, and selection is based on label ingredients. Raw meat-based diets (RMBD) have become increasingly commercially available, gaining popularity despite potential health risks. Reliability of RMBD based on label ingredients has not been investigated. Using quantitative polymerase chain reaction (qPCR), 9 canine and 9 feline commercial RMBD were assessed for reliability of species-specific animal DNA. Two separate batches of each diet were assessed for content consistency. The DNA of 1 or more unlisted animal species was identified in > 60% of diets, as was discrepancy between batches. The unlisted DNA most frequently detected was lamb in canine diets and turkey in feline diets. Based on these findings, use of commercially available RMBD cannot be recommended as an elimination diet in clinical diagnosis of CAFR.

Sesame, Pistachio, and Macadamia Nut: Development and Validation of New Allergenic Systems for Fast Real-Time PCR Application

Food allergy is a worldwide health problem that concerns infants to adults. The main health risk for sensitised individuals is due to the presence of traces of allergens as the result of an accidental contamination during food processing. The labelling of allergens such as sesame, pistachio, and macadamia nut on food products is mandatory according to Regulation (EU) N. 1169/2011; therefore, the development of suitable and specific analytical methodologies is advisable. The aim of this study was to perform a multi-allergen real-time PCR system that works well in fast mode at the same annealing temperature and with the same thermal profile. The real-time PCR was developed designing new, specific, and efficient primer and probe systems for the 2S albumingene for sesame and pistachio and for the vicilin precursorgene for macadamia nut. These systems were subjected to a robust intra-laboratory qualitative validation process prior to their application, by DNA extraction and fast real-time PCR, on some real market samples to reproduce a potential allergen contamination along the food chain. The developed system results were specific and robust, with a sensible limit of detection (0.005% for sesame; 0.004% for pistachio; 0.006% for macadamia nut). The performance and the reliability of the target systems were confirmed on commercial food samples. This molecular approach could be used as a screening or as a support tool, in association with the other widespread monitoring techniques (such as ELISA).

Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicons has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds.

Current analytical methods for porcine identification in meat and meat products

Authentication of meat products is critical in the food industry. Meat adulteration may lead to religious apprehensions, financial gain and food-toxicities such as meat allergies. Thus, empirical validation of the quality and constituents of meat is paramount. Various analytical methods often based on protein or DNA measurements are utilized to identify meat species. Protein-based methods, including electrophoretic and immunological techniques, are at times unsuitable for discriminating closely related species. Most of these methods have been replaced by more accurate and sensitive detection methods, such as DNA-based techniques. Emerging technologies like DNA barcoding and mass spectrometry are still in their infancy when it comes to their utilization in meat detection. Gold nanobiosensors have shown some promise in this regard. However, its applicability in small scale industries is distant. This article comprehensively reviews the recent developments in the field of analytical methods used for porcine identification.

Effect of low-temperature preservation on quality changes in Pacific white shrimp, Litopenaeus vannamei: a review

Shrimp has been widely accepted as an excellent resource for white meat due to its high-protein and low-fat content, especially low cholesterol. However, shrimps are highly perishable during preservation and retailing procedures due to the activities of enzymatic proteolysis, lipid oxidation, and microbial degradation. With increasing knowledge of and demands for safety, nutrition, and freshness of shrimp products, energy efficient, quality, maintained, and sustainable preservation technologies are needed. Low-temperature preservation, a practical processing method for improving the shelf life of food products, is widely used in the aquatic industry. This review focuses on the effects of low-temperature preservation on the quality changes in Litopenaeus vannamei. It considers physicochemical properties, sensory evaluation, melanosis assessment, and microbiological analysis. The perspectives of non-protein-based techniques on quality analysis of shrimps during preservation are also discussed. © 2019 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.

Detection of 12 Common Food-Borne Bacterial Pathogens by TaqMan Real-Time PCR Using a Single Set of Reaction Conditions

Food safety has become an important public health issue worldwide. However, conventional methods for detection of food-borne pathogens are complicated, and labor-intensive. Moreover, the sensitivity is often low, and it is difficult to achieve high-throughput detection. This study developed a TaqMan real-time polymerase chain reaction (PCR) assay for the simultaneous detection and quantification of 12 common pathogens in a single reaction, including Escherichia coli O157:H7, Listeria monocytogenes/ivanovii, Salmonella enterica, Vibrio parahaemolyticus, β-streptococcus hemolyticus, Yersinia enterocolitica, Enterococcus faecalis, Shigella spp., Proteus mirabilis, Vibrio fluvialis, Staphylococcus aureus, and Campylobacter jejuni in food and drinking water. Based on published sequence data, specific primers, and fluorescently-labeled hybridization probes were designed targeting based on the virulence genes of the 12 pathogens, and these primers and probes were optimized to achieve consistent reaction conditions. The assay was evaluated using 106 pure bacterial culture strains. There was no cross-reaction among the different pathogens. The analytical sensitivity was 1 copy/μL for E. coli O157:H7, L. monocytogenes/ivanovii, β-streptococcus hemolyticus, Shigella spp., P. mirabilis, and V. fluvialis, 10 copies/μL for S. enterica, V. parahaemolyticus, Y. enterocolitica, E. faecalis, S. aureus, and C. jejuni, respectively. The limit of detection (LOD) was 296, 500, 177, 56, 960, 830, 625, 520, 573, 161, 875, and 495 CFU/mL for E. coli O157:H7, L. monocytogenes/ivanovii, S. enterica, V. parahaemolyticus, β-streptococcus hemolyticus, Y. enterocolitica, E. faecalis, Shigella spp., P. mirabilis, V. fluvialis, S. aureus, and C. jejuni, respectively. The limit of detection for the assay in meat samples was 10³ CFU/g for V. parahaemolyticus and 10⁴ CFU/g for other 11 strains. Together, these results indicate that the optimized TaqMan real-time PCR assay will be useful for routine detection of pathogenic bacteria due to its rapid analysis, low cost, high-throughput, high specificity, and sensitivity.

Comparison of real-time PCR methods for quantification of European hake (Merluccius merluccius) in processed food samples

The quantification of species in commercial products is limited by analytical shortcomings, as most of them provide semiquantitative results. An exception is real-time PCR, which can provide quantitative results using hybridization probes. In the present work, this technique has been applied to the absolute, absolute-relative and relative quantification of the most valued hake species in European markets, Merluccius merluccius (European Hake). The best quantification results for this species in binary mixtures with non-target species (Merluccius capensis) and using a species-specific real-time PCR MMER_VIC system was achieved using a relative quantification approach (MLL as reference system). Absolute quantification using the MLL nuclear system has been demonstrated as appropriate for the quantification of the Merluccius genus in food model samples. This study reveals the impact of different reference systems (MLL and HAKE) in the absolute-relative and relative quantification approaches, showing that the nuclear MLL system performed better than the mitochondrial HAKE system.

From the Field to the Bottle—An Integrated Strategy for Wine Authenticity

The wine sector is one of the most economically important agro-food businesses. The wine market value is largely associated to terroir, in some cases resulting in highly expensive wines that attract fraudulent practices. The existent wine traceability system has some limitations that can be overcome with the development of new technological approaches that can tackle this problem with several means. This review aims to call attention to the problem and to present several strategies that can assure a more reliable and authentic wine system, identifying existent technologies developed for the sector, which can be incorporated into the current traceability system.

Q3: A Compact Device for Quick, High Precision qPCR

An accurate and easy-to-use Q3 system for on-chip quantitative real-time Polymerase Chain Reaction (qPCR) is hereby demonstrated, and described in detail. The qPCR reactions take place inside a single-use Lab-on-a-Chip with multiple wells, each with 5 to 15 µL capacity. The same chip hosts a printed metal heater coupled with a calibrated sensor, for rapid and accurate temperature control inside the reaction mixture. The rest of the system is non-disposable and encased in a 7 × 14 × 8.5 (height) cm plastic shell weighing 300 g. Included in the non-disposable part is a fluorescence read-out system featuring up to four channels and a self-contained control and data storage system, interfacing with an external user-friendly software suite. Hereby, we illustrate the engineering details of the Q3 system and benchmark it with seamlessly ported testing protocols, showing that Q3 equals the performance of standard commercial systems. Overall, to the best of our knowledge, this is one of the most mature general-purpose systems for on-chip qPCR currently available.

Detection of Korean Native Honey and European Honey by Using Duplex Polymerase Chain Reaction and Immunochromatographic Assay

Korean native honey (KNH) is much more expensive than European honey (EH) in Korea, because KNH is a favored honey which is produced less than EH. Food fraud of KNH has drawn attention of the government office concerned, which is in need of a method to differentiate between KNH and EH which are produced by the Asiatic honeybee, Apis cerana and the European honeybee, Apis mellifera, respectively. A method to discriminate KNH and EH was established by using duplex polymerase chain reaction (PCR) in this study. Immunochromatographic assay (IC) was examined to analyze the duplex PCR product. The DNA sequences of primers for the duplex PCR were determined by comparing cytochrome C oxidase genes of the two honey bee species. Chelex resin method was more efficient in extracting genomic DNA from honey than the other two procedures of commercial kits. The duplex PCR amplifying DNA of 133 bp were more sensitive than that amplifying DNA of 206 bp in detecting EH in the honey mixture of KNH and EH. Agarose gel electrophoresis and IC detected the DNA of 133 bp at the ratios of down to 1% and 5% EH in the honey mixture, respectively and also revealed that several KNH products distributed by internet shopping sites were actually EH. In conclusion, the duplex PCR with subsequent IC could also discriminate between KNH and EH and save time and labor.

On-site identification of meat species in processed foods by a rapid real-time polymerase chain reaction system

Correct labeling of foods is critical for consumers who wish to avoid a specific meat species for religious or cultural reasons. Therefore, gene-based point-of-care food analysis by real-time Polymerase Chain Reaction (PCR) is expected to contribute to the quality control in the food industry. In this study, we perform rapid identification of meat species by our portable rapid real-time PCR system, following a very simple DNA extraction method. Applying these techniques, we correctly identified beef, pork, chicken, rabbit, horse, and mutton in processed foods in 20min. Our system was sensitive enough to detect the interfusion of about 0.1% chicken egg-derived DNA in a processed food sample. Our rapid real-time PCR system is expected to contribute to the quality control in food industries because it can be applied for the identification of meat species, and future applications can expand its functionality to the detection of genetically modified organisms or mutations.

Electrochemical detection of magnetically-entrapped DNA sequences from complex samples by multiplexed enzymatic labelling: Application to a transgenic food/feed quantitative survey

Monitoring of genetically modified organisms in food and feed demands molecular techniques that deliver accurate quantitative results. Electrochemical DNA detection has been widely described in this field, yet most reports convey qualitative data and application in processed food and feed samples is limited. Herein, the applicability of an electrochemical multiplex assay for DNA quantification in complex samples is assessed. The method consists of the simultaneous magnetic entrapment via sandwich hybridisation of two DNA sequences (event-specific and taxon-specific) onto the surface of magnetic microparticles, followed by bienzymatic labelling. As proof-of-concept, we report its application in a transgenic food/feed survey where relative quantification (two-target approach) of Roundup Ready Soybean® (RRS) was performed in food and feed. Quantitative coupling to end-point PCR was performed and calibration was achieved from 22 and 243 DNA copies spanning two orders of magnitude for the event and taxon-specific sequences, respectively. We collected a total of 33 soybean-containing samples acquired in local supermarkets, four out of which were found to contain undeclared presence of genetically modified soybean. A real-time PCR method was used to verify these findings. High correlation was found between results, indicating the suitability of the proposed multiplex method for food and feed monitoring.

Ultrasensitive and rapid detection of β-conglutin combining aptamers and isothermal recombinase polymerase amplification

Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit β-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic β-conglutin allergen termed β-conglutin binding aptamer II (β-CBA II), facilitating ultrasensitive detection via isothermal amplification. Combining magnetic beads as the solid phase with Apta-RPA detection, the total assay time was reduced from 210 min to just 25 min, with a limit of detection of 3.5 × 10^-11 M, demonstrating a rapid and ultrasensitive generic methodology that can be used with any aptamer. Future work will focus on further simplification of the assay to a lateral flow format. Graphical Abstract Schematic representation of the rapid and novel bead-based Apta-RPA assay.