A novel reference real-time PCR assay for the relative quantification of (game) meat species in raw and heat-processed food

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.

Identification of Cross-Species Marker Peptides for the Detection of Mammalian and Poultry Meat in Vegan and Vegetarian Foods

Authentication of vegan and vegetarian foods is important since these increasingly popular food items could be adulterated with cheap meat to increase profit margins. In this study, nine marker peptides for the detection of meat (several species) were identified applying liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). These marker peptides enable the crucial differentiation of beef versus milk and chicken meat versus egg, demonstrated by the investigation of 19 commercial vegetarian meat substitutes containing milk and egg. Extensive experimental testing proved the presence of the cross-species meat marker peptides in 19 food-relevant types of mammals and poultry as well as their absence in more than 136 plant-based ingredients for the production of vegan and vegetarian foods. An authentic vegan sausage matrix based on an actual retail product was produced and spiked with 5.0%, w/w meat to confirm the high signal intensities and the heat stability of the marker peptides.

Design of Mismatch Primers to Identify and Differentiate Closely Related (Sub)Species: Application to the Authentication of Meat Products

Single-nucleotide polymorphisms (SNPs) are powerful molecular markers for the identification and differentiation of closely related organisms. A variety of methods can be used to determine the allele that is present at a specific locus in the genome, including real-time PCR by using an allele-specific primer. In order to increase the selectivity for the target allele, deliberate mismatch bases at the 3' end of the allele-specific primer may be introduced. This strategy has already been used for the identification and differentiation of microorganisms and plants. We have recently developed real-time PCR assays involving mismatch primers for the identification and differentiation of closely related deer species (red deer, fallow deer, sika deer) or the discrimination of wild boar and domestic pig in game meat products. These methods are applicable to detect meat species adulteration in food products.In this chapter, we offer a protocol for the design of PCR primer/probe systems suitable for meat species authentication in food. We address the retrieval and alignment of sequences, primer design by using a commercial software and the introduction of deliberate mismatch bases. In addition, we describe how the suitability of primer/probe systems can be tested in silico and in practice. We use the design of PCR primer/probe systems for wild boar and domestic pig as example.

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.

Real-Time PCR Assay for the Detection and Quantification of Roe Deer to Detect Food Adulteration-Interlaboratory Validation Involving Laboratories in Austria, Germany, and Switzerland

Game meat products are particularly prone to be adulterated by replacing game meat with cheaper meat species. Recently, we have presented a real-time polymerase chain reaction (PCR) assay for the identification and quantification of roe deer in food. Quantification of the roe deer content in % (w/w) was achieved relatively by subjecting the DNA isolates to a reference real-time PCR assay in addition to the real-time PCR assay for roe deer. Aiming at harmonizing analytical methods for food authentication across EU Member States, the real-time PCR assay for roe deer has been tested in an interlaboratory ring trial including 14 laboratories from Austria, Germany, and Switzerland. Participating laboratories obtained aliquots of DNA isolates from a meat mixture containing 24.8% (w/w) roe deer in pork, roe deer meat, and 12 meat samples whose roe deer content was not disclosed. Performance characteristics included amplification efficiency, level of detection (LOD_95%), repeatability, reproducibility, and accuracy of quantitative results. With a relative reproducibility standard deviation ranging from 13.35 to 25.08% (after outlier removal) and recoveries ranging from 84.4 to 114.3%, the real-time PCR assay was found to be applicable for the detection and quantification of roe deer in raw meat samples to detect food adulteration.

Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci

Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.

Applicability of a duplex and four singleplex real-time PCR assays for the qualitative and quantitative determination of wild boar and domestic pig meat in processed food products

Appropriate analytical methods are needed for the detection of food authentication. We investigated the applicability of a duplex real-time PCR assay targeting chromosome 1 and two singleplex real-time PCR assays targeting chromosome 9, both published recently, for the qualitative and quantitative determination of wild boar and domestic pig in processed food products. In addition, two singleplex real-time PCR assays targeting chromosome 7 were tested for their suitability to differentiate the two subspecies. Even by targeting the three genome loci, the probability of misclassification was not completely eliminated. Application of the real-time PCR assays to a total of 35 commercial meat products, including 22 goulash products, revealed that domestic pig DNA was frequently present, even in 14 out of 15 products declared to consist of 100% wild boar. Quantitative results obtained with the real-time PCR assays for wild boar (p < 0.001) and those for domestic pig (p < 0.001) were significantly different. However, the results obtained with the real-time PCR assays for wild boar (r = 0.673; p < 0.001) and those for domestic pig (r = 0.505; p = 0.002) were found to be significantly correlated. If the rules given in the paper are followed, the real-time PCR assays are applicable for routine analysis.

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

Poultry meat is consumed worldwide and is prone to food fraud because of large price differences among meat from different poultry species. Precise and sensitive analytical methods are necessary to control poultry meat products. We chose species-specific sequences of the cytochrome b gene to develop two multiplex real-time polymerase chain reaction (real-time PCR) systems: one for chicken (Gallus gallus), guinea fowl (Numida meleagris), and pheasant (Phasianus colchicus), and one for quail (Coturnix japonica) and turkey (Meleagris gallopavo). For each species, added meat could be detected down to 0.5 % w/w. No cross reactions were seen. For these two real-time PCR systems, we applied three different quantification methods: (A) with relative standard curves, (B) with matrix-specific multiplication factors, and (C) with an internal DNA reference sequence to normalize and to control inhibition. All three quantification methods had reasonable recovery rates from 43% to 173%. Method B had more accepted recovery rates, i.e., in the range 70-130%, namely 83% compared to 75% for method A or C.

Determination of content of camel milk in adulterated milk samples by normalized real-time polymerase chain reaction system based on single-copy nuclear genes

BACKGROUND

Compared with the traditional qualitative polymerase chain reaction (PCR), which only identifies the category of species, the quantitative PCR method provides a value, which is very important for appropriate penalty enforcement according to the extent of adulteration. However, most of the current quantitative PCR methods are based on mitochondrial genes, expressing different copy numbers in different cells and reducing the accuracy of quantitative results. In this study, single-copy nuclear housekeeping genes, instead of multicopy mitochondrial genes, were selected as both camel species-specific and reference genes to develop a novel normalized PCR system.

RESULTS

This system had an excellent linear correlation (R² = 0.9614) between camel milk content and Ct ratio (specific/reference genes), and allowed quantitative determination of the content of camel milk in adulterated milk samples. The accuracy was effectively validated using simulated adulterated samples with recoveries ranging from 90% to 120% and coefficient of variation less than 10%, exhibiting sufficient parameters of trueness and precision.

CONCLUSIONS

The normalized PCR system based on single-copy nuclear genes is a simple, rapid and reliable method for the determination of the content of camel milk in adulterated milk samples, and also provides technical support for appropriate penalty enforcement. © 2020 Society of Chemical Industry.

Coffea arabica and C. canephora discrimination in roasted and ground coffee from reference material candidates by real-time PCR

To produce specific desirable coffee blends, Coffea arabica and C. canephora are mixed each other, in some cases to suit consumer preference, but in others to reduce production costs. In this scenario, the aim of this work was to evaluate standard candidate reference materials (RMc) for analysis of different blends of roasted and ground coffee. For this purpose, we analyzed different percentages of C. arabica and C. canephora (100:0; 50:50; 25:75; and 0:100, respectively). These RMc samples were developed in a previous study with green coffee beans submitted to medium roasting. In this work, coffee species differentiation (C. arabica and C. canephora) was analyzed by real-time PCR, using specific primers previously developed, called ARA primers. The RMc material with 100% C. canephora did not present amplification, in contrast with the samples containing C. arabica, which all presented amplification. These results indicate the specificity of ARA primers for C. arabica and that the detection system assay can be used as a promising molecular tool to identify and quantify percentages of C. arabica in different coffee blends.

Tetraplex real-time PCR assay for the simultaneous identification and quantification of roe deer, red deer, fallow deer and sika deer for deer meat authentication

Analytical methods are needed for the identification and quantification of meat species to detect food adulteration. Since game meat is more expensive than meat from domesticated animal species, it is a potential target for adulteration. We present a tetraplex real-time PCR assay that allows the simultaneous determination of the content of roe deer, red deer, fallow deer and sika deer. The tetraplex assay showed only moderate cross-reactivity with closely related species. After optimization the tetraplex assay had a limit of detection of 0.1% (w/w) and a limit of quantification of 0.5% (w/w) for each of the four deer species. The tetraplex assay was found to be robust, slight modifications of the experimental setup did not lower its performance. Recoveries obtained by analyzing DNA mixtures and DNA isolates from model game sausages were similar to those obtained with the singleplex assays.

Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

Since game meat is more valuable and expensive than meat from domesticated animal species it is a potential target for adulteration. Analytical methods must allow the identification and quantification of meat species to be applicable for the detection of fraudulent labelling. We developed a real-time PCR assay for the authentication of sika deer (Cervus nippon) and products thereof. The primer/probe system amplifies a 71 bp fragment of the kappa-casein precursor gene. Since the target sequence contained only one sika deer-specific base, we introduced a deliberate base mismatch in the forward primer. The real-time PCR assay did not show cross-reactivity with 19 animal and 49 plant species tested. Low cross-reactivity was observed with red deer, fallow deer, reindeer and moose. However, with a ΔCt value of ≥11.79 between sika deer and the cross-reacting species, cross-reactivity will not affect the accuracy of the method. LOD and LOQ, determined by analysing serial dilutions of a DNA extract containing 1% (w/w) sika deer DNA in pig DNA, were 0.3% and 0.5%, respectively. The accuracy was evaluated by analysing DNA mixtures and DNA isolates from meat extract mixtures and meat mixtures. In general, recoveries were in the range from 70 to 130%.

Development and validation of a fallow deer (Dama dama)-specific TaqMan real-time PCR assay for the detection of food adulteration

The aim of the present study was to develop a real-time PCR assay for the identification and quantification of fallow deer (Dama dama) in food to detect food adulteration. Despite high sequence homology among different deer species, a fallow deer-specific primer/probe system targeting a fragment of the nuclear MC1-R gene was designed. This primer/probe system did not amplify DNA from 19 other animals and 50 edible plant species. Moderate cross-reactivity was observed for sika deer, red deer, roe deer, reindeer and wild boar. The LOD and LOQ of the real-time PCR assay were 0.1% and 0.4%, respectively. To validate the assay, DNA mixtures, meat extract mixtures, meat mixtures and model game sausages were analyzed. Satisfactory quantitative results were obtained when the calibration mixture was similar to the analyzed sample in both the composition and concentration of the animal species of interest.

Game meat authentication through rare earth elements fingerprinting

Accurate labelling of meat (e.g. wild versus farmed, geographical and genetic origin, organic versus conventional, processing treatment) is important to inform the consumers about the products they buy. Meat and meat products declared as game have higher commercial value making them target to fraudulent labelling practices and replacement with non-game meat. We have developed and validated a new method for authentication of wild rabbit meat using elemental metabolomics approach. Elemental analysis was performed using rapid ultra-trace multi-element measurement by inductively coupled plasma mass spectrometry (ICP-MS). Elemental signatures showed excellent ability to discriminate the wild rabbit from non-wild rabbit meat. Our results demonstrate the usefulness of metabolic markers -rare earth signatures, as well as other trace element signatures for game meat authentication.