Multiplex real-time PCR for the identification and quantification of DNA from duck, pig and chicken in Chinese blood curds

Machine-learning assisted modelling of multiple elements for authenticating edible animal blood food

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The critical elements for identifying species of the animal blood food were selected.

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Elemental fingerprint coupled with ELM were proposed for species identification of the animal blood food.

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The optimal ELM model for identifying the species of the animal blood food was constructed.

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The absolute and relative content of 25 elements in animal blood food were reported for the first time.

Elemental fingerprint coupled with machine learning modelling was proposed for species authentication of the edible animal blood gel (EABG). A total of 25 elements were determined by inductively coupled plasma mass spectrometry (ICP-MS) and atomic absorption spectroscopy (AAS) in 150 EABG samples prepared from five species of animals, namely duck, chicken, bovine, pig, and sheep. Extreme learning machine (ELM) models were constructed and optimized. Principal component analysis and Fisher linear discriminant analysis were comparatively utilized for dimension reduction of the crucial input elements selected via stepwise discriminant analysis and one-way ANOVA. The optimal ELM model was obtained with the crucial elements selected by one-way ANOVA from the relative content of the measured elements, which afforded accuracies of 98.0% and 96.0% for the training and test set, respectively. All findings suggest that elemental fingerprint accompanied by ELM have great potential in authenticating the edible animal blood food.

Inactivation of antibiotic resistant bacterium Escherichia coli by electrochemical disinfection on molybdenum carbide electrode

Antibiotic-resistant bacteria (ARB) pose a substantial threat to public health worldwide. Electrochemistry, as a low energy consumption and environmentally friendly technique, is ideal for inactivating ARB. This study explored the utility of electrochemical disinfection (ED) for inactivating ARB (Escherichia coli K-12 LE392 resistant to kanamycin, tetracycline, and ampicillin) and the regrowth potential of the treated ARB. The results revealed that 5.12-log ARB removal was achieved within 30 min of applying molybdenum carbide as the anode and cathode material under a voltage of 2.0 V. No ARB regrowth was observed in the cathode chamber after 60 min of incubation in unselective broth, demonstrating that the process in the cathode chamber was more effective for permanent inactivation of ARB. The mechanisms underlying the ARB inactivation were verified based on intercellular reactive oxygen species (ROS) measurement, membrane integrity detection, and genetic damage assessment. Higher ROS production and membrane permeability were observed in the cathode and anode groups (p < 0.001) compared to the control group (0 V). In addition, the DNA was more likely to be damaged during the ED process. Collectively, our results demonstrate that ED is a promising technology for disinfecting water to prevent the spread of ARB.

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.

An effective analytical droplet digital PCR approach for identification and quantification of fur-bearing animal meat in raw and processed food

Available nuclear gene sequences for meat detection are still rare and little applicability in the investigation of new types of meat adulteration such as fox, mink and raccoon dog was performed. In the present work, we developed a reliable qualitative and quantitative detection method for fur-bearing animal meat based on droplet digital PCR (ddPCR). Three sets of primers and probes targeted nuclear genes for fox, mink and raccoon dog were designed for ddPCR system; In addition, turkey was selected as internal reference to transform the copy numbers to the fraction of target species. Results indicated that the dynamic ranges of three fur-bearing animals were all from 1% to 90%; the limit of detection (LOD) and limit of quantification (LOQ) for three fur-bearing animals were same, with LOD 0.1% (w/w) and LOQ 1% (w/w). Moreover, we confirmed that different additives had no effect on quantification accuracy in the ddPCR assay.

Combination of Loop-Mediated Isothermal Amplification and AuNP-Oligoprobe Colourimetric Assay for Pork Authentication in Processed Meat Products

Pork adulteration is a major concern for Muslims and Jews whose diets are restricted by religious beliefs, as well as those who are allergic to pork meat and its derivatives. Accurate pork authentication is of great importance to assist this demographic group of people in making decision on their product purchase. The aim of this study was to develop a new analytical method for pork authentication in processed meat products based on a combination of loop-mediated isothermal amplification (LAMP) and AuNP-nanoprobe colourimetric assay. The LAMP conditions were first optimised to obtain the highest yield of amplified DNA products within the shortest time. Oligoprobe-functionalised AuNPs were then hybridised with LAMP-DNA amplicons and subsequently challenged with MgSO4 at a high concentration to induce AuNP aggregation. In the presence of pork DNA, the colloidal AuNP-probe remained unchanged in its red colour, which indicates the dispersion of AuNPs. In contrast, in the absence of pork DNA, the colour was changed to colourless as a result from the aggregation of AuNPs. The LAMP-AuNP-nanoprobe assay offers a high sensitivity with a limit of detection as low as 100 pg of pork DNA. The assay is highly specific to pork content without cross-reactivity with the other meat species tested. The assay developed herein can become a simple, inexpensive, precise, and rapid analytical tool for small laboratories or the general public interested in halal food authentication.

Triplex real-time PCR assay for the authentication of camel-derived dairy and meat products

Authentication of dairy and meat products is important to ensure fair competition, consumer benefit, and food safety. The large difference in price between camel and cow milk may be an incentive to adulterate camel dairy products with cow-derived foodstuffs. However, no studies so far have used triplex real-time PCR with an endogenous control to identify camel and cow origins in dairy and meat products. In this study, we developed a triplex real-time PCR assay based on amplification of mitochondrial 12S ribosomal DNA for the authentication of camel-derived dairy and meat products. This method was applied to identify camel and cow DNA in milk, yogurt, cheese, milk powder, milk beverage, meat products, and mixtures with milk and meat. Concentrations as low as 1 to 5% and 0.1% camel milk and meat, respectively, were detected in the mixtures, and 1 to 5% and 0.1% cow milk and meat, respectively, were identified via this approach. The limits of detection were 0.005 to 0.0025 ng, 0.05 to 0.001 ng, 0.001 to 0.0005 ng, and 0.00025 to 0.0001 ng of DNA in camel milk, camel yogurt, commercial camel milk beverage, and camel meat, and from 0.0025 to 0.001 ng, 0.5 to 0.001 ng, 1 to 0.05 ng, 0.01 ng, 0.001 ng, 0.0005 to 0.00025 ng, 0.0005 to 0.00025 ng, and 0.005 ng of DNA from cow milk, yogurt, cheese, acidic whey, milk powder, beef, beef jerky, and beef sausage, respectively. Different dairy and meat samples of camel and cow origins had a range of authentication limits and limits of detection. The designed triplex real-time PCR assay was shown to be a specific, sensitive, and efficient technique for the identification of camel and cow DNA in foodstuffs.

Quantitative Detection of Beef and Beef Meat Products Adulteration by the Addition of Duck Meat Using Micro Drop Digital Polymerase Chain Reaction

A single-copy specific primer was designed based on beef and duck samples and through drop digital polymerase chain reaction (ddPCR) for the quantitative analysis. Results revealed that the primers had no specific amplification with sheep, chicken, pork, or other species. Both the relationships between meat weight and DNA weight and between DNA weight and DNA copy number (C) were nearly linear within the dynamic range. To calculate the original meat weight from the DNA copy number, the DNA weight was used as the intermediate value to establish the following formulae: Mbeef = 0.058C − 1.86; Mduck = 0.0268C − 7.78. To achieve a good quantitative analysis, all species used in the experiment were made of lean meat. The accuracy of the method was verified by artificial adulteration of different proportions. Testing of the commercial samples indicated that adulteration is present in the market. The established digital PCR method provided an effective tool for monitoring the adulterated meat products and reducing the adulteration in the market.

TaqMan probe based multiplex quantitative PCR assay for determination of bovine, porcine and fish DNA in gelatin admixture, food products and dietary supplements

Detection of animal materials in gelatin-based products is required to address religious and cultural concerns, because porcine and bovine gelatins are prohibited in Halal, Kosher and Hindus consumer goods. In this paper, multiplex quantitative polymerase chain reaction (qPCR) assay using TaqMan probe was developed to discriminate bovine, porcine and fish gelatin species in a single assay platform. The assay was specific to cattle, pigs and fish, having been tested against 14 non-target species. The limit of detection, under gelatin admixed conditions, was 0.005 ng/µL. Finally, a pilot survey was undertaken testing 35 Halal branded processed food and dietary items. Out of 35 samples, only two were found to be positive for porcine species. The authenticity of these two qPCR products was confirmed by DNA sequencing analysis, which showed 99-100% similarity with Sus scrofa (Wild boar) species.

A multiplex PCR assay combined with capillary electrophoresis for the simultaneous detection of tropomyosin allergens from oyster, mussel, abalone, and clam mollusk species

Tropomyosin present in mollusk species is the most common allergen in humans and causes excessive immune responses. To simultaneously detect tropomyosin allergens in mollusk species, a multiplex PCR assay combined with capillary electrophoresis was developed for the detection of tropomyosin genes of oyster, mussel, abalone, and clam, and the 18S rRNA gene of eukaryotes. The developed multiplex PCR revealed specific amplicons of four mollusk species [oyster (Crassostrea gigas), 150 bp; mussel (Mytilus edulis), 119 bp; abalone (Haliotis discus hannai), 98 bp; clam (Ruditapes philippinarum), 76 bp] and an amplicon of universal eukaryotic primer (eukaryotes, 190 bp); the detection limit of DNA was confirmed to be 16 pg. This multiplex PCR assay was applied for monitoring commercially processed seafood products, achieving successful detection of tropomyosin genes in 19 processed seafood products in Korea. The developed assay is an efficient and useful method for detecting tropomyosin allergens from mollusk species in seafoods.

Insight into Rapid DNA-Specific Identification of Animal Origin Based on FTIR Analysis: A Case Study

In this study, a methodology has been proposed to identify the origin of animal DNA, employing high throughput extension accessory Fourier transform infrared (HT-FTIR) spectroscopy coupled with chemometrics. Important discriminatory characteristics were identified in the FTIR spectral peaks of 51 standard DNA samples (25 from bovine and 26 from fish origins), including 1710, 1659, 1608, 1531, 1404, 1375, 1248, 1091, 1060, and 966 cm⁻¹. In particular, the bands at 1708 and 1668 cm⁻¹ were higher in fish DNA than in bovine DNA, while the reverse was true for the band at 1530 cm⁻¹ was shown the opposite result. It was also found that the PO₂⁻ V_as/V_s ratio (1238/1094 cm⁻¹) was significantly higher (p < 0.05) in bovine DNA than in fish DNA. These discriminatory characteristics were further revealed to be closely related to the base content and base sequences of different samples. Multivariate analyses, such as principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were conducted, and both the sensitivity and specificity values of PLS-DA model were one. This methodology has been further validated by 20 meat tissue samples (4 from bovine, 5 from ovine, 5 from porcine, and 6 from fish origins), and these were successfully differentiated. This case study demonstrated that FTIR spectroscopy coupled with PLS-DA discriminant model could provide a rapid, sensitive, and reliable approach for the identification of DNA of animal origin. This methodology could be widely applied in food, feed, forensic science, and archaeology studies.

Quantitative Tetraplex Real-Time Polymerase Chain Reaction Assay with TaqMan Probes Discriminates Cattle, Buffalo, and Porcine Materials in Food Chain

Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.

A digital PCR method for identifying and quantifying adulteration of meat species in raw and processed food

Meat adulteration is a worldwide concern. In this paper, a new droplet digital PCR (ddPCR) method was developed for the quantitative determination of the presence of chicken in sheep and goat meat products. Meanwhile, a constant (multiplication factor) was introduced to transform the ratio of copy numbers to the proportion of meats. The presented ddPCR method was also proved to be more accurate (showing bias of less than 9% in the range from 5% to 80%) than real-time PCR, which has been widely used in this determination. The method exhibited good repeatability and stability in different thermal treatments and at ultra-high pressure. The relative standard deviation (RSD) values of 5% chicken content was less than 5.4% for ultra-high pressure or heat treatment. Moreover, we confirmed that different parts of meat had no effect on quantification accuracy of the ddPCR method. In contrast to real-time PCR, we examined the performance of ddPCR as a more precise, sensitive and stable analytical strategy to overcome potential problems of discrepancies in amplification efficiency discrepancy and to obtain the copy numbers directly without standard curves. The method and strategy developed in this study can be applied to quantify the presence and to confirm the absence of adulterants not only to sheep but also to other kinds of meat and meat products.

Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra

The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products.

Development of a sensitive and specific multiplex PCR method for the simultaneous detection of chicken, duck and goose DNA in meat products

Identifying the origin of animal species in manufactured meat products is of considerable economic, religious and sanitary importance. In this study, we developed a multiplex PCR method to simultaneously detect chicken, duck and goose DNA in meat products derived from beef, pork, mutton or quail. The PCR primers were designed based on the sequence of mitochondrial genes of each avian species, and the amplicon sizes were 131, 283 and 387bp for chicken, duck and goose, respectively. The method had no cross-reaction with DNA isolated from beef, mutton, pork or quail, and generated products at a target DNA content as low as 0.05ng, or a target meat content of 1% of total meat weight. Moreover, screening of 24 commercial meat samples using this method indicated that six, two and one samples were contaminated with chicken, duck, or both, respectively, suggesting its usefulness for the simultaneous identification of chicken, duck and goose DNA in commercial meat products.

A highly sensitive and specific tetraplex PCR assay for soybean, poultry, horse and pork species identification in sausages: development and validation

A tetraplex PCR assay was developed for a rapid and reliable identification of horse, soybean, poultry, and pork species in sausages simultaneously. The method merges the use of horse (Equus caballus), soybean (Glycine max), poultry (Gallus gallus), and pork (Sus scrofa) specific primers that amplify small fragments (horse; 85bp, soybean; 100bp, poultry; 183bp and pork; 212bp) of the mitochondrial cyt b, lectin, 12S rRNA and ATPase subunit 6 genes respectively. Good quality DNA was isolated from reference sausage to optimize the assay. Tetraplex analysis of the reference sausage samples showed that the detection limit of the assay was 0.01% for each species. Taken together, all data indicated that this tetraplex PCR assay was a simple, rapid, sensitive, specific, and cost-effective detection method for horse, soybean, poultry, and pork species in commercial sausages.

Determining the presence of chicken and turkey meat in selected meat products using realtime PCR method

The one of the most convenient method for the identification of animal species in raw and processed meat products is the examination of DNA sequences. Real-Time PCR are particularly suitable because even small fragments of DNA formed during heat processing of the meat can be amplified and identified. TaqMan Real-Time PCR is a rapid, convenient and sensitive assay for meat identification. For chicken and turkey meat identification we were using species-specific primers and TaqMan probe designed on the mitochondrial cytochrome b. The intensity of the fluorescence signal has risen at a variety of different samples. We analysed sixteen the samples of turkey meat products and we found the incidence of chicken at nine samples in the range of the detection range of the reaction0.1 to 100%.  Sample 8 fluorescence intensity exceeded the detection threshold in the 22.11 cycle (Cp = 22.11); Sample 6, (Cp = 23.19); Sample 1 in 27.08 cycle (Cp = 27.08); Sample 7 in 31,7 cycle (Cp = 31.7) and sample 5 in 32.32 cycle (Cp = 32.32). All Cp values for these samples fluorescence intensity exceeded the detection threshold in earlier cycles as sample the 100% turkey DNA. It follows that in the samples no. 8, 6, 1, 5, and 7 is in the range of chicken DNA detection range of the reaction, from 0.1 to 100%. Sample 11 in the cycle 27,08 (Cp = 27.08); Sample 10 in the cycle 27.8 (Cp = 27.8); sample 16 in 28.03 cycle (Cp = 28.03) and sample 13 in the cycle of 29.18 (Cp = 29.18). In recognition of the results of the monitoring of the content of chicken meat in meat products it is appropriate to further verification and testing detection kits used to work for possible use in practice since it has been found to be sufficient sensitivity and specificity to 30 cycle reaction.