Comparison of Real-Time PCR Quantification Methods in the Identification of Poultry Species in Meat Products

Development of real-time polymerase chain reaction for analysis of rat meat (Bandicota bengalensis) in beef meatballs for halal authentication

Background

Consumer awareness of food adulteration is increasing nowadays. Motivated by economic gain, unethical meat producers try to blend halal meat such as beef with non-halal meat like rat meat (RM).

Aim

This study aims to develop a real-time polymerase chain reaction (RT-PCR) analysis method to analyze the presence of RM in beef meatballs.

Methods

This research was carried out in the following stages: primer design, DNA isolation, analysis of DNA isolates, the optimization of primer annealing temperature, primer specificity test, sensitivity, and repeatability. The validated RT-PCR method was then used to analyze the marketed meatball samples.

Results

The result showed that the designed primer targeting on ND2 gene set rat mt-DNA (forward: ACTCCATATCTCTCACCATATTTCC; reverse: GGGTTAGGGTACTTAGGATTGTTAG), had good specificity at an optimal annealing temperature of 56.3oC over the other eight species. The developed RT-PCR method produces a limit detection value of 195.31 pg, coefficient of determination (R 2) for linearity of 0.983, amplification efficiency (E) of 100%, and CV value for amplification response of 1.8%. The result showed that the developed RT-PCR method did not detect the presence of RM DNA in eight marketed beef meatball samples.

Conclusion

The developed method meets the acceptance criteria for RT-PCR and can be used as a halal authentication method to identify the presence of RM in beef meatballs.

Mammalian and avian species quantification in homogenized foods: real time PCR and digital PCR as tools for label compliance controls

Currently food fraud and authenticity of products composition are topics of great concern; ingredients quantification could allow to identify small amounts of contaminats or voluntary addition of improper components. Many molecular methods are available for species identification in foodstuffs but, for a better application, they should not be affected by the interference of other ingredients. The main purpose of this work was to verify the Real Time PCR and the Digital PCR (dPCR) quantification performances on baby food samples, specifically selected for their high miscibility to limit variability; chicken was selected as target to verify the performance of quantification of methods after having spiked the same quantity in different baby foods. The other aims were: (1) to verify a constant genome copies ratio existence between mammalian and avian species (2) to verify the dPCR performance, set up on housekeeping, to quantify mammalian and avian species in commercial products. Digital PCR showed fewer differences respect to Real Time PCR, at the same 15% w/w chicken spiking level. Despite the constant difference between mammalian and avian genome copies, in samples with the same spiking weight, the confidence intervals increasing towards the extreme values, made impossible to use genome copies ratio as a sort of correction factor between species. Finally, the dPCR system using the myostatin housekeeping gene to determine the chicken content seemed reliable to verify the labelling compliance in meat-based commercial products.

Optimizing green approach to enhanced antioxidants from Thai pigmented rice bran using deep eutectic solvent-based ultrasonic-assisted extraction

Deep eutectic solvents (DES) have garnered significant attention as extraction media owing to their commendable attributes of being environmentally sustainable and the inherent adaptability of DES's versatile physical and chemical characteristics. The present study investigated the effects of deep eutectic solvents on the total contents of anthocyanin, phenolic, and flavonoids, as well as the antioxidant activity of Thai pigmented rice bran extract. The optimal extraction parameters for deep eutectic solvent-based ultrasonic-assisted extraction (DES-UAE) were also determined using the response surface methodology (RSM). The optimal conditions for the extraction of anthocyanins and other antioxidants from pigmented rice bran using a deep eutectic solvent were choline chloride: ethylene glycol (Ch:Eg) at a 1:2 ratio, mixed with 20 % water as a solvent. The ultrasonic-assisted extraction (UAE) at 37 kHz of frequency, 50 °C of temperature, 40 min of extraction time, and a 1:6 g/mL of solid-to-solvent ratio yielded a total anthocyanin content of 4.55 ± 0.09 mg C3G/g DW, a total phenolic content of 26.49 ± 0.62 mg GAE/g DW, a total flavonoid content of 6.57 ± 0.55 mg QE/g DW, and a percent inhibition of DPPH radical of 77.83 ± 1.51. By comparing the antioxidant content that was extracted from three cultivars of pigmented rice, it was found that Leum Pua black rice bran provided significantly higher antioxidant content compared to Hom Nin purple rice bran and Mali Dang red rice bran. This research suggests an achievable, eco-friendly, and effective method for preparing high-quality, consumer-safe Thai rice bran as a raw material for nutraceuticals.

Development of Seven New dPCR Animal Species Assays and a Reference Material to Support Quantitative Ratio Measurements of Food and Feed Products

Laboratory testing methods to confirm the identity of meat products and eliminate food fraud regularly rely on PCR amplification of extracted DNA, with most published assays detecting mitochondrial sequences, providing sensitive presence/absence results. By targeting single-copy nuclear targets instead, relative quantification measurements are achievable, providing additional information on the proportions of meat species detected. In this Methods paper, new assays for horse, donkey, duck, kangaroo, camel, water buffalo and crocodile have been developed to expand the range of species that can be quantified, and a previously published reference assay targeting the myostatin gene has been modified to include marsupials and reptiles. The accuracy of this ratio measurement approach was demonstrated using dPCR with mixtures of meat DNA down to 0.1%. However, the limit of detection (LOD) of this approach is not just determined by the assay targets, but by the samples themselves, with food or feed ingredients and processing impacting the DNA yield and integrity. In routine testing settings, the myostatin assay can provide multiple quality control roles, including monitoring the yield and purity of extracted DNA, identifying the presence of additional meats not detected by the suite of species-specific assays and potentially estimating a sample-specific LOD based on measured copy numbers of the myostatin target. In addition to the myostatin positive control assay, a synthetic DNA reference material (RM) has been designed, containing PCR targets for beef, pork, sheep, chicken, goat, kangaroo, horse, water buffalo and myostatin, to be used as a positive template control. The availability of standardised measurement methods and associated RMs significantly improves the reliability, comparability and transparency of laboratory testing, leading to greater confidence in results.

Quantification of Pork, Chicken, Beef, and Sheep Contents in Meat Products Using Duplex Real-Time PCR

Accurate methods for meat speciation and quantification are essential for ensuring the supply of safe and wholesome meat and composite products with animal origins to negate the potential associated hazards, aid classification of consignments at the import control system, and thwart food fraud committed for financial gain. To better enhance meat safety control and combat food fraud, this study developed two duplex real-time polymerase chain reaction (real-time PCR) systems specifically designed for chicken, pork, sheep, and beef, using single-copy, chromosomally encoded, species-specific gene sequences to accurately measure the content of each meat type in meat products. DNA extracted from the raw and boiled reference materials prepared in varying proportions (ranging from 1% to 75%) were used in the development of the duplex assay to derive calibration factors to determine the meat content in different meat products. The method was further validated using proficiency test samples and market monitoring samples. Our findings showed that this method exhibits high specificity and sensitivity, with a significant accuracy range of 0.14% to 24.07% in quantifying the four meat types in both raw and processed meat products. Validation results further confirmed the effectiveness of our method in accurately quantifying meat content. Thus, we have demonstrated the duplex qPCR assays as promising approaches for implementation in routine analysis to strengthen meat safety control systems and combat meat fraud, thereby safeguarding consumer health and trust in the meat industry.

A Novel Universal Primer Multiplex Real-Time PCR (UP-M-rtPCR) Approach for Specific Identification and Quantitation of Cat, Dog, Fox, and Mink Fractions Using Nuclear DNA Sequences

Adulteration of meat with carnivorous animals (such as cats, dogs, foxes, and minks) can cause ethical problems and lead to disease transmission; however, DNA quantitative methods for four carnivorous species in one tube reaction are still rare. In this study, a carnivore-specific nuclear DNA sequence that is conserved in carnivorous animals but has base differences within the sequence was used to design universal primers for its conserved region and corresponding species-specific probes for the hypervariable region. A novel universal primer multiplex real-time PCR (UP-M-rtPCR) approach was developed for the specific identification and quantitation of cat, dog, fox, and mink fractions in a single reaction, with a 0.05 ng absolute limit of detection (LOD) and 0.05% relative LOD. This approach simplifies the PCR system and improves the efficiency of simultaneous identification of multiple animal-derived ingredients in meat. UP-M-rtPCR showed good accuracy (0.48-7.04% relative deviation) and precision (1.42-13.78% relative standard deviation) for quantitative analysis of cat, dog, fox, and mink DNA as well as excellent applicability for the evaluation of meat samples.

An Inexpensive CRISPR-Based Point-of-Care Test for the Identification of Meat Species and Meat Products

The growing demand for and supply of meat and meat products has led to a proportional increase in cases of meat adulteration. Adulterated meat poses serious economic and health consequences globally. Current laboratory methods for meat species identification require specialized equipment with limited field applications. This study developed an inexpensive, point-of-care Loop-Mediated Isothermal Amplification (LAMP)-CRISPR/Cas12a colorimetric assay to detect meat species using a Texas Red-labelled single-strand (ssDNA) reporter. As low as 1.0 pg/µL of the porcine NADH4, the chicken NADH dehydrogenase subunit 2 (ND2) and the duck D-loop genes was detectable under white, blue and ultraviolet light. The test turnaround time from DNA extraction to visualization was approximately 40 min. The assay accurately detected pure and mixed-meat products in the laboratory (n = 15) and during a pilot point-of-care test (n = 8) in a food processing factory. The results are 100% reproducible using lateral flow detection strips and the real-time PCR detection instrument. This technology is fully deployable and usable in any standard room. Thus, our study demonstrates that this method is a straightforward, specific, sensitive, point-of-care test (POCT) adaptable to various outlets such as customs, quarantine units and meat import/export departments.

Identification of Mammalian and Poultry Species in Food and Pet Food Samples Using 16S rDNA Metabarcoding

The substitution of more appreciated animal species by animal species of lower commercial value is a common type of meat product adulteration. DNA metabarcoding, the combination of DNA barcoding with next-generation sequencing (NGS), plays an increasing role in food authentication. In the present study, we investigated the applicability of a DNA metabarcoding method for routine analysis of mammalian and poultry species in food and pet food products. We analyzed a total of 104 samples (25 reference samples, 56 food products and 23 pet food products) by DNA metabarcoding and by using a commercial DNA array and/or by real-time PCR. The qualitative and quantitative results obtained by the DNA metabarcoding method were in line with those obtained by PCR. Results from the independent analysis of a subset of seven reference samples in two laboratories demonstrate the robustness and reproducibility of the DNA metabarcoding method. DNA metabarcoding is particularly suitable for detecting unexpected species ignored by targeted methods such as real-time PCR and can also be an attractive alternative with respect to the expenses as indicated by current data from the cost accounting of the AGES laboratory. Our results for the commercial samples show that in addition to food products, DNA metabarcoding is particularly applicable to pet food products, which frequently contain multiple animal species and are also highly prone to adulteration as indicated by the high portion of analyzed pet food products containing undeclared species.

A Simple and Reliable Single Tube Septuple PCR Assay for Simultaneous Identification of Seven Meat Species

Multiplex PCR methods have been frequently used for authentication of meat product adulteration. Through screening of new species-specific primers designed based on the mitochondrial DNA sequences, a septuple PCR method is ultimately developed and optimized to simultaneously detect seven species including turkey (110 bp), goose (194 bp), pig (254 bp), sheep (329 bp), beef (473 bp), chicken (612 bp) and duck (718 bp) in one reaction. The proposed method has been validated to be specific, sensitive, robust and inexpensive. Taken together, the developed septuple PCR assay is reliable and efficient, not only to authenticate animal species in commercial meat products, but also easily feasible in a general laboratory without special infrastructures.