Development of a monoclonal antibody specific to cooked mammalian meats

Bushmeat Species Identification: Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow (LF) Strip for Identification of Formosan Reeves' Muntjac (Muntiacus reevesi micrurus)

Simple Summary

Illegal hunting of wild animals and the consumption of bushmeat are recognized not only as a threat to biodiversity, but also as a risk for transmitting zoonotic diseases. Illegal sales of meat products from Formosan Reeves’ muntjac (Muntiacus reevesi micrurus) is a growing issue in Taiwan, bringing forth the demand for a fast and cost-effective technique for meat species identification. In this study, a new recombinase polymerase amplification combined with a lateral flow strip to identify Formosan Reeves’ muntjac in meat products was described. This method only requires minimal sample preparation and an isothermal heating process. The result can be interpreted by the naked eye within 30 min. The system we designed efficiently detected a variety of meat products, and no cross-reactions were observed with other animal species. This simple assay provides a sensitive and specific method to identify bushmeat sources in various meat products, which holds the potential for on-field application in the future.

Abstract

The identification of animal species of meat in meat products is of great concern for various reasons, such as public health, religious beliefs, food allergies, legal perspectives, and bushmeat control. In this study, we developed a new technique to identify Formosan Reeves’ muntjac in meat using recombinase polymerase amplification (RPA) in combination with a lateral flow (LF) strip. The DNA extracted from a piece of Formosan Reeves’ muntjac meat was amplified by a pair of specific primers based on its mitochondrial cytochrome b gene for 10 min at a constant temperature ranging from 30 to 45 °C using RPA. Using the specific probe added to the RPA reaction system, the amplified products were visualized on the LF strip within 5 min. The total operating time from quick DNA extraction to visualizing the result was approximately 30 min. The RPA-LF system we designed was efficient when using boiled, pan-fried, roasted, stir-fried, or stewed samples. The advantages of simple operation, speediness, and cost-effectiveness make our RPA-LF method a promising molecular detection tool for meat species identification of either raw or variously cooked Formosan Reeves’ muntjac meat. It is also possible to apply this method to identify the meat of other wildlife sources.

Identification of a broad spectrum of mammalian and avian species using the short fragment of the mitochondrially encoded cytochrome b gene

Mitochondrial DNA (mtDNA), especially the gene for cytochrome b (MT-CYB), has been found to be highly informative for species identification. In this study, we present the results of the analysis of a 127 bp long fragment of MT-CYB, amplified using universal primers, variable enough to be used for species identification and discrimination, even in highly degraded animal samples. The total number of analyzed species in this study was 30, including 17 mammalian and 13 bird species. Using a newly created primer pair, we successfully amplified and sequenced the target sequence in almost all tested species. The amplification was incomplete in just two species, and as a result, partial, but still variable sequences, were obtained. Using the target fragment we successfully identified all tested samples. Initial results suggested that the intraspecies genetic diversity of the target region, in all tested species, was low - from 0 to 4.72%. The interspecies genetic diversity of the target region, crucial for successful discrimination, showed relatively high diversity, ranging from 8.36% to 42.52%. Given its short length, the target region should be used for species determination, particularly in samples that are degraded or are low in DNA quantity.

Detection and quantification of beef and pork materials in meat products by duplex droplet digital PCR

Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos taurus) and pork (Sus scrofa) in a single digital PCR reaction tube. Mixed meat samples of known composition were used to test the accuracy and applicability of this method. The limit of detection (LOD) and the limit of quantification (LOQ) of this detection and quantification system were also identified. We conclude that our dddPCR detection and quantification system is suitable for quality control and routine analyses of meat products.

Development of a real-time PCR assay to control the illegal trade of meat from protected capercaillie species (Tetrao urogallus)

A rapid and highly species-specific real-time polymerase chain reaction (PCR) assay has been developed for the detection of capercaillie DNA (Tetrao urogallus) in meat and meat mixtures. The method combines the use of capercaillie-specific primers, that amplify a 142bp fragment of the mitochondrial 12S rRNA gene, and a positive control primer pair that amplifies a 141bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. SYBR(®) Green dye or TaqMan(®) fluorogenic probes were used to monitor the amplification of the target genes. Results obtained with the use of TaqMan(®) probes as detection platform increased the specificity of the real-time PCR assay in comparison with the results obtained using SYBR(®) Green. The proposed real-time PCR assay represents a rapid and straightforward method for the accurate identification of capercaillie that could be used by law enforcement agencies as a tool for the control of poaching and illegal trade of meat from this protected species.

Species identification of Tanzanian antelopes using DNA barcoding

Efficient tools for consistent species identification are important in wildlife conservation as it can provide information on the levels of species exploitation and assist in solving forensic-related problems. In this study, we evaluated the effectiveness of the mitochondrial cytochrome c oxidase subunit I (COI) barcode in species identification of Tanzanian antelope species. A 470 base-pair region of the COI gene was examined in 95 specimens representing 20 species of antelopes, buffalo and domestic Bovidae. All the Tanzanian species showed unique clades, and sequence divergence within species was <1%, whereas divergence between species ranged from 6.3% to 22%. Lowest interspecific divergence was noted within the Tragelaphus genus. Neighbour-joining phylogenetic analyses demonstrated that the examined COI region provided correct and highly supported species clustering using short fragments down to 100 base-pair lengths. This study demonstrates that even short COI fragments can efficiently identify antelope species, thus demonstrating its high potential for use in wildlife conservation activities.

Sequence of specific mitochondrial 16S rRNA gene fragment from Egyptian buffalo is used as a pattern for discrimination between river buffaloes, cattle, sheep and goats

Characterization of molecular markers and the development of better assays for precise and rapid detection of domestic species are always in demand. This is particularly due to recent food scares and the crisis of biodiversity resulting from the huge ongoing illegal traffic of endangered species. The aim of this study was to develop a new and easy method for domestic species identification (river buffalo, cattle, sheep and goat) based on the analysis of a specific mitochondrial nucleotide sequence. For this reason, a specific fragment of Egyptian buffalo mitochondrial 16S rRNA gene (422 bp) was amplified by PCR using two universal primers. The sequence of this specific fragment is completely conserved between all tested Egyptian buffaloes and other river buffaloes in different places in the world. Also, the lengths of the homologous fragments were less by one nucleotide (421 bp) in case of goats and two nucleotides (420 bp) in case of both cattle and sheep. The detection of specific variable sites between investigated species within this fragment was sufficient to identify the biological origin of the samples. This was achieved by alignment between the unknown homologous sequence and the reference sequences deposited in GenBank database (accession numbers, FJ748599-FJ748607). Considering multiple alignment results between 16S rRNA homologous sequences obtained from GenBank database with the reference sequence, it was shown that definite nucleotides are specific for each of the four studied species of the family Bovidae. In addition, other nucleotides are detected which can allow discrimination between two groups of animals belonging to two subfamilies of family Bovidae, Group one (closely related species like cattle and buffalo, Subfamily Bovinae) and Group two (closely related species like sheep and goat, Subfamily Caprinae). This 16S DNA barcode character-based approach could be used to complement cytochrome c oxidase I (COI) in DNA barcoding. Also, it is a good tool for identification of unknown sample belonging to one of the four domestic animal species of family Bovidae quickly and easily.

Using species-specific repeat and PCR-RFLP in typing of DNA derived from blood of human and animal species

Species determination of tissue specimens, including blood, is an important component of forensic analysis to distinguish human from animal remains. DNA markers based on a method of species-specific PCR and amplifying the 359-base pair (bp) fragment of the mitochondrially encoded cytochrome-b gene and then digestion with the TaqI restriction enzyme were developed for detection and discrimination of human, cattle, buffalo, horse, sheep, pig, dog, cat and chicken blood samples. The results reveal that PCR-amplification of the gene encoding the species-specific repeat (SSR) region generated 603 bp in cattle and buffalo, 221 bp in horse, 374 bp in sheep, <or=100 bp in pig, 808 bp in dog, 672 bp in cat and 50 bp in chicken. Restriction analysis of the amplified 359-bp portion of the cytochrome-b gene using the TaqI restriction enzyme results in species-specific restriction fragment length polymorphism (RFLP) between buffalo, cattle and human. Two different bands were generated in buffalo (191 and 168 bp) and human (209 and 150 bp), with no digestion in cattle (359 bp). Cytochrome-b is a highly conserved region and consequently a good molecular marker for diagnostic studies. Therefore, the two complementary techniques, SSR-PCR and PCR-RFLP, could be used successfully as routine methods in forensics for sensitive, rapid, simple and inexpensive identification of the species in bloodstains.

Fast differentiation of meats from fifteen animal species by liquid chromatography with electrochemical detection using copper nanoparticle plated electrodes

A simple, rapid and reliable method based on high-performance liquid chromatography with electrochemical detection was developed to routinely differentiate among meat products from fifteen food animal species. Samples from cattle, pigs, goats, deer, horses, chickens, ducks, ostriches, salmon, cod, shrimp, crabs, scallops, bullfrogs and alligators each exhibited unique electrochemical profiles. Species-specific markers exhibited reproducible peak retention times with coefficients of variation less then 6% across different runs, body regions and subjects. The method requires no derivatization or extraction steps and may be applicable to fresh or cooked meats. Incubation of fresh beef, pork or chicken at room temperature for 24h or repeated freezing and thawing changed the intensity but not the pattern of species-specific peaks. In conclusion, this method appears suitable for rapid differentiation of meats from various food animal species and demonstrates the utility of electrochemical detection to supplement existing immunochemical and molecular biological methods. The possibility of using this method to detect adulteration and degradative changes of meat proteins is discussed.

Development of novel heminested PCR assays based on mitochondrial 16s rRNA gene for identification of seven pecora species

BACKGROUND

Characterization of molecular markers and the development of better assays for precise and rapid detection of wildlife species are always in demand. This study describes a set of seven novel heminested PCR assays using specific primers designed based on species-specific polymorphism at the mitochondrial 16S rRNA gene for identification of Blackbuck, Goral, Nilgai, Hog deer, Chital, Sambar and Thamin deer.

RESULTS

The designed heminested PCR assays are two consecutive amplifications of the mitochondrial 16S rRNA gene. In the first stage, approximately 550 bp region of the 16S rRNA gene was amplified by PCR using template DNA and universal primers. In the second stage, a species-specific internal region of the 16S rRNA gene was amplified by PCR using the amplicon of the first PCR along with one universal primer and another species-specific primer as the reverse or forward primer. The amplicon generated after two consecutive amplifications was highly unique to target species. These assays were successfully validated for sensitivity, specificity, and ruggedness under a wide range of conditions.

CONCLUSION

The validation experiments confirm that the designed heminested PCR assays for identification of the seven species are highly specific, sensitive, reliable and provide a reproducible method allowing analysis of low copy number DNA recovered from decomposed or highly processed tissues. The assays for identification of other species could be devised by extrapolating the principle of designed heminested PCR.

Caillary electrophoresis for the analysis of meat authenticity

In this overview, different meat authenticity issues are presented, as well as a wide variety of methods available for meat authentication. Unlike chromatographic, traditional gel electrophoretic, or immunological methods, which have been routinely used in analytical laboratories, the application of capillary electrophoresis (CE) is relatively new in solving meat authentication issues. Several unique CE applications based on meat protein fingerprinting are discussed for the analysis of meat species in unheated meat products. For protein data interpretation, pattern recognition is used to account for the natural variability present within the same meat species. While gel DNA-based methods are widely used for determining meat species in heat processed products, few DNA-based methods utilizing CE have been reported. Moreover, the methods reported are qualitative or semiquantitative. Thus, the need for quantitative competitive PCR CE methods in the determination of meat species is addressed. For the determination of meat extenders, CE methods were either protein-based or based on specific markers. Polyphenols are used as specific markers for soy detection and hydroxyproline is used as a specific marker for collagen determination. Finally, the potential of electrophoretically mediated miroanalysis (EMMA) for the detection of meat that may have been previously frozen and retailed as "fresh" is highlighted.

Diagnostic polymorphisms in the mitochondrial cytochrome b gene allow discrimination between cattle, sheep, goat, roe buck and deer by PCR-RFLP

Background

As an alternative to direct DNA sequencing of PCR products, random PCR-RFLP is an efficient technique to discriminate between species. The PCR-RFLP-method is an inexpensive tool in forensic science, even if the template is degraded or contains only traces of DNA from various species.

Results

Interspecies-specific DNA sequence polymorphisms in the mitochondrial cytochrome b gene were analyzed using PCR-RFLP technology to determine the source (i.e., species) of blood traces obtained from a leaf.

Conclusions

The method presented can be used for the discrimination of cattle (Bos taurus), sheep (Ovis aries), goat (Capra hircus), roe buck (Capreolus capreolus) and red deer (Cervus elaphus).

Development of a specific monoclonal antibody for grouper (Epinephelus guaza) identification by an indirect enzyme-linked immunosorbent assay

Identification of fish species adulteration is important for consumer protection and the enforcement of food-labeling laws. A monoclonal antibody (MAb) generated against soluble muscle proteins from grouper (Epinephelus guaza) has been used in two indirect enzyme-linked immunosorbent assay (ELISA) formats (microtiter plates and immunostick tubes) for the rapid authentication of grouper fillets. The 3D12 MAb was produced with the use of the hybridoma technique and tested against several commonly consumed fish species by ELISA. The 3D12 MAb specifically reacted with grouper samples and could be useful for the discrimination of grouper among other, less-valued, fish species sold in the marketplace.

Quantitative PCR detection of pork in raw and heated ground beef and pâté

Quantitative estimates are important to establish whether pork adulteration in ground beef and pâté is accidental or intentional. A PCR procedure has been developed and evaluated to quantify pork in heated and nonheated meat and pâtés by densitometry using a specific and sensitive repetitive DNA element. Thirty, twenty-five, and twenty PCR cycles were carried out to find the best standard curve and correlation between pork content and band intensity. Twenty cycles showed the best results, quantifying degree contamination up to 1% pork in beef (heated and nonheated) and pork in duck pâté with a minimum error. Finally, fraud was found in commercial pâtés.

Beef- and bovine-derived material identification in processed and unprocessed food and feed by PCR amplification

This research developed and evaluated a PCR procedure to detect beef in heated and unheated meat, sausages, and canned food, using a specific and sensitive method. To confirm the effectiveness and specificity of this fragment, we tested 45 cattle blood DNA samples (from different breeds) and obtained positive results. With 125 samples tested from other species, the specific beef amplification was not detected. Feed components intended for cattle nutrition were also checked, and bovine-derived material was detected. Using this method we can detect the degree of contamination up to 0.01% raw beef in pork. In the same way, 1% beef was detected in cooked meat mixtures and bovine-derived material in concentrate mixtures. Beef has been identified in both heated and unheated meat products, sausages, canned food, and hamburgers. In conclusion, specific PCR amplification of a repetitive DNA element seems to be a powerful technique for the identification of beef in processed and unprocessed food, because of its simplicity, specificity and sensitivity. Furthermore, feed components intended for cattle nutrition can be checked. The procedure is also much cheaper than other methods based on RFLPs-PCR, immunodiffusion, and other techniques that need expensive equipment.

Random amplified polymorphic DNA fingerprints for identification of species in poultry pâté

Because some fraudulent or unintentional mislabeling occurs that can be undetected, resulting in lower quality pâté, and because some population groups, for philosophical or religious reasons, do not wish to eat meat from certain species, a new procedure was developed and evaluated to detect pâté species composition by randomly amplified polymorphic DNA (RAPD). The RAPD method was used to generate fingerprint patterns for pork, chicken, duck, turkey, and goose meats. Ten DNA samples from pork, chicken, turkey, and duck meats were tested to confirm the effectiveness and specificity. Specific results for each species were obtained by the RAPD method. Sensitivity of the method was studied by DNA dilution in each species, detecting as little as 250 pg of DNA. Isolations of DNA from 30 pâtés (tinned and untinned) were carried out, and an optimal DNA was obtained for using as template DNA in polymerase chain reaction (PCR). The RAPD-PCR pattern was useful to identify species composition of pork, duck, duck-pork, goose, and poultry pâtés. This study demonstrates the usefulness of RAPD fingerprinting to distinguish between species in pâtés.

Detection and analysis of animal materials in food and feed

Bovine spongiform encephalopathy (BSE) belongs to a group of progressively degenerative neurological diseases known as transmissible spongiform encephalopathies (TSEs) associated with a variant form of Creutzfeldt-Jakob disease in humans. TSEs are fatal diseases caused by prions (proteinaceous infectious particle) and are characterized by an incubation period that may range from several months to several years, depending on the host. Because BSE is spread through animal feed, the main strategy for preventing the establishment and spread of BSE is to prohibit the use of proteins derived from mammalian tissue in feed for ruminant animals. Enforcement of these regulations relies on the ability to identify the presence of prohibited proteins in ruminant feed. The methods to detect bovine products in rendered and cooked materials are based on analyses of DNA, bone, or protein. In this article, we discuss the current methodology as well as other potentially useful methods of analysis of animal material in food. While methods are generally useful, none specifically distinguish between prohibited bovine material and allowable bovine products, such as milk or blood. Furthermore, all these methods are hampered by the fact that the rendering process involves heat treatment that denatures and degrades proteins and DNA. There is a need for improving existing methods and developing new methods to overcome these two limitations.