Species-specific PCR for the identification of ruminant species in feedstuffs

Cross-contamination in canine and feline dietetic limited-antigen wet diets

Background

Adverse food reactions (AFRs) are defined as abnormal responses to an ingested food or food additive. Diagnosis and treatment of AFRs consist of the complete elimination of these ingredients in the dietary trial. Previous studies have demonstrated the presence of undeclared ingredients in commercial limited-antigen dry food diets that can compromise the results and efficacy of dietary elimination trails. The aim of this study was to assess a selection of commercial canine and feline dietetic limited-antigen wet foods for the potential cross-contamination of animal proteins from origins not mentioned on the label.

Results

Eleven canine and feline dietetic limited-antigen wet foods (9 novel animal protein foods, 1 vegetarian and 1 hydrolyzed) were analyzed by polymerase chain reaction (PCR) to detect the presence DNA of animal and vegetal origins. PCR analysis confirmed the contamination of 6 of the 11 (54.5%) limited-antigen wet diets with undeclared animal protein. One of these 6 diets was solely composed of animal protein sources completely unrelated to those declared on the label. None of the foods containing horse meat or fish were contaminated, and neither were the vegetarian or the hydrolyzed food products. Moreover, the results show that had zoological class primers only been used to check for cross-class contaminations, as are generally used in the pet food industry for in-house checks, the apparent contamination rate would have been significantly underestimated: less than 20% (3/11), instead of the actual rate of 54.7% using species-specific primers.

Conclusion

This study reveals a high rate of cross-contamination in dietetic limited-antigen wet canine and feline foods, as previously described for dietetic dry limited-antigen foods (reported to be more than 80%). These results add new fuel to the discussion about the potential causes underlying the failure of elimination diets, since animal protein contaminants may actually be present in the commercial dietetic limited-antigen diets. AFRs may therefore occur as a result of inadequate practices in the pet food industry.

A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification

There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.

Rapid Identification of Meat Species by the Internal Extractive Electrospray Ionization Mass Spectrometry of Hemoglobin Selectively Captured on Functionalized Graphene Oxide

Hemoglobin (Hb) present in the blood and meat juice samples was selectively adsorbed by graphene oxide (GO) particles functionalized with amylopectin (AP) and was sensitively detected by direct internal extractive electrospray ionization mass spectrometry (iEESI-MS) analysis for the identification of meat type. Various samples including the whole blood samples of chicken, duck, sheep, mouse, pigeon, turtledove, and meat juice mixtures were successfully identified based on the difference in molecular composition of Hb reflected in MS. The adulteration of sheep blood with only 2% chicken blood could be detected, which demonstrated the high chemical specificity of the approach. The established method is featured by the high speed of analysis (4 min per sample, including the analyte extraction and sample loading), high sensitivity, minimal sample preparation, and low sample consumption (0.9 μL of whole blood or 300 mg of raw meat). In perspective, the reported method can be extended for the sensitive detection of trace analytes in complex matrices in broad molecular range by using the selective enrichment on functionalized graphene oxide particles followed by iEESI-MS analysis.

Development and validation of a universal primer pair for the simultaneous detection of eight animal species

In the present study, we developed a novel simplex PCR assay for the simultaneous detection of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig and camel. A unique pair of universal primers was designed to target mitochondrial DNA variable regions in the eight animal species, generating, 787, 763, 563, 512, 507, 491, 455 and 385bp long fragments for goat, sheep, deer, buffalo, cattle, yak, pig and camel, respectively. The assay showed no cross-reactivity with other common domestic animals, and was validated by sequencing and enzyme digestion. Detection limit for DNA samples from the eight animal species varied between 6 and 20pg in a 20μl PCR mixture. Interestingly, the newly developed method successfully identified 170 commercial meat products, and is simple, fast, sensitive, specific, and cost-effective. Therefore, it could be used for the detection of goat, sheep, deer, buffalo, cattle, yak, pig, and camel species in foodstuffs.

Rapid detection of bovine adipose tissue using lateral flow strip assay

Currently no rapid immunoassays are developed to identify the species content of fat tissue in mixtures. We report a simple protocol enabling the effective detection of bovine fat in highly processed materials using a lateral flow (LF) immunoassay which targets a ruminant-specific muscle protein. A portion (50 gm) of muscle-free fat samples was rendered to separate the molten fat from the proteinaceous residue, then soluble proteins were extracted from the solid residue with 0.5 mol/L NaCl for the LF analysis. The assay could detect 2% bovine fat-in-pork fat, 1% bovine fat-in-porcine meat-and-bone meal, and 0.5% bovine fat-in-soy meal mixtures. Rendered bovine fat could be detected up to 213°C. These results demonstrate that low levels of bovine fat tissue can be detected in processed materials using an immunoassay based on the presence of the muscle protein which serves as a species marker in the fat tissue.

Rapid bovine and caprine species identification in ruminant feeds by duplex real-time PCR melting curve analysis using EvaGreen fluorescence dye

A duplex real-time PCR assay with melting curve analysis, using the EvaGreen fluorescence dye, was developed for rapid and reliable identification of bovine and caprine in ruminant feeds. The method merges the use of bovine (Bos taurus) and caprine (Capra hircus) specific primers that amplify small fragments (bovine 96 bp and caprine 142 bp) of the mitochondrial 16S rRNA and 12S rRNA genes, respectively. DNA was isolated from heat-treated meats (133 °C/3 bar for 20 min) mixtures of bovine and caprine and was used to optimize the assay. Gene products of caprine and bovine produced two distinct melting peaks simultaneously at 82 and 86.8 °C, respectively. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The aim of this study was to develop a duplex real-time PCR assay followed by a melt curve step for sensitive, rapid, specific, and cost-effective detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies.

Development of qualitative and quantitative PCR analysis for meat adulteration from RNA samples

Total RNA samples were used to establish qualitative and quantitative PCR-based methods for assessing meat adulteration. The primers were designed based on the mRNA sequences of troponin I (TnI), mitochondrial ribosomal protein (MRP) and tropomodulin genes to distinguish chicken, pork, goat, beef and ostrich. There was no cross reaction between the primers, and the detection limit of the cDNA template was 0.01 and 20 ng in simplex PCR and multiplex PCR, respectively. In the low temperature storage test, the detection limits of cDNA template with 10 and 1 ng were determined at 4 °C and -80 °C. In quantitative assay, the precision of real-time PCR analysis expressed as a coefficient of variation (CV) ranged from 0.25% to 5.24% and the trueness, expressed as an error, ranged from 0.28% to 6.98% for adulteration. Thus, herein, we provided alternative tools for the assessment of meat adulteration using mRNA-based PCR methods.

Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA

Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be 85.56±0.07℃ for cattle, 84.96±0.08℃ for pig, and 85.99±0.05℃ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); 84.91±0.11℃ for goat and 83.90±0.11℃ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and 86.31±0.23℃ for chicken, 88.66±0.12℃ for duck, and 84.49±0.08℃ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from 10 pg/μL to 100 fg/μL levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

Species identification of Asini Corii Collas (donkey glue) by PCR amplification of cytochrome b gene

Asini Corii Collas (ACC; donkey glue) is a crude drug used to promote hematopoiesis and arrest bleeding. Because adulteration of the drug with substances from other animals such as horses, cattle, and pigs has been found, we examined PCR methods based on the sequence of the cytochrome b gene for source species identification. Two strategies for extracting DNA from ACC were compared, and the ion-exchange resin procedure was revealed to be more suitable than the silica-based one. Using DNA extracted from ACC by the ion-exchange resin procedure, PCR methods for species-specific detection of donkey, horse, cattle, and pig substances were established. When these species-specific PCR methods were applied to ACC, amplicons were obtained only by the donkey-specific PCR. Cattle-specific PCR detected as little as 0.1% admixture of cattle glue in the ACC. These results suggest that the species-specific PCR methods established in this study would be useful for simple and easy detection of adulteration of ACC.

Influences on the sensitivity of real-time PCR for the detection of bovine DNA in heat-sterilised feedstuffs

The present study evaluated two previously developed methods for amplification of bovine mtDNA segments of 109 and 271 base pairs (bp) by real-time polymerase chain reaction (PCR). Beef samples were sterilised experimentally at different temperatures (126 degrees C, 129 degrees C, 132 degrees C and 135 degrees C). These experimentally sterilised beef samples and nine commercial meat and bone meals (MBM) were mixed to a reference plant concentrate in strengths of 50%, 10%, 5%, and 1%. The results of the following PCR showed that the Bos-109 real-time PCR assay was able to detect all the experimental beef samples with exception of the mixtures of beef heated experimentally to 135 degrees C. In mixtures of industrial MBM bovine DNA were always found. Comparatively, the beef sterilised at 135 degrees C and 132 degrees C (and their respective mixtures) and the mixture containing 1% of beef sterilised at 129 degrees C were not detectable with the PCR assay amplifying a target of 271 bp. Using this PCR mixtures of industrial MBM were only weakly detected. The low concentrated mixtures of the extremely processed MBM-1 and MBM-2 even reported negative. These results indicate that the detectability of bovine DNA is strongly influenced by the degree of the thermal treatment. Only the PCR assay amplifying relatively short fragments of a multi-copy mitochondrial target was reliable for the detection of correctly heated MBM in mixed feed.

Novel TaqMan real-time polymerase chain reaction assay for verifying the authenticity of meat and commercial meat products from game birds

Species-specific real-time polymerase chain reaction (PCR) assays using TaqMan probes have been developed for verifying the labeling of meat and commercial meat products from game birds, including quail, pheasant, partridge, guinea fowl, pigeon, Eurasian woodcock and song thrush. The method combines the use of species-specific primers and TaqMan probes that amplify small fragments (amplicons <150 base pairs) of the mitochondrial 12S rRNA gene, and an endogenous control primer pair that amplifies a 141-bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. Analysis of experimental raw and heat-treated binary mixtures as well as of commercial meat products from the target species demonstrated the suitability of the assay for the detection of the target DNAs.

Real-time PCR for quantitative detection of bovine tissues in food and feed

A real-time PCR approach with the SYBR Green detection system has been developed for the quantitative detection of bovine tissues in food and feedstuffs. The method combines the use of bovine-specific primers, which amplify an 84-bp fragment of the mitochondrial 12S rRNA gene, and universal primers, which amplify a 140-bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. The 18S rRNA primers are used as endogenous controls for the total content of PCR-amplifiable DNA in the sample. The specificity of the primers was tested against 18 animal species, including mammals, birds, and fish, as well as 6 plant species. Analysis of experimental bovine tissues-oats mixtures demonstrated the suitability of the assay for the detection of bovine DNA in mixtures containing as low as 0.1% of bovine tissues. The performance of the method is not affected by severe heat treatment (up to 133 degrees C for 20 min at 300 kPa). The reported PCR assay could be very useful for detecting bovine-derived ingredients in raw and heat-treated food and feedstuffs.