Rapid identification of deer products by multiplex PCR assay

Attempts were made to establish one-step multiplex PCR assay for the identification of the widely used species in deer products (sika deer, wapiti, red deer and reindeer). Primers were designed from tandem repeat region of D-loop and well-conserved region of 16S rDNA after alignment of the available sequences in the GenBank database. The primers generated specific fragments of 307 bp in length for sika deer, 307 and 246 bp for wapiti, 272 bp for Tarim red deer, 230 bp for red deer and 141 bp for reindeer, respectively. The detection limit was 0.05 ng for sika deer and wapiti, 0.1 ng for Tarim red deer, 0.5 ng for red deer and 0.02 ng for reindeer. The results demonstrated that the fraudulent phenomenon is epidemic in the substitution of deer products, in especially antler, penis, foetus and tendon products. Hence, this multiplex PCR provided a useful and sensitive technique to identify the sources of deer products.     

Mitochondrial DNA enrichment for species identification and evolutionary analysis

 Nucleic acid-based species identification often targets the mitochondrial encoded cytb gene. However, polymerase chain reaction (PCR)- restriction fragment length polymorphism (RFLP) analysis using universal primers sometimes leads to ambiguous results, which are due to the presence of nuclear encoded pseudo-cytb genes. Such ambiguities were succesfully avoided using a newly developed method for the enrichment of mitochondrial DNA. In addition, a mitochondrial cytb-specific PCR system was designed allowing the unambiguous identification of game meat. Received: 24 February 1998     

A rapid and high-throughput real-time PCR assay for species identification: application to stockfish sold in Italy

In some parts of Italy, there is a tradition of eating special, highly prized species of cod, fished and dried in Norway. In order to safeguard the value of this food product, in 2005, the Italian government legislated that the commercial term “stockfish” can only be attributed to Gadus morhua (Gm). In this study, we present an improved real-time PCR assay for efficient identification of Gm with respect to other gadiforms of commercial interest. The method is applied to 437 stockfish samples, collected in various Italian regions, in order to verify whether labelling regulations had been respected and to report instances of fraud in the Italian stockfish market. The PCR method employed here allowed rapid and economical identification of the species, with a very high percentage of correct identifications.     

Molecular identification of the black tiger shrimp (Penaeus monodon), the white leg shrimp (Litopenaeus vannamei) and the Indian white shrimp (Fenneropenaeus indicus) by PCR targeted to the 16S rRNA mtDNA

Polymerase chain reaction-based methodologies have been developed for the identification of three commercially-relevant penaeid shrimp species, these were: Litopenaeus vannamei, Penaeus monodon and Fenneropenaeus indicus in food products. Such three species represent more than 80% of the whole farmed shrimp production worldwide and may be fraudulently replaced by species exhibiting lower value such as Litopenaeus stylirostris, Penaeus semisulcatus and Fenneropenaeus merguiensis, respectively. For it, preliminary sequencing of a mitochondrial sequence of ca. 530 bp in the 16S rRNA/tRNA^Val mitochondrial region was performed in nearly 20 penaeid shrimp species of commercial relevance. Careful analysis of such sequences allowed the design of primers PNVF/PNVR, which allowed the combined identification of P. monodon and L. vannamei, and PNIF/PNIR, which allowed the specific identification of F. indicus. In addition, P. monodon and L. vannamei could be easily differentiated by either restriction with TspE1 or by amplification with novel primers MPNF/MPNR, specific for P. monodon. The proposed specific methods improve current general identification methods of these species based on more general RFLP analyses. In addition, these methods can be easily completed in less than 8 h.     

A DNA method for qualitative identification of plant raw materials in feedstuff

This research developed a simple and not expensive DNA method for the qualitative identification of plant raw materials used as feed mixtures. Specific simple sequence tagged (STS) markers were developed to detect faba bean (Lectin A gene), field pea (Convicilin A gene), grain sorghum (UDP-glucosyltransferase gene) and barley (Hordoindoline-a gene), whereas identification of durum and common wheat (lipid transfer protein gene), soybean (Gly m Bd 30K allergen gene) and maize (invertase gene) was carried out using markers available from the literature. Cross-reactivity of the primer pairs was also checked against oat, rye, kidney bean and lentil. The method was effectively applied to the analysis of flour mixtures and extruded feedstuff. It could be included in traceability and certification of animal feeding systems within high quality animal production chains which are strictly related to the production area by the valorisation of locally grown raw materials.     

Molecular identification of cephalopod species by FINS and PCR-RFLP of a cytochrome b gene fragment

Identification of commercial species is a relevant issue to assure the correct labeling of seafood products. In this work two different molecular techniques, FINS (Forensically Informative Nucleotide Sequencing) and PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) were developed to identify 8 cephalopod species (families Loliginidae and Ommastrephidae) employing a fragment of the cytochrome b gene. DNA amplification for all of the species was carried out with a new set of specific primers designed in this study for cephalopods. FINS is a technique based on DNA sequencing, while PCR-RFLP allows direct species identification by comparing specific DNA restriction patterns. Both techniques are useful for cephalopod species identification. 17 food products (mainly "squid rings") were analyzed and the species employed for their manufacture identified by FINS.     

A quick and simple method for the identification of meat species and meat products by PCR assay

The polymerase chain reaction (PCR) was applied to identify six meats (cattle, pig, chicken, sheep, goat and horse) as raw materials for products. By mixing seven primers in appropriate ratios, species-specific DNA fragments could be identified by only one multiplex PCR. A forward primer was designed on a conserved DNA sequence in the mitochondrial cytochrome b gene, and reverse primers on species-specific DNA sequences for each species. PCR primers were designed to give different length fragments from the six meats. The products showed species-specific DNA fragments of 157, 227, 274, 331, 398 and 439 bp from goat, chicken, cattle, sheep, pig and horse meats, respectively. Identification is possible by electrophoresis of PCR products. Cattle, pig, chicken, sheep and goat fragments were amplified from cooked meat heated at 100 or 120°C for 30 min, but horse DNA fragments could not be detected from the 120°C sample. Detection limits of the DNA samples were 0.25 ng for all meats.     

A real-time PCR method for the detection and quantification of lupin flour in wheat flour-based matrices

Lupin flour is growingly being used in bakery products, mainly as a soybean protein substitute. The aim of the present work was to detect and quantify the presence of lupin flour in wheat-based foods using a newly set up qPCR system based on SYBR green. Although DNA sequence information for lupin is scarce, it has been possible to design a primer pair highly specific for the target gene and devoid of any primer-dimers amplification capacity. Lupin flour revealed to be a difficult matrix, since large amounts of compounds tend to co-purify with DNA, even adopting well established extraction protocols. Nonetheless, the primers used allowed to reach high PCR efficiencies and did not show any cross-reactivity with DNAs extracted from various plant and animal foods. The sensitivity achieved was 7 pg of lupin DNA, corresponding to a percentage of less than 0.1% of lupin flour in the foods.     

Application of species-specific PCR for the identification of dried bonito product (Katsuobushi)

The species-specific PCR (polymerase chain reaction) method was developed to identify the species of dried bonito product (Katsuobushi) produced from Euthynnus pelamis, E. affinis, Auxis rochei, A. thazard, and Sarda orientalis. The 1141 bp complete mitochondrial cytochrome b genes of five bonito species and other five related Scombridae species were established, and then five pairs of species-specific primer were designed to amplify short length fragments among bonito species. The developed species-specific PCR method was successfully applied to authenticate species of commercial dried bonito products. Hence, this method really provided a useful and academic technique to identify the sources of bonito product.     

Survey of the authenticity of prawn and shrimp species in commercial food products by PCR-RFLP analysis of a 16S rRNA/tRNA mitochondrial region

A novel PCR-RFLP method was evaluated as a tool to assess the incidence of incorrect labelling of prawns and shrimps in commercial food products. The whole method can be performed in less than 8 h in only one day of work. PCR amplification with primers 16Scru4/16Scru3, targeted to the amplification of a ca. 530 bp region of 16S rRNA and tRNA^Val mitochondrial genes, was coupled to restriction analysis with AluI, TaqI or HinfI. Forty-one commercial food products were considered. The molecular method considered allowed the identification of up to 17 different prawn and shrimp species in all the processed products considered. Seven (28%) of the 25 food products declaring one or more species in their labels were incorrectly labelled. Authentication was successfully assessed in commercial peeled products subjected to industrial processing, in which none of the products displayed labelling at species level. Overall, incorrect labelling was detected in 10 (24.4%) of the 41 commercial products tested, while another 16 samples (39%) exhibited incomplete labelling. The molecular method evaluated in this study proved to be a rapid and easy-to-perform two-step analytical approach to achieve species identification of commercial whole specimens of frozen prawns and shrimps and in peeled processed products where such raw materials are included as added-value ingredients.     

PCR assay for the identification of animal species in cooked sausages

A species-specific PCR assay was developed for the detection of low levels of pork, horse and donkey meat in cooked sausages. Oligonucleotid primers were designed for amplification of species-specific mitochondrial DNA sequences of each species and detected the presence of 0.01 ng of template DNA in water. When applying the assay to DNA extracts from sausages samples that were prepared from binary meat mixtures, it was possible to detect each species when spiked in any other species at the 0.1% level. In conclusion, it can be suggested that this assay can be used to determine mislabelled and/or fraudulent species substitution in comminuted meat products.     

Polymerase chain reaction assay for identification of chicken in meat and meat products

The aim of this study was to develop polymerase chain reaction (PCR) assay for specific detection of chicken meat using designed primer pair based on mitochondrial D-loop gene for amplification of 442 bp DNA fragments from fresh, processed and autoclaved meat and meat products. The PCR result was further verified by restriction digestion with HaeIII and Sau3AI enzymes for specific cutting site in amplified DNA fragments. The specificity of assay was cross tested with DNA of cattle, buffalo, sheep, goat, pig, duck, guinea fowl, turkey and quail, where amplification was observed only in chicken without cross reactivity with red meat species. However positive reaction was also observed in quail and turkey. In this study, no adverse effects of cooking and autoclaving were found on amplification of chicken DNA fragments. Thus, the detection limits was found to be less than 1% in admixed meat and meat products. The developed assay was found specific and sensitive for rapid identification of admixed chicken meat and meat products processed under different manufacturing conditions.     

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

A polymerase chain reaction (PCR) method based on the nucleotide sequence variation in the 12S ribosomal RNA mitochondrial gene has been developed for the specific identification of bovine, ovine and caprine DNAs in feedstuffs. The primers designed generated specific fragments of 84, 121 and 122pb length for bovine, ovine and caprine species, respectively. The specificity of the primers designed was tested against 30 animal species including mammals, birds and fish, as well as eight plant species. Analysis of experimental feedstuffs demonstrated that 0.1% of raw and heated bovine, ovine or caprine tissues can be easily detected using the species-specific primers developed. The performance of this method is not affected by prolonged heat treatment, and consequently it could be very useful to verify the origin of the raw materials in products submitted to denaturing technologies, for which other methods cannot be applied.     

Polymerase chain reaction (PCR) in the quality and safety assurance of food: Detection of soya in processed meat products

A new method for the specific and sensitive detection of soya (Glycine max) in processed meat products has been developed using polymerase chain reaction (PCR) technology. The presence of soya deoxyribonucleic acid (DNA) from several soya protein concentrates was determined with two pairs of specific oligonucleotides yielding a 414-bp (bp=base pair) fragment and an internal 118-bp fragment amplified from the soya lectinLe1 gene. The test detected DNA from textured soya protein concentrates in meat products at a level of 1% and was confirmed by a commercially available enzyme-linked immunosorbent assay (ELISA).     

A multiplex magnetic capture hybridisation and multiplex Real-Time PCR protocol for pathogen detection in seafood

Seafood could become a source of bacterial pathogens by exposure to contaminated water or through processing practices, thus representing a public health hazard. Conventional culture-based analytical methods take several days to be completed, while the molecular rapid identification of bacterial pathogens is crucial for effective disease control. The developed application consist of a multiplex magnetic capture hybridisation (mMCH) assay for the simultaneous isolation of Salmonella spp. and Listeria monocytogenes DNA from seafood, using paramagnetic amino-modified nanoparticles with capture oligonucleotides, and a triplex Real-Time PCR with an Internal Amplification Control (IAC), in accordance with ISO 22174. The detection probability was 100% with 10 genome equivalents of each target species co-amplified in the same reaction. The complete molecular procedure was tested on raw and smoked salmon fillets artificially contaminated with known amounts of one or both target bacteria (1–10³ cfu/g), directly or after culture enrichment, and compared for equivalence with the standard methods. Results revealed a complete agreement between the two approaches, with a sensitivity of 1 cfu/g, in enriched samples, and higher sensitivity (10²–10³ cfu/g) of the molecular method in samples examined before culture enrichment. The proposed procedure was also able to identify a natural contamination by L. monocytogenes in smoked salmon with a considerable shortening of time.     

Development and validation of a real-time PCR detection method for celery in food

As from 25 November 2005 onwards, a list of ingredients with known allergenic potential has to be labeled according to Directive 2003/89/EC, including celery and products thereof. In order to provide appropriate detection methods a novel real-time polymerase chain reaction (PCR) system for the specific and sensitive detection of DNA from celery (Apium graveolens) was developed and validated. Specificity was confirmed by testing DNA derived from more than 50 food relevant organisms. Sensitivity was demonstrated on the basis of a calibration curve plotting the corresponding Ct-values against DNA amounts ranging from 1 to 1000 copies. Due to the lack of certified reference material the applicability of the method was assessed by analysis of sausages spiked with defined amounts of grounded celery seed. The limit of detection (LOD) examined exemplarily for emulsion-type sausages was 5–10 mg/kg. Analysis of celery-containing commercial products demonstrated the performance potential and limitations of the new real-time PCR system.     

Validation and comparison of a sandwich ELISA,two competitive ELISAs and a real-time PCR method for the detection of lupine in food

Methods applied in food allergen analysis should be specific, sensitive and applicable to both raw and highly processed foods. The performance of the most commonly used methods, ELISA and real-time PCR, may, however, be influenced by food processing steps, e.g., heat treatment. The present study compares the applicability of four in-house developed methods, one sandwich ELISA, two competitive ELISAs and a real-time PCR method, for the detection of lupine in four different food matrices, comprising bread, biscuits, rice patties and noodles. In order to investigate the influence of food processing on the detectability, not only the heat treated model foods but also the corresponding doughs were analysed. The sandwich ELISA proved to be the most sensitive method. The LOD was found to be 10 ppm lupine, independent from the food matrix and independent if the dough or the heat treated food was analysed. In addition, the methods were applied to the analysis of commercial foodstuffs differing in their labelling.     

A PCR-microarray method for the screening of genetically modified organisms

A new method to screen and to identify genetically modified organisms (GMO) is presented in this paper. It is based on the detection of multiple genetic elements common to GMO by their amplification via PCR followed by direct hybridisation of the amplicons on microarray. The pattern of the elements is then compared to a database of the composition of EU-approved GMO and an identification of the GMO is then proposed. The limit of detection of the method was ≤0.1% GMO content (w/w) expressed as the amount of target DNA present in the template for single unprocessed material. The DNA targets were detected both in reference materials and in mixtures with the same detection limit. The specificity for the detection of the different elements was found to be very good with no cross-reaction even in samples with two GMO present at different concentrations. The paper presents examples of GMO identification and discusses the potential and limitation of such approaches and how they can facilitate the work of private and enforcement detection laboratories.     

Validation of a method for the detection of five species,serogroups, biotypes and virulence factors of Vibrio by multiplex PCR in fish and seafood

In this work a sequential multiplex PCR system was designed and validated for the detection of most frequent foodborne pathogen Vibrio species in fish and seafood (Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio alginoliticus and Vibrio mimicus). The method proposed functions in a hierarchical way, being composed of an end-point multiplex PCR to detect the presence of DNA belonging to the studied species, followed by multiplex PCR and fragment analysis allowing the viability assessment of the detected strains. The final multiplex PCR step of the method may be applied if identification of the serogroup, biotype and/or virulence factor level is necessary. Forty samples of commercial fish and seafood products were used at the method validation stage. Sixty three marine organism samples obtained from various estuarine areas of Spain including shrimps, crabs, bivalve mollusks and fishes were screened for presence of Vibrio species and 2 mussel samples were found positive for V. parahaemolyticus. On the whole, the proposed method is robust and readily adaptable in routine molecular diagnostic laboratories, allowing monitoring and simultaneous detection of all these bacterial pathogens in seafood samples, reducing the expenses and time consumed by other analytical methods.     

Development of a real-time PCR protocol for the species origin confirmation of isolated animal particles detected by NIRM

At present, European legislation prohibits totally the use of processed animal proteins in feed for all farmed animals (Commission Regulation (EC) No. 1234/2003–extended feed ban). A softening of the feed ban for non-ruminants would nevertheless be considered if alternative methods could be used to gain more information concerning the species origin of processed animal proteins than that which can be provided by classical optical microscopy. This would allow control provisions such as the ban of feeding animals with proteins from the same species or intra-species recycling (Regulation (EC) No. 1774/2002). Two promising alternative methods, near-infrared microscopy (NIRM) and real-time polymerase chain reaction (PCR), were combined to authenticate, at the species level, the presence of animal particles. The paper describes the improvements of the real-time PCR method made to the DNA extraction protocol, allowing five PCR analyses to be performed with the DNA extracted from a single particle.