Two quantitative multiplex real-time PCR systems for the efficient GMO screening of food products

According to the EU and Swiss food legislation, only deregulated traits of transgenic plants are allowed to be imported and sold to the consumer. In order to control imports of soya and maize products from retailers, efficient and reliable methods for the detection and quantification are a prerequisite. The screening for specific DNA elements characteristic of transgenic plants is crucial for further analysis and has a major impact on the efficiency of the whole analysis workflow. To allow laboratories to efficiently and reliably screen food products for transgenic plant products, two novel multiplex real-time polymerase chain reaction (PCR) systems were developed and validated. One system determines DNA contents from maize, soya, cauliflower mosaic virus (CaMV) 35S promoter (P35S), NOS terminator from Agrobacterium tumefaciens and CaMV, and the second PCR system simultaneously detects DNA sequences from figwort mosaic virus promoter (PFMV), from bar gene of Streptomyces hygroscopicus, from gene coding for phosphinothricin acetyltransferase (PAT) and from a DNA construct of enolpyruvyl shikimate phosphate synthase gene (CP4-EPSPS) and Arabidopsis thaliana (CPT2). The tests exhibit good specificity and a limit of detection of at least 0.1 % for all analytes.     

A novel real-time polymerase chain reaction (PCR) method for the detection of walnuts in food

A real-time polymerase chain reaction (PCR)-based method for the detection of the walnut (Juglans regia) component in food is described here. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with walnut-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the jug r2, a major allergen gene of walnut. The method was positive for 8 varieties of walnut and negative for all other tested plant materials used in food industry, including pecan nuts. The intrinsic detection limit of the method was 0.24 ng walnut DNA. Using a series of model pastry samples with defined walnut contents, a practical detection limit of 0.01% walnut content was estimated. Practical applicability of the PCR method was tested by the analysis of 13 food samples (bakery and confectionery products), out of which two cakes were found to contain walnuts although they were not adequately labelled. The presented PCR method is useful for sensitive and selective detection of walnuts in food samples and can be performed in one working day.     

Quantitative competitive PCR for the detection of genetically modified soybean and maize

 The surveillance of food labelling concerning genetically modified organisms (GMOs) requires DNA-based analytical techniques. Present assay systems allow the detection of GMO in food; however, they do not permit their quantitation. In this study, we report the development of quantitative competitive polymerase chain reaction (QC-PCR) systems for the detection and quantitation of the Roundup Ready soybean (RRS) and the Maximizer maize (MM) in food samples. Three DNA fragments that differ from the GMO-specific sequences by an insertion were constructed and used as internal standards in the PCR. These standards were calibrated by co-amplifying with mixtures containing RRS DNA and MM DNA, respectively. The calibrated QC-PCR systems were applied to nine commercial food samples containing RRS DNA and to three certified RRS flour mixtures in order to elucidate whether these food samples contain more or less than 1% RRS DNA. Finally, the GMO contents of four samples that were found to contain more than 1% RRS were determined by QC-PCR using various amounts of standard DNA. Received: 13 January 1998 / Revised version: 4 March 1998     

Multiplex real-time PCR for the simultaneous detection and quantification of DNA from three transgenic rice species and construction and application of an artificial oligonucleotide as reference molecule

According to the EU and Swiss legislation for food, only approved traits of transgene plants are allowed to be imported and sold to the consumer. In order to control imports of rice and rice products from retailers, dealers and importing companies, efficient and reliable methods for the detection and quantification are a prerequisite. Therefore, a novel pentaplex real-time polymerase chain reaction system was developed and validated for the quantitative determination of three genetically modified rice lines at once. This system simultaneously determines DNA contents of the phospholipase-gen, a rice species specific gene, the 35S:BAR-construct, as the promotor of different transgene rice lines and the specific systems for LL62, LL601 and Bt-63-rice (Shanyou63). The test exhibits a good specificity and sensitivity for the transgenes in the range of 0.01–1%. It proved its efficiency and reliability in daily routine. Due to the lack of appropriate reference material for the Bt-63-rice, a reference oligonucleotide was artificially constructed. This oligonucleotide proved its applicability in diagnostic analysis.     

A novel multiplex PCR assay for rapid and simultaneous detection of five pathogenic bacteria: Escherichia coli O157:H7, Salmonella, Staphylococcus aureus, Listeria monocytogenes, and Vibrio parahaemolyticus

Rapid and sensitive detection techniques for foodborne pathogens are important to the food industry. However, traditional detection methods rely on bacterial culture in combination with biochemical tests, a process that typically takes 4 to 7 days to complete. Thus, this study was conducted to address the issue of time lag inherent in traditional methods by developing a novel PCR assay for each of five foodborne pathogenic bacteria. This new system consists of a simultaneous screening method using multiplex PCR in a single reaction tube for the rapid and sensitive detection of each of the five bacteria. Specific primers for multiplex PCR amplification of the Shiga-like toxin (verotoxin type II), femA (cytoplasmic protein), toxR (transmembrane DNA binding protein), iap (invasive associative protein), and invA (invasion protein A) genes were designed to allow simultaneous detection of Escherichia coli O157:H7, Staphylococcus aureus, Vibrio parahaemolyticus, Listeria monocytogenes, and Salmonella, respectively. To confirm the specificity of each primer pair for the respective target gene, three types of experiments were carried out using boiled cell lysates and their DNAs. In the multiplex PCR with mixed DNA samples, specific bands for corresponding genes were simultaneously detected from a single reaction. The detection of all five foodborne pathogenic bacteria could be completed in less than 24 h with this novel PCR method.     

Evaluation of TaqMan PCR assay for detecting Salmonella in raw meat and shrimp.

We evaluated the TaqMan Salmonella amplification/detection kit from PE Applied Biosystems, which uses a polymerase chain reaction (PCR) assay for rapid detection of Salmonella in food samples. This system uses the 5' nuclease activity of Taq DNA polymerase, which digests an internal fluorogenic probe to monitor the amplification of the target gene. The system's sensitivity and specificity were evaluated using 42 serotypes of 68 Salmonella strains isolated from fecal samples from patients in Tokyo, Japan, and 39 non-Salmonella strains in 22 genera. There were no false-negative or false-positive results. This PCR assay can detect 3 CFU per PCR tube of Salmonella in pure culture (120 CFU/ml of TSB culture). PCR signals were attenuated with artificially contaminated shrimp, but a similar detection limit was obtained. TaqMan's performance was tested with 100 meat and chicken samples purchased from stores in Tokyo. Overall, two of the DNA extraction protocols (the Chelex and EnviroAmp methods) worked equally well, with some exceptions. Of the 100 samples analyzed, 10 were positive for Salmonella with both conventional culture methods and the kit and 89 were negative with both. One sample was negative by the culture method but positive by the kit assay. These results indicate that TaqMan is a reliable and rapid method for Salmonella analysis in the food industry. With this system, food samples can be analyzed for Salmonella in less than 20 h.     

Evaluation of a polymerase chain reaction-based test for detecting Salmonella spp. in food samples: Probelia Salmonella spp

A commercially available polymerase chain reaction (PCR) kit was evaluated for the detection of Salmonella spp. in food samples. The test combines PCR amplification and sandwich hybridization of the amplified DNA in microtiter plates. The sensitivity and specificity was evaluated with 52 Salmonella strains and 51 non-Salmonella strains and showed that the test was entirely reliable. The threshold sensitivity was 10(2) CFU/ml. The limit of detection of dead cells that determines the minimum detection level of dead cells in food samples was superior to 10(6) CFU/25 g, a level rarely achieved in naturally contaminated samples. After an 18-h pre-enrichment step, the test could detect viable Salmonella in artificially contaminated food samples, even for the lower contamination level (3 CFU/25 g). There was complete agreement between the PCR test and the ISO 6579 bacteriological reference method with artificially contaminated samples. Regarding the accuracy of the results obtained from 253 naturally or noncontaminated foods and from 32 artificially contaminated foods, the agreement percentage was 99.6%. The fidelity of the technique was evaluated in a collaborative study with eight European laboratories and showed a correlation of 98.4%.     

Incidence and polymerase chain reaction assay of Listeria monocytogenes from raw milk in Gyeongnam Province of Korea.

A total of 50 raw milk samples from Gyeongnam Province of Korea were examined for the incidence of Listeria monocytogenes between July 1998 and August 1998. L. monocytogenes isolated by biochemical test was confirmed by polymerase chain reaction (PCR) with two sets of primers designed from the invasion-associated protein (iap) gene. After standard PCR with external primers, the amplified DNA was confirmed by a second round of PCR with internal primers (nested PCR). Both the external and internal primers generated 468-bp and 287-bp products. respectively. Only one (G9 strain) of the three suspect samples that tested positive in biochemical tests for L. monocytogenes from 50 raw milk samples was also PCR positive. Following this procedure. PCR-positive G9 strain was confirmed by Southern blot using the 287-bp internal iap probe again. The detection limit of G9 strain by standard PCR assay was as few as 102 cells, equivalent to approximately I pg of L. monocytogenes DNA. These PCR assays may be useful for novel detection as well as rapid confirmation for L. monocytogenes from food samples and the field.     

Quantitative real‐time PCR assays to detect DNA degradation in soy‐based food products

BACKGROUND: Polymerase chain reaction (PCR)‐based DNA diagnostics have grown in importance for assessing food quality and safety. PCR diagnostic reliability and sensitivity depend on the quality of the DNA extractions, including the extent of DNA degradation and the presence of PCR inhibitors. RESULTS: An approach has been described that quantifies the extent of DNA degradation in soy food samples using anchored real‐time PCR (qPCR) assays that amplify target sequences ranging from < 100 to > 1000 bp, based on two endogenous soy sequences. DNA degradation was quantified for model foods produced in the laboratory (cooked soy meal, tofu) as well as purchased soy‐containing food products. Considerably less than 1% of the total DNA extracted from samples was available for amplification of the longest amplicons (830 and 1022 bp) from the most highly processed food products (e.g., soy‐based infant formula). CONCLUSION: The utility of anchored qPCR assays was demonstrated for characterizing the amount of DNA that is available for amplifying different‐length PCR products from a range of soy‐containing processed food products. This approach should be useful for estimating the amount of amplifiable DNA in food ingredients in cases where food processing has caused degradation of DNA. Copyright © 2009 Society of Chemical Industry     

珠江三角洲地区副溶血性弧菌遗传多样性和致病性相关研究

副溶血性弧菌(Vibiro parahaemolyticus)是一种常见的食源性致病菌,本文研究了珠江三角洲地区副溶血性弧菌的遗传多样性。从54株副溶血性弧菌出发,研究了它们的API20E生化反应、抗生素耐药性、O抗原血清型,进行了ERIC-PCR分子分型,并检测了两种毒力基因tdh和trh的分布。54株副溶血性弧菌可被分为6个生化反应类群,主要类群为Biochem-A;菌株对萘啶酮酸、环丙沙星、氯霉素均不耐药,而对氨苄青霉素耐药率最高,耐药率0.88;O抗原血清型分别为O1、O2、O3、O4、O5、O6、O8、O10、O11,O2为主要血清型,O3为临床主要血清型;ERIC-PCR分子分型将54株菌分成47个型别,ERIC-PCR图谱相似性大于0.80的类群有12个,没有明显的优势类群;有12株副溶血性弧菌为tdh阳性,阳性率为0.22,其中10株为临床来源菌株;有2株副溶血性弧菌为trh阳性,阳性率为0.04,均为食品分离株。珠三角地区食品和临床来源的副溶血性弧菌具有丰富的遗传多样性。     

Quantitative competitive (QC) PCR for quantification of porcine DNA

Many meat products nowadays may contain several species in different proportions. To protect consumers from fraud and misdeclarations, not only a qualitative but also a quantitative monitoring of ingredients of complex food products is necessary. DNA based techniques like the polymerase chain reaction (PCR) are widely used for identification of species but no answer to the proportional amount of a certain species could be given using current techniques. In this study we report the development and evaluation of a quantitative competitive polymerase chain reaction (QC-PCR) for detection and quantification of porcine DNA using a new porcine specific PCR system based on the growth hormone gene of sus scrofa. A DNA competitor differing by 30 bp in length from the porcine target sequence was constructed and used for PCR together with the target DNA. Specificity of the new primers was evaluated with DNA from cattle, sheep, chicken and turkey. The competitor concentration was adjusted to porcine DNA contents of 2 or 20% by coamplification of mixtures containing porcine and corresponding amounts of bovine DNA in defined ratios.     

A novel real-time polymerase chain reaction (PCR) method for the detection of hazelnuts in food

A real-time PCR (polymerase chain reaction)-based method for the detection of hazelnuts (nuts of Corylus avellana or C. maxima) in confectionery and bakery products is described. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with hazelnut-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the hsp1 gene encoding for a low molecular weight heat-shock protein. The method was positive for five hazelnut varieties approved in Slovakia and negative for all other tested plant materials used in food industry including peanuts, walnuts, almonds, pistachio nuts, cashews and chestnuts. The intrinsic detection limit of the method was 13 pg hazelnut DNA, which corresponds to approximately 27 genome equivalents (1C). Using a series of model pastry samples with defined hazelnut contents, a practical detection limit of 0.01% (w/w) hazelnut was determined. Practical applicability of the PCR method was tested by the analysis of 20 food samples (confectionery and bakery products) along with ELISA. For all of the food samples, identical results were obtained by both methods, which conformed to the labelling. The presented PCR method is useful for sensitive and selective detection of hazelnuts in food samples and can be performed in one working day.     

Methods for rapid separation and concentration of bacteria in food that bypass time-consuming cultural enrichment

The rapid detection of pathogenic organisms that cause foodborne illnesses is needed to insure food safety. Conventional methods for the detection of pathogens in foods are time-consuming and labor-intensive. New advanced rapid methods (i.e., polymerase chain reaction, DNA probes) are more sensitive and selective than conventional techniques, but many of these tests are inhibited by food components, rendering them dependent on slow cultural enrichment. The need for alternative methods that will rapidly separate and concentrate bacteria directly from food samples, thereby reducing the time required for these new rapid detection techniques, is evident. Separation and concentration methods extract target bacteria from interfering food components and/or concentrate bacteria to detectable levels. This review describes several methods used to separate and/or concentrate bacteria in food samples. Several methods discussed here, including centrifugation and immunomagnetic separation, have been successfully used, individually and in combination, to rapidly separate and/or concentrate bacteria from food samples in less time than is required for cultural enrichment.     

A novel real-time polymerase chain reaction method for the detection of pecan nuts in food

A real-time PCR-based method for the detection of the pecan (Carya illinoiensis) component in food is described. The method consists of DNA isolation by chaotropic solid phase extraction and the subsequent PCR with pecan-specific primers and a TaqMan fluorescent probe. The primers and the probe are targeted to the putative gene for allergenic vicilin-like seed storage protein of pecan. The method was positive for 10 pecan varieties and negative for all other tested plant materials used in food industry, including walnut. The intrinsic detection limit of the method was 1 pg pecan DNA which corresponds to 1.2 haploid genome copies. Using a series of model pastry samples with defined pecan contents, a practical detection limit of 0.01% (w/w) pecan was estimated. Practical applicability of the PCR method was tested by the analysis of 13 food samples; no discrepancies between the declared and detected pecan contents were found. The presented PCR method is useful for sensitive and selective detection of pecans in food samples and can be performed in one working day.     

Differentiation of animal species in food by oligonucleotide microarray hybridization

Oligonucleotide microarray hybridization analysis of polymerase chain reaction (PCR) products from the mitochondrial cytochrome b gene DNA was applied to identify different animal species in meat and cheese food samples. A pair of universal primers binding to conserved regions of the vertebrate mitochondrial cytochrome b gene was used to amplify a 377 bp fragment with internal regions of high inter-species variability. PCR products of cattle, pig, chicken, turkey, sheep and goat were unequivocally identified by hybridization with species-specific probe sequences immobilized on an oligonucleotide microarray. In meat samples, 0.1% admixtures of beef or chicken meat were still detectable. By using this new PCR-based DNA chip hybridization for the analysis of 24 commercial food samples from routine control, the simultaneous species composition of mixtures with up to four different species could be determined in a single experiment. The results agreed well with those from the reference methods performed at the local food control authority, which are a combination of enzyme-linked immunosorbent assay (ELISA), species-specific PCR and PCR–RFLP (restriction fragment length polymorphism). Thus, the DNA chip hybridization analysis of cytochrome b PCR products offers a new way for rapid and sensitive species differentiation in food.     

PCR方法快速鉴别食品中肉的种类

本文针对食品中肉成分种类鉴别开发了一种快速灵敏的PCR检测方法,可检测食品中是否存在猪肉、牛肉、羊肉以及鸡肉等成分。采用微波助提法提取样品中DNA,简化了前处理步骤,可在短时间内完成从多种不同类型肉与肉制品中提取肉成分DNA。为了评价方法的可靠性与灵敏度,猪肉以及掺入了不同比例浓度猪肉成分的食品样品采用本方法进行了核酸提取与PCR分析。检测结果表明,方法可检测出低至含有0.5%浓度的猪肉成分的混合样品。随机抽取50份不同类型的市面食品样品,检测出5份食品含有猪肉成分,7份食品中含有牛肉成分,5份食品中含有羊肉成分。该样品前处理方法、DNA提取方法以及PCR检测方法可广泛应用于食品中肉成分种类的检测鉴别。     

Detection of genetically modified soybean DNA in refined vegetable oils

In this study, four different protocols were tested for their ability to extract DNA from blended refined vegetable oils: the in-house prepared Wizard and CTAB methods and the methods based on the use of the commercial kits Wizard^® Magnetic DNA purification system for food and Nucleospin^® for food. The performance of the extraction protocols was determined by end-point polymerase chain reaction (PCR) targeting the soybean lectin gene with primers suitable for the amplification of small fragments and confirmed by real-time PCR with specific hydrolysis probes. From the tested protocols, the Nucleospin method was the only one able to produce amplifiable DNA from refined vegetable oils. To verify the presence of Roundup Ready^® (RR) soybean, event-specific primers were used for end-point PCR assays. The amplification of trace amounts of RR soybean by real-time PCR confirmed the label statements of two samples. The results highlight the importance of the DNA extraction protocol and the critical choice of PCR primers on processed food matrices, such as refined oils. Considering the few reports and difficulties pointed out in the literature to obtain amplifiable DNA from refined vegetable oils, the present results can be a step forward in the traceability of refined oils regarding authenticity issues and genetically modified organism detection.     

鱼翅类食品中鲨鱼成分PCR鉴定方法研究

本文针对鱼翅中的鲨鱼成分进行检测鉴定开发了一种快速灵敏的PCR检测方法,可检测鱼翅类食品中是否存在鲨鱼成分。根据鲨鱼线粒体的细胞色素亚基I基因序列设计了鲨鱼特异性引物,扩增长度为228 bp;为了评价方法的特异性,将设计的引物分别针对22份鱼翅样品DNA和37种其它种类DNA进行PCR检测,结果显示,只在鲨鱼鱼翅中能检测出特异的228 bp条带,其它37种物种中均无条带检出。为了评价方法的灵敏度,将鱼翅DNA中掺入了不同比例土豆DNA的样品采用本方法进行了PCR分析,显示方法可检测灵敏度为0.1%(m/m)。随机抽取45份不同类型的鱼翅样品,检测出22份鲨鱼翅均含鲨鱼成分,而21份仿鱼翅均不含鲨鱼成分而含有植物成分。该样品前处理方法、DNA提取方法以及PCR检测方法可广泛应用于食品中鲨鱼成分检测鉴定。     

Collaborative Study of a T-nos Real-Time PCR Method for Screening of Genetically Modified Organisms in Food Products

In the EU the presence of genetically modified organisms (GMO) in food is controlled by the Member States official laboratories within their national inspection and monitoring programs. The most frequently used approach to detect the presence of GMO material in different food matrices is the PCR-based screening for the CaMV 35S promoter and the nos terminator (T-nos) DNA sequence from Agrobacterium tumefaciens. A real-time PCR method for detection of T-nos and its validation in a collaborative trial study is described in this paper. The PCR system amplifies a 84 bp fragment and showed to be sensitive to detect at least 5 copies of the T-nos DNA sequence. The assay was adapted for use in real-time PCR instruments using plastic reaction vials and glass capillaries, respectively. A total of 24 laboratories participated in the study and each laboratory received 18 DNA blind samples prepared from GMO certified reference materials (0.1 % and 0.5 % NK601 maize) and from a non-GM maize flour. All samples containing NK603 maize DNA were correctly classified as T-nos positive by the participating laboratories. For the blank samples (0 % GMO) only three false-positive results were reported. A detailed evaluation of the results of the collaborative trial study is described. Received: March 19, 2007     

Collaborative Study of a T-nos Real-Time PCR Method for Screening of Genetically Modified Organisms in Food Products

In the EU the presence of genetically modified organisms (GMO) in food is controlled by the Member States official laboratories within their national inspection and monitoring programs. The most frequently used approach to detect the presence of GMO material in different food matrices is the PCR-based screening for the CaMV 35S promoter and the nos terminator (T-nos) DNA sequence from Agrobacterium tumefaciens. A real-time PCR method for detection of T-nos and its validation in a collaborative trial study is described in this paper. The PCR system amplifies a 84 bp fragment and showed to be sensitive to detect at least 5 copies of the T-nos DNA sequence. The assay was adapted for use in real-time PCR instruments using plastic reaction vials and glass capillaries, respectively. A total of 24 laboratories participated in the study and each laboratory received 18 DNA blind samples prepared from GMO certified reference materials (0.1 % and 0.5 % NK601 maize) and from a non-GM maize flour. All samples containing NK603 maize DNA were correctly classified as T-nos positive by the participating laboratories. For the blank samples (0 % GMO) only three false-positive results were reported. A detailed evaluation of the results of the collaborative trial study is described.