Droplet Digital PCR (ddPCR) Analysis for the Detection and Quantification of Cow DNA in Buffalo Mozzarella Cheese

Double-Tube Multiplex TaqMan Real-Time PCR for the Detection of Eight Animal-Derived Dairy Ingredients

Milk and dairy products represent important sources of nutrition in our daily lives. The identification of species within dairy products holds importance for monitoring food adulteration and ensuring traceability. This study presented a method that integrated double-tube and duplex real-time polymerase chain reaction (PCR) with multiplex TaqMan probes to enable the high-throughput detection of animal-derived ingredients in milk and dairy products. The detection system utilized one pair of universal primers, two pairs of specific primers, and eight animal-derived specific probes for cow, buffalo, goat, sheep, camel, yak, horse, and donkey. These components were optimized within a double-tube and four-probe PCR multiplex system. The developed double-tube detection system could simultaneously identify the above eight targets with a detection limit of 10-0.1 pg/μL. Validation using simulated adulterated milk samples demonstrated a detection limit of 0.1%. The primary advantage of this method lies in the simplification of the multiplex quantitative real-time PCR (qPCR) system through the use of universal primers. This method provides an efficient approach for detecting ingredients in dairy products, providing powerful technical support for market supervision.

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.

An instrument-free, integrated micro-platform for rapid and multiplexed detection of dairy adulteration in resource-limited environments

In dairy industry, expensive yak's milk, camel's milk, and other specialty dairy products are often adulterated with low-cost cow's milk, goat's milk and so on. Currently, the detection of specialty dairy products typically requires laboratory settings and relies on skilled operators. Therefore, there is an urgent need to develop a multi-detection technology and on-site rapid detection technique to enhance the efficiency and accuracy of the detection of specialty dairy products. In this study, we introduced a fully integrated and portable microfluidic detection platform called Sector Self-Driving Microfluidics (SDM), designed to simultaneously detect eight common species-specific components in milk. SDM integrated nucleic acid extraction, purification, loop-mediated isothermal amplification (LAMP), and lateral flow strip (LFS) detection functions into a closed microfluidic system, enabling contamination-free visual detection. The SDM platform used a constant-temperature heating plate, powered by a mobile battery, eliminated the need for additional power support. The SDM platform achieved nucleic acid enrichment and transfer through magnetic force and liquid flow driven by capillary forces, operating without external pumps. The standalone SDM platform could detect dairy components with as low as 1% content within 1 h. Validation with 35 commercially available samples demonstrated 100% specificity and accuracy compared to the gold standard real-time PCR. The SDM platform provided the dairy industry with an efficient, convenient, and accurate detection tool, enabling rapid on-site testing at production facilities or sales points. This facilitated real-time monitoring of quality issues during the production process, quickly identifying potential risks and preventing substandard products from entering the market.

Novel and Sensitive Touchdown Polymerase Chain Reaction Assays for the Detection of Goat and Sheep Milk Adulteration with Cow Milk

Milk is the most consumed liquid food in the world due to its high nutritional value and relatively low cost, characteristics that make it vulnerable to adulteration. One of the most common types of milk adulteration involves the undeclared addition of cow's milk to milk from other mammalian species, such as goats, sheep, buffalo or donkeys. The incidence of such adulteration not only causes a crisis in terms of commercial market and consumer uncertainty but also poses a risk to public health, as allergies can be triggered by proteins in undeclared cow's milk. In this study, a specific qualitative touchdown (TD) PCR method was developed to detect the undeclared addition of cow's milk in goat and sheep milk based on the discrimination of the peak areas of the melting curves after the modification of bovine-specific primers. The developed methodology has high specificity for the DNA templates of other species, such as buffalos and donkeys, and is able to identify the presence of cow's milk down to 1%. Repeatability was tested at low bovine concentrations of 5% and 1% and resulted in %RSD values of 1.53-2.04 for the goat-cow assay and 2.49-7.16 for the sheep-cow assay, respectively. The application of this method to commercial goat milk samples indicated a high percentage of noncompliance in terms of labeling (50%), while a comparison of the results to rapid immunochromatographic and ELISA kits validated the excellent sensitivity and applicability of the proposed PCR methodology that was able to trace more adulterated samples. The developed assays offer the advantage of multiple detection in a single run, resulting in a cost- and time-efficient method. Future studies will focus on the applicability of these assays in dairy products such as cheese and yogurt.

Duplex Droplet Digital PCR Assay for Quantification of Hepatitis E Virus in Food

Hepatitis E virus (HEV) represents an emerging risk in industrialized countries where the consumption of contaminated food plays a pivotal role. Quantitative real-time RT-PCR (RT-qPCR) is one of the most suitable methods for the detection and quantification of viruses in food. Nevertheless, quantification using RT-qPCR has limitations. Droplet digital PCR (ddPCR) provides the precise quantification of nucleic acids without the need for a standard curve and a reduction in the effect on virus quantification due to the presence of inhibitors. The objectives of the present work were (i) to develop a method for the absolute quantification of HEV in swine tissues based on ddPCR technology and provide internal process control for recovery assessment and (ii) to evaluate the performance of the method by analyzing a selection of naturally contaminated wild boar muscle samples previously tested using RT-qPCR. The method was optimized using a set of in vitro synthesized HEV RNA and quantified dsDNA. The limit of detection of the developed ddPCR assay was 0.34 genome copies/µL. The analysis of the wild boar samples confirmed the validity of the ddPCR assay. The duplex ddPCR method showed no reduction in efficiency compared to individual assays. The method developed in the present study could represent a sensitive assay for the detection and absolute quantification of HEV RNA in food samples with the advantage of presenting the co-amplification of internal process control.

Assessment of cheese frauds, and relevant detection methods: A systematic review

Dairy products are widely consumed in the world due to their nutritional and functional characteristics. This group of food products are consumed by all age groups due to their health-giving properties. One of these products is cheese which has a high price compared to other dairy products. Because of this, it can be prone to fraud all over the world. Fraud in food products threatens the world's food safety and can cause serious damage to human health. There are many concerns among food authorities in the world about the fraud of food products. FDA, WHO, and the European Commission provide different legislations and definitions for fraud. The purpose of this review is to identify the most susceptible cheese type for fraud and effective methods for evaluating fraud in all types of cheeses. For this, we examined the Web of Science, Scopus, PubMed, and ScienceDirect databases. Mozzarella cheese had the largest share among all cheeses in terms of adulteration due to its many uses. Also, the methods used to evaluate different types of cheese frauds were PCR, Spectrometry, stable isotope, image analysis, electrophoretic, ELISA, sensors, sensory analysis, near-infrared and NMR. The methods that were most used in detecting fraud were PCR and spectrometry methods. Also, the least used method was sensory evaluation.

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.

Animal Species Authentication in Dairy Products

Milk is one of the most important nutritious foods, widely consumed worldwide, either in its natural form or via dairy products. Currently, several economic, health and ethical issues emphasize the need for a more frequent and rigorous quality control of dairy products and the importance of detecting adulterations in these products. For this reason, several conventional and advanced techniques have been proposed, aiming at detecting and quantifying eventual adulterations, preferentially in a rapid, cost-effective, easy to implement, sensitive and specific way. They have relied mostly on electrophoretic, chromatographic and immunoenzymatic techniques. More recently, mass spectrometry, spectroscopic methods (near infrared (NIR), mid infrared (MIR), nuclear magnetic resonance (NMR) and front face fluorescence coupled to chemometrics), DNA analysis (real-time PCR, high-resolution melting analysis, next generation sequencing and droplet digital PCR) and biosensors have been advanced as innovative tools for dairy product authentication. Milk substitution from high-valued species with lower-cost bovine milk is one of the most frequent adulteration practices. Therefore, this review intends to describe the most relevant developments regarding the current and advanced analytical methodologies applied to species authentication of milk and dairy products.