Identification of species-specific DNA in feedstuffs

The Development of a Risk Assessment Model for Inedible Rendering Plants in Canada: Identifying and Selecting Feed Safety-Related Factors

The Canadian Food Inspection Agency (CFIA) is developing an establishment-based risk assessment model to categorize rendering plants that produce livestock feed ingredients (ERA-Renderer model) according to animal and human health risks (i.e., feed safety risks) and help in determining the allocation of inspection resources based on risk. The aim of the present study was to identify and select feed-safety-related factors and assessment criteria for inclusion in the ERA-Renderer model. First, a literature review was performed to identify evidence-based factors that impact the feed safety risk of livestock feed during its rendering processes. Secondly, a refinement process was applied to retain only those that met the inclusion conditions, such as data availability, lack of ambiguity, and measurability. Finally, an expert panel helped in selecting factors and assessment criteria based on their knowledge and experience in the rendering industry. A final list of 32 factors was developed, of which 4 pertained to the inherent risk of a rendering plant, 8 were related to risk mitigation strategies, and 20 referred to the regulatory compliance of a rendering plant. A total of 179 criteria were defined to assess factors based on practices in the Canadian rendering industry. The results of this study will be used in the next step of the model development to estimate the relative risks of the assessment criteria considering their impact on feed safety. Once implemented, the CFIA's ERA-Renderer model will provide an evidence-based, standardized, and transparent approach to help manage the feed safety risks in Canada's rendering sector.

Single tube multiplex PCR assay for the identification of banned meat species

Food adulteration has a direct impact on public health, religious faith, fair-trades, and wildlife. In the present study, a reliable and sensitive assay has been developed for verifying meat adulteration in food chain. The multiplex PCR system was optimised for identification of chicken, cow/buffalo, sheep/goat, horse/donkey, pork, and dog DNAs in a single reaction mixture simultaneously. The primers were designed using 12 S rRNA gene sequences with fragment size in the range of 113 bp to 800 bp, which can be easily visualised on agarose gel electrophoresis making the technique economical. After validation of accuracy, specificity, and sensitivity, commercially available meat products (n = 190) were screened, comprising both raw and cooked meat samples. The results demonstrated a high rate of adulteration (54.5%) in meat products. The technique developed here can be easily used for screening of different meat products for export and import purposes as well as for food inspection and livestock diagnostic laboratories.

A simple and sensitive two-tube multiplex PCR assay for simultaneous detection of ten meat species

A sensitive and reliable technique for meat species identification is required to prevent food adulteration, particularly in meat production. This work developed an optimized multiplex PCR assay for simultaneous identification of five commonly consumed and five commonly banned meat species in meat products. We designed primers that specifically amplified mitochondrial ATPase subunit 8 gene regions of different lengths of bovine, ovine, swine, chicken, turkey, cat, dog, mouse and human DNAs. The developed multiplex PCR assay proved to be specific, sensitive down to 30pg DNA per reaction, reproducible and economical. It could be used with a variety of raw meats and processed food samples and is easily applicable in a routine laboratory analysis without specific sophisticated equipment.

Droplet digital polymerase chain reaction (ddPCR) assays integrated with an internal control for quantification of bovine, porcine, chicken and turkey species in food and feed

Food adulteration and feed contamination are significant issues in the food/feed industry, especially for meat products. Reliable techniques are needed to monitor these issues. Droplet Digital PCR (ddPCR) assays were developed and evaluated for detection and quantification of bovine, porcine, chicken and turkey DNA in food and feed samples. The ddPCR methods were designed based on mitochondrial DNA sequences and integrated with an artificial recombinant plasmid DNA to control variabilities in PCR procedures. The specificity of the ddPCR assays was confirmed by testing both target species and additional 18 non-target species. Linear regression established a detection range between 79 and 33200 copies of the target molecule from 0.26 to 176 pg of fresh animal tissue DNA with a coefficient of determination (R²) of 0.997–0.999. The quantification ranges of the methods for testing fortified heat-processed food and feed samples were 0.05–3.0% (wt/wt) for the bovine and turkey targets, and 0.01–1.0% (wt/wt) for pork and chicken targets. Our methods demonstrated acceptable repeatability and reproducibility for the analytical process for food and feed samples. Internal validation of the PCR process was monitored using a control chart for 74 consecutive ddPCR runs for quantifying bovine DNA. A matrix effect was observed while establishing calibration curves with the matrix type under testing, and the inclusion of an internal control in DNA extraction provides a useful means to overcome this effect. DNA degradation caused by heating, sonication or Taq I restriction enzyme digestion was found to reduce ddPCR readings by as much as 4.5 fold. The results illustrated the applicability of the methods to quantify meat species in food and feed samples without the need for a standard curve, and to potentially support enforcement activities for food authentication and feed control. Standard reference materials matching typical manufacturing processes are needed for future validation of ddPCR assays for absolute quantification of 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.

Development of PCR primers for the detection of porcine DNA in feed using mtATP6 as the target sequence

In Japan, PCR identification of species-specific, animal group-specific and plant DNA is employed as part of the audit program to ensure compliance with the feed ban in place for the control of bovine spongiform encephalopathy (BSE). Since October 2001, animal proteins other than dairy proteins, egg proteins and gelatin have been prohibited to be used in feed for ruminants. Meat-and-bone meal (MBM) derived from poultry, pig and/or fish is allowed to be used in feed for poultry, pigs and fish. Porcine MBM is permitted in feed for domestic animals other than cattle since April 2005. Given the fact that pigs and cattle are the two major sources of MBM in Japan, the identification of porcine DNA with high specificity and sensitivity has become increasingly important to ensure that MBM products are free from ruminant materials. Two PCR primer sets (PPA8 and PPA6) were newly designed using mtATP8 and mtATP6 as the target sequences, with relatively short amplification sizes. PPA8 and PPA6 were able to specifically detect porcine DNA with the detection limits of 0.01% and 0.001% of porcine MBM in feed, respectively. PPA6 was superior to PPA8 in terms of detection of DNA damaged/fragmented during rendering procedures. The PCR method using these primer sets is registered as the official analytical method for feed in Japan.

Real-time PCR detection and identification of prohibited mammalian and avian material in animal feeds

A method for the detection and identification of "prohibited" mammalian or avian material in animal feed was developed and assessed through the analysis of DNA. A generic real-time PCR assay was designed to detect the presence of mammalian and avian mitochondrial DNA 16S rRNA genes in animal feed samples. Samples positive with this screening method were further investigated using identification assays to detect the 16S rRNA gene from bovine, ovine, porcine, and avian species and to determine whether the DNA originated from species whose material is prohibited from inclusion in farmed animal feed. An internal positive control was coamplified in the 16S real-time PCR assays to monitor PCR amplification efficiency and avoid potential false-negative results. Using vegetable-based feed standards spiked with meat and bone meal generated with a commercial rendering process, 0.1% meat and bone meal could be detected using the general and species-specific 16S assays. The species-specific assays had 100% specificity for the homologous target species. The 16S real-time PCR assays were evaluated alongside existing tests based on protein evaluation or microscopic examination for a wide range of commercial animal feed samples. In total, 111 (0.76%) of 14,678 samples examined contained prohibited material based on the results from at least one of these tests. However, most positive results did not represent noncompliance because they were associated with samples of pet food, which can legitimately contain material prohibited for use in food for farmed animals. The species-specific 16S assays confirmed the presence of prohibited material in 75% of the 111 samples, whereas the existing protein and microscope tests confirmed the presence of this material in 25 and 54% of the samples, respectively.

Detection of ruminant meat and bone meals in animal feed by real-time polymerase chain reaction: result of an interlaboratory study

The commercialization of animal feeds infected by prions proved to be the main cause of transmission of bovine spongiform encephalopathy (BSE). Therefore, feed bans were enforced, initially for ruminant feeds, and later for all feeds for farmed animals. The development and validation of analytical methods for the species-specific detection of animal proteins in animal feed has been indicated in the TSE (Transmissible Spongiform Encephalopathies) Roadmap (European Commission. The TSE (Transmissible Spongiform Encephalopathy) roadmap. URL: http://europa.eu.int/comm/food/food/biosafety/bse/roadmap_en.pdf, 2005) as the main condition for lifting the extended feed ban. Methods based on polymerase chain reaction (PCR) seem to be a promising solution for this aim. The main objective of this study was to determine the applicability of four different real-time PCR methods, developed by three National expert laboratories from the European Union (EU), for the detection and identification of cattle or ruminant species in typical compound feeds, fortified with meat and bone meals (MBM) from different animal species at different concentration levels. The MBM samples utilized in this study have been treated using the sterilization condition mandatory within the European Union (steam pressure sterilization at 133 degrees C, 3 bar, and 20 min), which is an additional challenge to the PCR methods evaluated in this study. The results indicate that the three labs applying their PCR methods were able to detect 0.1% of cattle MBM, either alone or in mixtures with different materials such as fishmeal, which demonstrates the improvement made by this technique, especially when compared with results from former interlaboratory studies.

Detection of land animal remains in fish meals by the polymerase chain reaction-restriction fragment length polymorphism technique

In the present study a technique was developed with the aim of guaranteeing the composition and security of fish meals, since it allows verification of whether these meals contain land animal remains. The method is based on polymerase chain reaction (PCR) and length polymorphism, followed by a restriction fragment length polymorphism (RFLP). Specific primers for every species were designed and calibrated, generating exclusively a PCR product with a specific size when DNA for each species was present in the sample. This technique allows the detection of land animal remains in fish meals, specifically cow, chicken, pig, horse, sheep, and goat. The identity of the PCR products can be confirmed by RFLP analysis using only one restriction enzyme. The selected restrictase generated one characteristic restriction profile for every species included in this study. The detection limit of this method was calculated by using mixtures of fish meals in different proportions and meal that exclusively contained remains of one of these land species studied. The analytical strategy herein proposed was applied to fish and meat meals, giving good results, both in the analyzed standards and in commercial samples.

Effective PCR detection of animal species in highly processed animal byproducts and compound feeds

In this paper we present a polymerase chain reaction (PCR)-based method for detecting meat and bone meal (MBM) in compound feedingstuffs. By choosing adequate DNA targets from an appropriate localisation in the genome, the real-time PCR method developed here proved to be robust to severe heat treatment of the MBM, showing high sensitivity in the detection of MBM. The method developed here permits the specific detection of processed pig and cattle materials treated at 134 degrees C in various feed matrices down to a limit of detection of about 0.1%. This technique has also been successfully applied to well-characterised MBM samples heated to as high as 141 degrees C, as well as to various blind feed samples with very low MBM contents. Finally, the method also passed several official European ring trials.

Application of quantitative real-time PCR in the detection of prion-protein gene species-specific DNA sequences in animal meals and feedstuffs

This study describes a method for quantitative and species-specific detection of animal DNA from different species (cattle, sheep, goat, swine, and chicken) in animal feed and feed ingredients, including fish meals. A quantitative real-time PCR approach was carried out to characterize species-specific sequences based on the amplification of prion-protein sequence. Prion-protein species-specific primers and TaqMan probes were designed, and amplification protocols were optimized in order to discriminate the different species with short PCR amplicons. The real-time quantitative PCR approach was also compared to conventional species-specific PCR assays. The real-time quantitative assay allowed the detection of 10 pg of ruminant, swine, and poultry DNA extracted from meat samples processed at 130 degrees C for 40 min, 200 kPa. The origin of analyzed animal meals was characterized by the quantitative estimation of ruminant, swine, and poultry DNA. The TaqMan assay was used to quantify ruminant DNA in feedstuffs with 0.1% of meat and bone meal. In conclusion, the proposed molecular approach allowed the detection of species-specific DNA in animal meals and feedstuffs.

Conventional and real-time PCR-based approaches for molecular detection and quantitation of bovine species material in edible gelatin

The majority of edible gelatin in Europe is derived from pigskin, but a significant portion is extracted from bovine tissue. Because of the bovine spongiform encephalopathy crisis, consumers might be concerned about the gelatin used in various products. To assure consumers of the quality and safety of edible gelatin, European Union directive 1999/724/EC described general guidelines for gelatin production, including requirements for documentary proof confirming that raw materials are from animals fit for human consumption. Analytical methods to confirm gelatin documentation or raw material animal species source in the finished product are lacking. In this study, several published species-specific PCR systems were evaluated as potential molecular methods for determining the origin of the raw material used in making gelatin. A recently validated bovine species-specific PCR primer set targeting the ATPase 8 subunit gene in bovine mitochondrial DNA was suitable for detection of bovine material in gelatin. This PCR primer set was optimized using conventional and real-time PCR approaches. An evaluation of these two PCR methods confirmed the high specificity for the adopted primer set in various gelatin matrices of known origin. The inclusion of bovine gelatin in pork or fish gelatin can be detected at 0.1 to 0.001%. These PCR assays are potential molecular detection tools that can be used to routinely detect bovine gelatin either alone or as an inclusion in gelatin made from other species.

Food and forensic molecular identification: update and challenges

The need for accurate and reliable methods for animal species identification has steadily increased during past decades, particularly with the recent food scares and the overall crisis of biodiversity primarily resulting from the huge ongoing illegal traffic of endangered species. A relatively new biotechnological field, known as species molecular identification, based on the amplification and analysis of DNA, offers promising solutions. Indeed, despite the fact that retrieval and analysis of DNA in processed products is a real challenge, numerous technically consistent methods are now available and allow the detection of animal species in almost any organic substrate. However, this field is currently facing a turning point and should rely more on knowledge primarily from three fundamental fields--paleogenetics, molecular evolution and systematics.

Quantitative detection of species-specific DNA in feedstuffs and fish meals

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species-derived material in concentrate feed mixtures and fish meals.