Development of sensitive and specific multiplex PCR method for the detection of microcystin producing cyanobacteria in spirulina food supplements

Food Science and Biotechnology - Spirulina has emerged as the next-generation dietary supplement owing to its health benefits. Despite the advantages, there have been reports of contamination by...     

A highly sensitive real-time PCR system for quantification of wheat contamination in gluten-free food for celiac patients

A quantitative real-time PCR system (Q-PCR) for the detection and quantification of wheat DNA in food for celiacs has been developed and optimised. The DNA was extracted with a new procedure, based on the SDS/Guanidine–HCl/Proteinase K method, but faster, with a higher yield and enough purity to avoid an additional purification step. This is the first report that compares the information provided by a Q-PCR technique with the prolamin levels determined with the most frequently used commercially available ELISA, based on the R5 monoclonal antibody. With the exception of some hydrolysed and highly processed food samples (such as beers, syrups, malt extracts, breakfast cereals…), the rest of the food with prolamin levels above the R5 ELISA quantification limit (1.5 mg/kg) have given positive signals with the Q-PCR system. Moreover, some food samples with prolamin levels below 1.5 mg/kg have also given positive signals with the Q-PCR system, indicating a better sensitivity of the DNA technique. Therefore, the developed Q-PCR system can be used as a non-immunological tool in order to confirm, by the “DNA pathway”, the presence of wheat in food not only for celiacs but also for individuals with wheat allergy.     

Development and applications of real-time PCR standards for GMO quantification based on tandem-marker plasmids

The need to comply with mandatory thresholds introduced for the labeling of GM food and feed by recent European Regulations is increasing the interest for reliable standards for GMO quantification. Certified reference materials (CRMs) for the different GMO lines are an essential element to calibrate measurement systems adopted to quantify GM ingredients. Unfortunately, conventional CRMs are affected not only by their high production costs but also by time consuming production and certification procedures. At the moment CRMs are available only for few of the GMOs authorized in Europe. In addition, latest developments in European legislation makes conceivable that the number of different authorized GM lines to be analysed will increase significantly, raising the need for additional CRMs. In the field of GMO detection and quantification, plasmids have been demonstrated to represent a cheap and reliable alternative to conventional CRMs. Here we describe the production of tandem-marker plasmids containing simultaneously specific target sequences for the GMO of interest and a species-specific reference marker sequence in a 1:1 ratio have been developed and used as real-time PCR standards. Strengths and weaknesses of these novel standards are discussed in detail.E. Mattarucchi and F. Weighardt: first authors     

Comparison of gene nature used in real-time PCR for porcine identification and quantification: A review

Pork adulteration has been a major concern nowadays for Halal verification. Unintentional pork inclusion by contamination in highly processed food materials involves a minute amount of porcine DNA to be detected, emphasizing the need of specific and sensitive method for porcine detection. Real-time PCR is a widely used technique for species identification that can serve this purpose besides providing a powerful quantification method. Incorporation of a highly sensitive and specific probe can greatly improve the specificity and sensitivity of the assay. However, derivation of PCR primers, either from nuclear DNA (nDNA) or mitochondrial DNA (mtDNA) can relatively affect the sensitivity and specificity of the reaction as well as the quantitative measurement. In this review, both types of DNA are compared in terms of their characteristics and their influence on species identification and quantification using real-time PCR.     

Detection and quantification of Aspergillus westerdijkiae in coffee beans based on selective amplification of beta-tubulin gene by using real-time PCR

Aspergillus westerdijkiae is a new species of fungus that was recently dismembered from Aspergillus ochraceus taxon. Most isolates of A. westerdijkiae are able to produce large amounts of a mycotoxin called ochratoxin A (OA). OA has been found in food and beverages, such as coffee. A. westerdijkiae is very similar to A. ochraceus, and several isolates previously identified as A. ochraceus are now identified as A. westerdijkiae. By using sequences of the beta-tubulin gene, we analyzed several isolates from Brazilian coffee bean samples, previously identified as A. ochraceus, to compare with those of A. westerdijkiae. In fact, most (84%) were identified as A. westerdijkiae. Since this species consistently produces large amounts of OA, we developed a specific primer-pair for detecting and quantifying it in coffee beans by using real-time PCR. The primers Bt2Aw-F 5'TGATACCTTGGCGCTTGTGACG and Bt2Aw-R 5'CGGAAGCCTAAAAAATGAAGAG provided an amplicon of 347 bp in all A. westerdijkiae isolates, and no cross-reaction was observed using DNA from A. ochraceus. The sensitivity of real-time PCR was more than 100 times higher than the cfu technique.     

Targeting a polyketide synthase gene for Aspergillus carbonarius quantification and ochratoxin A assessment in grapes using real-time PCR

Aspergillus carbonarius is an ochratoxin producing fungus that has been considered to be responsible of the ochratoxin A (OTA) contamination in grapes and wine. In order to monitor and quantify A. carbonarius, a specific primer pair Ac12RL_OTAF/Ac12RL_OTAR has been designed from the acyltransferase (AT) domain of the polyketide synthase sequence Ac12RL3 to amplify 141 bp PCR product. Among the mycotoxigenic fungi tested, only A. carbonarius gave a positive result. This specific primer pair was also successfully employed in real-time PCR conjugated with SYBR Green I dye for the direct quantification of this fungus in grape samples. A positive correlation (R(2)=0.81) was found between A. carbonarius DNA content and OTA concentration in 72 grape samples, allowing for the estimation of the potential risk from OTA contamination. Consequently, this work offers a quick alternative to conventional methods of OTA quantification and mycological detection and quantification of A. carbonarius in grapes.     

阪崎肠杆菌zpx基因的分子信标一实时PCR技术研究

目的建立分子信标-实时PCR技术检测婴幼儿乳粉中阪崎肠杆菌的快速方法。方法在PCR反应体系中加入分子信标探针,探针的5’端标记FAM,3’端标记TAMRA,建立阪崎肠杆菌zpx基因分子信标-实时PCR技术快速检测方法。结果检测方法特异性强,无非特异性扩增;分子信标-实时PCR反应体系DNA灵敏度为180fg/PCR反应体系,纯阪崎肠杆菌菌液的检出限为102 CFU/ml,无交叉反应;以此反应体系检测23份样品,其中2份为阳性,余未检出,与传统检测方法结果一致。结论分子信标-实时PCR检测体系快速、灵敏度高、特异性强,可用于婴幼儿乳粉中阪崎肠杆菌的快速检测。     

基于内参系统的阪崎肠杆菌实时荧光定量PCR检测方法的建立

根据阪崎肠杆菌ompA靶基因设计特异性引物和探针,并加入内参(IAC),建立能够实时监控反应过程的荧光定量PCR检测方法。结果表明,该方法对阪崎肠杆菌基因组DNA的最低检测限为1pg;对细菌的最低检测限为1×10~4 CFU;对含有靶基因质粒的最低检测限为10~3拷贝;Ct值与模板拷贝数均呈良好的线性关系(R~2=0.999)。人工污染试验结果表明,在初始菌量为10CFU/25g奶粉样品时,采用水洗加试剂盒法和水煮法提取DNA,阪崎肠杆菌均在增菌10h时检出。研究结果为进一步优化和完善阪崎肠杆菌分子生物学方法的标准化提供了参考。     

A novel poisson distribution-based approach for testing boundaries of real-time PCR assays for food pathogen quantification

The validation of quantitative real-time PCR systems and above all, proof of the detection limit of this method, is a frequently and intensively discussed topic in food pathogen detection. Among proper sample collection, assay design, careful experimental design, execution of real-time PCR, and data analysis, the validation of the method per se ensuring reliable quantification data is of prime importance. The purpose of this study was to evaluate a novel validation tool for real-time PCR assays, based on the theoretical possibility of the amplification of a single DNA target. The underlying mathematical basis for the work is Poisson distribution, which describes patterns of low particle numbers in a volume. In this context, we focused on the quantitative aspect of real-time PCR for the first time. This allowed for demonstration of the reliable amplification of a lone target DNA molecule and the demonstration of the distinct discrimination between integer molecular numbers when using low initial copy numbers. A real-time PCR assay amplifying a 274-bp fragment of the positive regulatory protein A locus of Listeria monocytogenes was used for this work. Evidence for a linear range of quantification from a single target copy to 10 ng of target DNA was experimentally demonstrated, and evidence for the significance of this novel validation approach is presented here.     

A simulation approach to assess the minimal number of real-time PCR replicates for GM quantification

The quantification of genetically modified (GM) ingredients in food and feed typically uses real-time quantitative PCR (RT-QPCR). In recent years a multitude of new RT-QPCR assays have facilitated increased method performance. The level of sample replication within these assays is a fundamental aspect that needs to be considered to produce results with high confidence. In this paper we describe the use of a modelling approach as applied to GM and RT-QPCR data sets, to objectively assesses the effect of different levels of PCR replication in terms of the variability associated with a result, and demonstrate that it is possible to use a reduced level of replication without a subsequent reduction in the confidence of a result. Using an example data set, we show it is possible to reduce the sample level of replication from six to three PCR replicates, without a significant change in the mean value of the result. The use of such an approach can facilitate the use of the minimum number of replicates in order to produce an accurate result, thus saving on important resources involved in quantification assays.     

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.     

Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines interlaboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention was placed on the influence of the DNA isolation step and effect of simplex and multiplex amplification approaches on interlaboratory variability. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol.     

Food matrix standards for the quantification of allergenic food ingredients using real-time PCR

For the quantification of food allergens by real-time polymerase chain reaction (PCR), food matrix standards with defined levels of spiked allergenic food ingredients can be used. The production and homogeneity testing of selected materials as sausages, cookies and sauce hollandaise powder is described. Except for egg and milk, all relevant allergenic ingredients were spiked to each material. Allergens were spiked and quantified as food ingredients, for example, peanut or lupine flour, at levels of 5–400 mg/kg. Material with sufficient homogeneity could be produced even at low levels of 5–10 mg of the allergenic ingredient per kilogram. The effect of the food matrix on allergen quantification was checked. The bias caused by this effect was in an acceptable range for the tested materials. The materials produced within this study were used as samples and for calibration in inter-laboratory validation studies for the quantification of allergenic food ingredients by real-time PCR. The results of this study are a contribution how to produce such reference materials for allergen analysis in the near future. Before threshold or action values of allergens in food are set, the availability of reference materials is essential.     

Identification of meat species by TaqMan-based real-time PCR assay

In this study, a convenient, sensitive and specific real-time PCR assay was described for the species identification and their quantification in raw and cooked meat products. Specific primers and TaqMan probes were designed on the mitochondrial ND2, ND5 and ATP 6-8 genes for donkey, pork and horse, respectively, and the performance of the method was tested. In the results, no cross-reaction was observed between the donkey and pork species specific primer-probe systems and non-target species (bovine, ovine, chicken and turkey). Only one cross reaction was observed between the horse species specific primer-probe set and 100 ng pork DNA at the ct 33.01 level (corresponding to 0.01 ng horse DNA). The real-time quantitative assay used in this study allowed the detection of as little as 0.0001 ng template DNA from pure meat for each species investigated and experimental meat mixtures. In conclusion, it can be suggested that the TaqMan probe assay used in this research might be a rapid and sensitive method for the routine meat species identifications studies in raw or cooked meat products.     

应用多重实时荧光PCR检测蜡样芽胞杆菌毒力基因

目的:建立一种快速、准确、简便的蜡样芽胞杆菌毒力基因检测方法,为蜡样芽胞杆菌更深入的研究提供依据和便利。方法:采用TaqMan探针法设计了三重hblA,hblC,hblD基因,三重nheA,nheB,nheC基因,三重ces,entFM,bceT基因的多重实时荧光PCR体系检测蜡样芽胞杆菌毒力基因。结果:多重体系对蜡样芽胞杆菌毒力基因的检测具有良好的特异性和灵敏性,其最低检出限为63 CFU/mL。结论:利用上述体系对蜡样芽胞杆菌的毒力基因进行检测能够省时省力,特异性、灵敏性良好,具有实际应用价值。     

Development of a real-time PCR assay for detection and quantification of enterotoxigenic members of Bacillus cereus group in food samples

A highly sensitive real-time PCR (qPCR) procedure, targeting the phosphatidylcholine-specific phospholipase C gene (pc-plc), was developed for specific detection and quantification of strains belonging to Bacillus cereus group. The target region was selected based on the enterotoxigenic profiles of 75 Bacillus strains. The inclusivity and exclusivity of the RTi-PCR assay were assessed with 59 isolates of the B. cereus group, 16 other Bacillus spp., and 4 non-Bacillus strains. The assay was also used to construct calibration curves for different food matrices, and it had a wide quantification range of 6 log units using both serial dilutions of purified DNA and calibrated cell suspensions of B. cereus CECT 148^T. The detection limit for B. cereus in artificially contaminated liquid egg and reconstituted infant formula was about 3 CFU per reaction or 60 CFU/ml of food, with a relative accuracy of 86.27% to 116.12% in artificially contaminated liquid egg. Naturally contaminated food samples were tested for the presence of B. cereus with the standard method, a conventional PCR and the new developed RTi-PCR assay. Results showed that the new developed RTi-PCR assay is very suitable for detection and quantification of strains of B. cereus group in food samples without an enrichment step.     

荧光定量PCR法计数农家干酪中动物双歧杆菌乳酸亚种

分别利用荧光定量PCR及平板菌落计数法计数农家干酪中双歧杆菌的菌体数,通过对结果的比较分析,建立一种适用于快速、敏感、特异的检测干酪中双歧杆菌活菌数的方法。利用传统工艺制备双歧杆菌农家干酪,在其贮存期间分别采用荧光定量PCR及平板菌落计数法计数干酪中双歧杆菌的数量。其中,在利用荧光定量PCR法检测时,对影响PCR定量准确的因素进行系统研究,包括设计双歧杆菌引物,并对引物特异性进行评价、考察,从干酪基质中提取DNA的数量和质量,建立标准曲线。引物特异性验证结果表明,引物专一性强。采用试剂盒法从干酪样品中提取DNA的纯度较好,OD_(260)/OD_(280)均在1.75~1.82之间。除贮存第1天外,荧光定量PCR法计数结果比平板计数法高0.39%~2.25%,未见显著差异。荧光定量PCR具有灵敏、特异、简便和快速的特点,可用于干酪中双歧杆菌的定量检测。     

基于实时荧光PCR对肉制品中羊肉的精确定量

该研究将实时荧光定量PCR技术(real-time fluorescence quantitative PCR,r PCR)与微滴式数字PCR技术(micro-droplet digital PCR,dd PCR)相结合,利用dd PCR建立拷贝数和羊肉质量的函数关系,确立了基于r PCR定量检测羊肉含量的方法。特异性实验结果表明,除绵羊和山羊外,非目标物种DNA未出现特异性扩增;灵敏度实验结果表明,该方法的最低检出限为0. 01 ng/μL;通过对已知成分的混合样品和市售样品的检测表明,该方法能够对含量在5%以上的羊肉进行准确定量。因此,该方法在肉制品中羊肉含量检测和掺假鉴别方面具有较好应用潜力。     

Rapid, specific, and sensitive detection of spoilage molds in orange juice using a real-time Taqman PCR assay

The outgrowth of spoilage organisms, including molds and yeasts, results in significant financial loss to the food industry and wastes natural resources. The objective of this study was to develop a rapid, specific, and sensitive real-time PCR method for detecting spoilage molds during screening of raw materials and final product quality control analysis. The 18S rRNA gene was used to develop PCR primers and probe. With this set of primers and probe, less than 1,000 mold cells per milliliter of orange juice (10 cells per reaction) were detected with the real-time PCR system within 6 to 7 h. No cross-reactivity was found with other common foodborne bacteria, yeasts, or food ingredients. This technique is significantly faster than current detection and identification procedures, which take from days to weeks.     

First ring-trial validation of real-time PCR methods for the quantification of allergenic food ingredients

The first interlaboratory validation of two food allergen quantification methods using real-time PCR is described. Methods for the specific detection and quantification of soybean and white mustard in boiled sausages were used. Matrix-based calibrants spiked with defined amounts of soybean and white mustard were applied for quantitative evaluation. The lowest spike level of 10?mg soybean and white mustard per kilogram could reproducibly be detected. Recovery in spiked sausages was between 82 and 99?% for soy and between 80 and 93?% for mustard. Reproducibility standard deviation was in the range that would be acceptable, for example, for quantitative GMO analytical methods (<35?%).