Quantitative competitive PCR for the detection of genetically modified organisms in food

Present polymerase chain reaction (PCR) detection methods only allow the qualitative detection of GMO in food without quantitation of the GMO content. Clearly, the availability of quantitative detection methods for GMO analysis is an important prerequisite for the introduction of threshold limits for GMOs in food. PCR is well known to be quantitative if internal DNA standards are co-amplified together with the target DNA. This quantitative competitive (QC) PCR was first described in the early nineties and is widely used nowadays.

We have developed and evaluated QC–PCR systems for the quantitative detection of Roundup Ready^TM soybean (RRS) and Maximizer maize (MM) in food samples. Three DNA fragments differing from the GMO specific sequences by DNA insertions were constructed and used as internal standards in QC–PCR. These standards were calibrated by co-amplifying with mixtures containing defined amounts of RRS DNA and MM DNA, respectively. The calibrated QC–PCR systems were applied to several commercial food samples containing RRS and to three certified RRS flour mixtures (Fluka standards). Recently, quantitative methods for the detection of RRS were successfully tested in a collaborative study involving twelve European control laboratories. Thus, QC–PCR methods will allow to survey “de minimis thresholds” of GMOs in food.     

A general multiplex-PCR assay for the general detection of genetically modified soya and maize

The use of genetically modified organisms (GMOs) as food and in food products is becoming more and more widespread. The European Union has implemented a set of very strict procedures for the approval to grow, import and/or utilize GMOs as food or food ingredients. Thus, analytical methods for the detection of GMOs are necessary in order to verify compliance with labelling requirements. In the past few years, different PCR-based methods for the specific detection of the most economically important GMOs have been proposed. A molecular screening method based on multiplex-PCR that involves amplification of specific soya or maize sequences from plant DNA and the amplification of 35S promoter and NOS terminator for the detection of genetically modified soya and maize was developed. The m-PCR assay discriminated the GMO very quickly, reproducibly and in a cost saving and less time-consuming way. It is a flexible assay to conduce a preliminary GMO screening for detection of genetically modified soya and maize.     

Prevalence of genetically modified foods (GM foods) in the United Arab Emirates

The real and/or perceived risks of genetically modified organisms (GMO) prompted food safety regulators to label the GM products. Although there are no legislations on GM labeling and cultivation of GM crops in the UAE, the present study aims to monitor the status of GM foods in the UAE market using Light cycler real time PCR technology and GMO screening kit. The yield and purity of DNA extracted by CTAB method was higher when compared to Qiagen plant kit with an exception of soya products for which Qiagen kit yielded better results.Out of 128 samples tested, 16 were positive for plant, 35S promoter and Tnos fragment. In conclusion, GMO screening assay applied in this study confirms the presence of genetically modified food in the UAE market. The rapidly growing GM market with multiple events and the threat from unapproved events signifies the value of surveillance program for monitoring the status of GM foods.     

Detection methods for genetically modified crops

Due to the market introduction of genetically modified crops (GMOs) as the Roundup Ready (RR) soya and Bt corn, the European food industry came face to face with the question of the use and labeling requirements on GMO crops and its derivatives. Although even today, no defined European legislation is available, a definitive need for detection methods exists. Both DNA and protein based methods have been developed and applied for the detection of RR soya beans and its derivatives. For the CP4 synthase, synthetic peptides corresponding with the antigenic and non-homologous parts of the CP4 synthase were synthesized and mono-specific anti-CP4 synthase monoclonal antibodies were prepared by hybridoma technology. The monoclonal antibodies were able to detect the CP4 synthase in the RR soya using Western blotting analysis. Detection limits were found between 0.5% and 1%. The method is currently validated for half-and final products. The applied DNA methodology was making use of polymerase chain reactions (PCR) using sets of primers along the gene encoding the Agrobacterium CP4 synthase. DNA extraction and purification conditions were examined on a case-by-case approach for a scala of soya products (lecithin, oil, soybean meal, soy protein isolates etc.), half-products and final consumer products. Detection limits were found between 0.01% and 0.1%. In this paper a comparison will be made between the two types of methods in relation to sample preparation, sensitivity, validation and the use for half-products and final consumer products.     

A multiplex nested PCR assay for the simultaneous detection of genetically modified soybean,maize and rice in highly processed products

The use of genetically modified organisms (GMOs) as food products becomes more and more widespread. The European Union has implemented a set of very strict procedures for the approval to grow, import and/or utilize GMOs as food or food ingredients. Thus, analytical methods for detection of the GMOs are necessary in order to verify compliance with labeling requirements. There are few effective screening methods for highly processed GM (genetically modified) products. Four genes (CP4-EPSPS, Cry1A(b), BAR, and, PAT) are common exogenous genes used in commercialized transgenic soybean, maize, and rice. In the present study, a multiplex nested polymerase chain reaction (PCR) method was developed to simultaneously detect the four exogenous genes and one endogenous gene in two runs. We tested eleven representative highly processed products samples (soya lecithin, soya protein powder, chocolate beverage, infant rice cereal, soybean refine oil, soybean salad oil, maize oil, maize protein powder, maize starch, maize jam) using the developed method, and amplicons of endogenous gene and transgenic fragments were obtained from all the processed products except for soybean refined oil, soybean salad oil and maize oil, and the sensitivity was 0.005%. These results indicate that multiplex nested PCR is appropriate for qualitative detection of transgenic soybean, maize and rice in highly processed products except for refined oil.     

Detection of Roundup Ready soy in highly processed products by triplex nested PCR

Till now, there still has not an effective detection method for the highly processed GM (genetically modified) products. A novel method of the triplex nested PCR, was developed for the sensitive detection of several foreign genes (Lectin, CaMV 35S, CTP, CP4-EPSPS, NOS) in highly processed products. We detected seven representative highly processed products (soya lecithin, soya protein powder, chocolate beverage, infant rice cereal, crude soybean oil, soybean refine oil, soybean salad oil) by the triplex nested PCR. The first triplex PCR cannot detect the insert signals in the processed products, and the sensitivity is 0.5%. However the second triplex PCR, which can simultaneously detect RR soybean targets with a sensitivity of 0.005% in the triplex nested PCR. The result indicates the advanced level of the method for the GM products detection. It is a flexible assay to detect the RR soybean in highly processed products.     

Traceability of genetically modified Roundup Ready soybean: A case study on sampling and analytical uncertainty along processing chain

A study on the fate of Genetically Modified (GM) Roundup Ready soybean (RRS) was undertaken on the following products: flour, protein flour, lecithin, crude and refined oil, broken grain, hull and expander of an industrial soybean manufacturing plant, with the aim to evaluate the possible effects of processing on the reliability of control plans. A sampling control plan was applied to all the products of the industrial manufactory plant. The best sampling point was identified based on the lowest impact of the analytical and sampling uncertainty.The best “fit for purpose” sampling point for the accurate evaluation of the Genetically Modified Organism (GMO) concentration measurement was identified in the processed products, e.g. flour and protein flour, thanks to the homogeneity on RRS in the batch and the better yield and quality of the extracted DNA.This study presents a practical approach to assess the two main factors that affect the reliability of the control plans: analytical and sampling uncertainty. The work was undertaken on GM soybean derived products, nevertheless the conclusions we reached could be also applied to verify compliance with GMO labelling threshold.     

Comparison of simplex and duplex real-time PCR for the quantification of GMO in maize and soybean

This paper focuses on the determination of the GMO content of maize and soybean samples using real-time PCR, comparing simplex and duplex PCR. The total DNA content of samples was determined by amplifying part of a maize gene encoding a lipid transfer protein, or part of a soybean lectin gene. The transgenic DNA was quantified by amplifying part of the CaMV 35S promoter. The importance of preparation and conservation of standards as well as the relevance of DNA extraction protocol on the variability of results are discussed. For the determination of low GMO content, limitation in the number of copies of the target gene to be amplified is considered. For samples with a theoretical GMO content of 1%, corresponding to the legal threshold for labelling, the value determined by duplex real-time PCR ranged from 0.85% to 1.20%. Both real-time simplex and duplex PCRs allowed identification of GMO free samples without ambiguity.     

Identification and verification of porcine DNA in commercial gelatin and gelatin containing processed foods

Gelatin, derived from bovine and porcine sources, has been used in many foods and pharmaceutical products. To ensure the compliance of food products with halal regulations, the reliable analytical methods are very much required. In this study, polymerase chain reaction (PCR) assay using species-specific primers was performed to evaluate the halal authenticity of commercial pure gelatin and gelatin-containing processed food products. Based on the specificity and cross-reactivity results of the seven species-specific primers by conventional PCR, the porcine species primer No. 2 was selected and it was able to detect species DNA in 12 out of 36 processed foods. The cloning, sequencing, and blasting at NCBI confirmed the presence of pork DNA in 5 out of 12 porcine DNA positive food samples. The maximum identity (homology) with pork sequence available in NCBI Gene Bank for the five samples ranged from 87% to 97% and the Query Cover ranged from 94% to 100%. The real-time PCR assay detected more positive samples (27 positive amplifications) compared to 12 positive samples with conventional PCR using porcine specific primer No. 2. PCR using species specific primers is a very useful and effective technique for halal authenticity of gelatin and gelatin-containing food products.     

A validated strip-based lateral flow assay for the confirmation of sheep-specific PCR products for the authentication of meat

Molecular methods, such as PCR and real-time PCR, have been developed to detect species in meat and meat products. Despite good specificity and sensitivity, they are not widely implemented in food control programs due to complex operation or financial reasons. In the present study, a simple, rapid and affordable method, Sheep-PCR-Strip [Sheep specific polymerase chain reaction-Strip], was developed for the authentic identification of raw and heat-treated mutton. The assay is based on PCR amplification of sheep DNA, followed by detection of the PCR product by a strip format; the result can be read within 5 min by the naked eye. There is a real advantage of the strip approach rather in the reduced time (5 min versus electrophoresis) and avoidance of chemicals (e.g. ethidiumbromide). The sensitivity of the Sheep-PCR-Strip test was established to be 0.01% for the detection of adulterated meat; the limit of detection (LOD) was up to 0.01 pg of sheep DNA. The assay was also specific for sheep, and no cross-reactions were observed in other non-target species. It is a promising new tool for sheep identification and can be rapidly modified for other meat detection and widely used for solving problems related to food quality assurance, species authentication and traceability.     

Quantitative analysis of genetically modified organisms (GMO) in processed food by PCR-based methods

Two different PCR-based approaches for the quantitative analysis of genetically modified organism (GMO) – components in foods are presented using Soybean derived samples as an example. The first method – a double competitive PCR – is well suited to determine threshold levels of GMO content in food. The other – PCR on-line measurement – is suited to determine ratios of transgenic versus non-transgenic component. Both methods provide a means to alleviate the problems of standardisation encountered with simple qualitative PCR approaches and will allow to cope with threshold levels for GMO, once issued by legislative bodies.     

Disposable genosensor, a new tool for the detection of NOS-terminator, a genetic element present in GMOs

Legislation enacted worldwide to regulate the presence of genetically modified organisms (GMOs) in crops, foods and ingredients, necessitated the development of reliable and sensitive methods for GMO detection. An indicator based electrochemical disposable genosensor for the voltammetric detection of NOS-terminator, a genetic element present in GMOs is described as a possible substitute method for the common technique of gel electrophoresis and fluorescent image analysis. The biosensor relies on the immobilization of the 25-mer single stranded oligonucleotides (probe) related to NOS-terminator DNA sequence and the relative binding of this sequence with the polymerase chain reaction (PCR) amplified samples from certified reference material (CRM) of Roundup Ready soybean (Fluka) at a screen printed electrode (SPE). The extent of hybridization between the probe and target DNA is determined by using square wave voltammetry (SWV) with moving average baseline correction and methylene blue (3,7-bis(dimethylamino)phenothiazin-5-ium chloride, MB), as the hybridization indicator. The difference between the MB signals, obtained from the hybrid modified and probe modified SPEs, is used to detect GMOs from PCR amplified DNA samples. Numerous factors affecting the hybridization and indicator binding reactions are optimized to maximize the sensitivity.     

Screening new gene markers for gluten detection in foods

In the present work, three DNA sequences encoding wheat proteins (α2-gliadin, agglutinin isolectin and thioredoxin h) were compared to trace gluten-containing cereals in food products. Quantitative real-time PCR methods using hydrolysis probes were successfully developed to target the three sequences for the detection of wheat DNA. The comparison of the three systems highlights the best sensitivity when tracing the α2-gliadin marker sequence, showing an absolute limit of detection (LOD) of 2 pg of wheat DNA and a relative LOD of 0.005% (50 mg/kg) of wheat in soybean, which corresponds to 4.5 mg/kg of gluten. All the systems reveal high specificity for detecting other gluten-containing cereals, such as barley and rye. Therefore, the developed real-time PCR systems can be used as non-immunological tools to confirm the presence of gluten-containing cereals in foods, towards the safety of celiac patients and wheat allergic individuals.     

Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) for halal verification

Pork identification in four types of food products, which are sausages and the casings, bread and biscuits, using species-specific polymerase chain reaction (PCR) detection of a conserved region in the mitochondrial (mt) 12S ribosomal RNA (rRNA) gene was developed. Genomic DNA of the food products were successfully extracted except for the casing samples, where no genomic DNA was detected. The extracted genomic DNA was then subjected to PCR amplification targeting the specific regions of the 12S rRNA gene. The genomic DNA from the food products were found to be of good quality and produced clear PCR products on the amplification of 12S rRNA gene of 387 base pairs (bp) from pork species. The species-specific PCR identification yielded excellent results for identification of pork derivatives in food products and it is a potentially reliable and suitable technique in routine food analysis for halal certification.     

Results of an interlaboratory assessment of a screening method of genetically modified organisms in soy beans and maize

The preliminary results on an interlaboratory trial on the detection of genetically modified organisms (GMO) are presented. The method applied is based on the detection of modified DNA using the polymerase chain reaction (PCR) for amplification. The amplified fragments analysed are derived from the 35S promotor and the NOS terminator used for modification and are present in 26 from the 28 GMOs currently already approved or under approval by the competent authorities. This method fits as a screening method indicating the presence of GMO in food. However, it does not allow an identification of the kind of GMO present in the samples. Samples of soybean and maize flour containing 0%, 0.1%, 0.5% and 2% GMO had been prepared for this study and are also already commercially available. In this paper the combined results from 27 laboratories are presented, indicating that on average the probability of false positive or false negative results is only about 1% for soybeans and below 5% for maize.     

Detection of gluten-containing cereals in flours and “gluten-free” bakery products by polymerase chain reaction

A polymerase chain reaction-based method for the detection of gluten-containing cereals in flours and “gluten-free” bakery products was optimized and its intralaboratory validation was carried out. The optimized method involved DNA isolation by chaotropic solid-phase extraction and PCR with primers of Dahinden et al. [Dahinden I., von Büren M., Lüthy J., 2001. A quantitative competitive PCR system to detect contamination of wheat, barley and rye in gluten-free food for coeliac patients. European Food Research and Technology 212, 228–233]. Using purified DNA, intrinsic detection limit of 42 ± 12 pg was determined, which corresponds to 10° genome copies. By the analysis of a panel of 26 European wheat cultivars and flours from six non-gluten-containing plants, which are commonly used for the production of gluten-free bakery products, inclusivity of 100% and exclusivity of 100% were determined. By the analysis of model samples of soya flour and cakes, detection limit of 0.1% (w/w) of fine wheat flour was determined, which is suitable for the analysis of “gluten-free” food products, as it is approximately equivalent to the limit of 10 mg per 100 g for gluten stated by Codex Alimentarius. The method was successfully applied to four samples of flours and 13 brands of biscuits designated “gluten-free”, out of which two flours and one brand of biscuits were found positive for gluten-containing cereals. The method proved to be suitable for routine use, it was relatively straightforward and could be completed in one working day.     

Development of a real time PCR assay for detection of allergenic trace amounts of peanut (Arachis hypogaea) in processed foods

Peanut allergic reactions can result from the ingestion of even very small quantities of peanut and represent a severe threat to the health of sensitized individuals. In order to protect the allergic consumer, efficient and reliable methods are required for the detection of allergenic ingredients. For this purpose, we have developed a TaqMan real-time PCR method for specific detection of peanut in commercial food products. The assay uses two genetic makers in the Arah2 (125 bp) and ITS1 (90 bp) gene respectively, and TaqMan probes. The nuclear 18S rRNA gene was employed as a positive amplification control. Results obtained on sensitivity of both Arah2 and ITS primers with mixtures spiked with different concentrations of the target showed detection levels of 10 and 0.1 ppm, respectively. The applicability of the real-time PCR protocol to detect the presence of peanut DNA in commercial food products was determined through analysis of 123 different commercial products with the ITS primers which aimed higher sensitivity than Arah2 primer pair. The performance of the real-time PCR proposed herein allows a highly sensitive detection of peanut DNA in all the different food products, which declared to contain peanut material as well as in others were the presence of peanut or its traces wasn't declared in the labeling.     

Development of a PCR protocol to detect ochratoxin A producing moulds in food products

Ochratoxin A (OTA) is a mycotoxin produced by several Penicillium and Aspergillus species growing in food commodities. To prevent OTA in foods it is necessary to have rapid and specific methods for early detection of producing moulds regardless of species and genera. In this work a PCR method to detect ochratoxigenic moulds has been developed. For this purpose, 75 mould strains belonging to species usually reported in food products were used. Their OTA production was checked by micellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). A specific amplicon of 459 bp was detected by using the designed PCR protocol only in the OTA producing strains. The detection limit of the developed PCR protocol was estimated for 25 pg of mould DNA from pure cultures and from about 10²–10⁴ cfu/g when it was evaluated directly on artificially inoculated food. Its functionality in naturally infected samples was also demonstrated. In conclusion, the developed PCR method could be used for detecting ochratoxigenic moulds in foods and consequently for monitoring these moulds in the HACCP programs.     

Microbiological safety of kinema, a fermented soya bean food

Kinema is a fermented soya bean food of Nepal and the hilly regions of North-eastern States of India. Generally, the fermentation is dominated by Bacillus spp. that often cause alkalinity and desirable stickiness in the product. The present study was undertaken in a limited number of commercial (market) kinema samples to test for the presence of foodborne pathogens and their properties. Bacillus cereus was present in numbers exceeding 10⁴ cfu/g product in five of the tested 15 market samples. Enterobacteriaceae and coliform bacteria exceeded 10⁵ cfu/g in 10 of the 15 samples. Escherichia coli exceeding 10⁵ cfu/g was found in two samples. Staphylococcus aureus was not detected in any of the tested samples. Of 31 isolated typical and atypical strains of B. cereus, 18 representative strains were tested qualitatively for the ability to produce diarrhoeal type enterotoxin (BCET) using an Oxoid BCET-RPLA test kit. Overall, BCET was formed by 12 strains in BHIG (brain heart infusion broth +1% glucose), by seven strains on sterilized cooked rice, and by five strains on sterilized cooked soya beans. Semi-quantitative tests on BCET revealed that levels exceeding 256 ng/g soya beans, produced by single pure culture inoculation with the isolated B. cereus strains, were reduced to ≤ 8 ng/g by frying kinema in oil, a common procedure when making kinema curry. It was also shown in a mixed pure culture experiment that a kinema strain B. Subtilis DK-W1, is able to suppress growth and BCET formation by a selected toxin producing strain (BC7-5) of B. cereus. It is concluded that the traditional way of making kinema and its culinary use in curries is safe. However, for novel applications of kinema, safety precautions are advisable.     

Simultaneous detection of Escherichia coli O175:H7, Salmonella spp., and Listeria monocytogenes by multiplex PCR

The wide application of nucleic acid amplification techniques and the increasing industrial interest toward rapid methods has led to the development and application of PCR based methods for the detection of microbial pathogens in food. In the present paper we describe the development of a multiplex PCR method for simultaneous detection of Salmonella enterica serovar Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7 in a complex food matrix (liquid whole egg).Four different DNA extraction procedures were evaluated for their application on food and, among these, Chelex resin combined with a DNA purification step were found to better perform on the food system considered.A multiplex PCR system was developed, based on the evaluation and combination of published primer sets, and applied to the simultaneous detection of the target pathogens plus an internal amplification control, both in culture media and in a model food system.The overall system proposed, based on an overnight enrichment step followed by DNA isolation and multiplex PCR, was satisfactorily tested for its specificity and sensitivity and allowed the detection of the presence of bacterial DNA and the identification of the target pathogens down to 10 cells/25 g liquid whole egg.