Simultaneous and sensitive detection of three foodborne pathogens by multiplex PCR, capillary gel electrophoresis, and laser-induced fluorescence

The simultaneous detection of Staphylococcus aureus, Listeria monocytogenes, and Salmonella spp. has been approached by a new multiplex PCR-based procedure followed by capillary gel electrophoresis with laser-induced fluorescence detection (multiplex-PCR-CGE-LIF). As compared to slab gel electrophoresis, the use of CGE-LIF improved from 10- to 1000-fold the sensitivity of the multiplex PCR analysis, allowing the detection of 2.6 x 10(3) cfu mL(-1) of S. aureus, 570 cfu mL(-1) of L. monocytogenes, and 790 cfu mL(-1) of Salmonella in artificially inoculated food, without enrichment. Following 6 h of enrichment, as low as 260, 79, and 57 cfu mL(-1) of S. aureus, L. monocytogenes, and Salmonella, respectively, were detected. The CGE-LIF method is shown to be reproducible, providing relative standard deviation (RSD) values lower than 0.8% for analysis time and lower than 5.8% for peak areas. The multiplex-PCR-CGE-LIF proved a powerful analytical tool to detect various food pathogens simultaneously in a fast, reproducible, and sensitive way.     

Simultaneous confirmatory analysis of different transgenic maize (zea mays) lines using multiplex polymerase chain reaction-restriction analysis and capillary gel electrophoresis with laser induced fluorescence detection

A novel analytical procedure based on the combination of multiplex PCR, restriction analysis, and CGE-LIF to unambiguosly and simultaneously confirm the presence of multiple lines of genetically modified corn is proposed. This methodology is based on the amplification of event-specific DNA regions by multiplex PCR using 6-FAM-labeled primers. Subsequently, PCR products are digested by a mixture containing specific restriction endonucleases. Thus, restriction endonucleases selectively recognize DNA target sequences contained in the PCR products and cleave the double-stranded DNA at a given cleavage site. Next, the restriction digest is analyzed by CGE-LIF corroborating the length of the expected restriction fragments, confirming (or not) the existence of GMOs. For accurate size determination of the DNA fragments by CGE-LIF a special standard DNA mixture was produced in this laboratory for calibration. The suitability of this mixture for size determination of labeled DNA fragments is also demonstrated. The usefulness of the proposed methodology is demonstrated through the simultaneous detection and confirmatory analysis of samples containing 0.5% of GA21 and MON863 maize plus an endogenous gene of maize as control.     

Detection of genetically modified maize by the polymerase chain reaction and capillary gel electrophoresis with UV detection and laser-induced fluorescence

In this paper, the possibilities of capillary gel electrophoresis (CGE) to detect transgenic maize in flours are shown. The method is based on the extraction and amplification by the polymerase chain reaction (PCR) of a specific DNA fragment from transgenic maize and its subsequent analysis by CGE with UV detection or laser-induced fluorescence (LIF). Some useful considerations regarding the optimization of DNA extraction and amplification conditions are given. Also, a comparison is established between the two CGE protocols for DNA detection based on ultraviolet absorption (CGE-UV) and LIF (CGE-LIF). The requirements, advantages, and limitations of both CGE methods are discussed. To our knowledge, this is the first paper on the use of CGE-LIF to detect transgenic food.     

Interlaboratory transfer of a PCR multiplex method for simultaneous detection of four genetically modified maize lines: Bt11, MON810, T25, and GA21

The number of cultured hectares and commercialized genetically modified organisms (GMOs) has increased exponentially in the past 9 years. Governments in many countries have established a policy of labeling all food and feed containing or produced by GMOs. Consequently, versatile, laboratory-transferable GMO detection methods are in increasing demand. Here, we describe a qualitative PCR-based multiplex method for simultaneous detection and identification of four genetically modified maize lines: Bt11, MON810, T25, and GA21. The described system is based on the use of five primers directed to specific sequences in these insertion events. Primers were used in a single optimized multiplex PCR reaction, and sequences of the amplified fragments are reported. The assay allows amplification of the MON810 event from the 35S promoter to the hsp intron yielding a 468 bp amplicon. Amplification of the Bt11 and T25 events from the 35S promoter to the PAT gene yielded two different amplicons of 280 and 177 bp, respectively, whereas amplification of the 5' flanking region of the GA21 gave rise to an amplicon of 72 bp. These fragments are clearly distinguishable in agarose gels and have been reproduced successfully in a different laboratory. Hence, the proposed method comprises a rapid, simple, reliable, and sensitive (down to 0.05%) PCR-based assay, suitable for detection of these four GM maize lines in a single reaction.     

Identification of goose,mule duck,chicken, turkey,and swine in foie gras by species-specific polymerase chain reaction

A specific Polymerase Chain Reaction (PCR) has been developed for the identification of goose (Anser anser), mule duck (Anas platyrhynchos x Cairina moschata), chicken (Gallus gallus), turkey (Meleagris gallopavo), and swine (Sus scrofa domesticus) in foie gras. A forward common primer was designed on a conserved DNA sequence in the mitochondrial 12S ribosomal RNA gene (rRNA), and reverse primers were designed to hybridize on species-specific DNA sequences of each species considered. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose, mule duck, chicken, turkey, and swine in foie gras. Analysis of experimental mixtures demonstrated that the detection limit of the assay was approximately 1% for each species analyzed. This genetic marker can be very useful for the accurate identification of these species, avoiding mislabeling or fraudulent species substitution in foie gras.     

不同细菌饲喂细菌线虫对土壤细菌数量、活性以及群落结构的影响

The effects of bacterial-feeding nematodes on bacterial number, activity, and community composition were studied through a microcosm experiment using sterilized soil inoculated with soil bacteria （soil suspension） and with bacteria and three species of bacterial-feeding nematodes （ Cephalobus persegnis, Protorhabditis filiformis, and Caenorhabditis elegans）. Catalyzed reporter deposition-fluorescence in situ hybridization, CO2 evolution, and denaturing gradient gel electrophoresis （DGGE） of PCR ampli- fied 16S rRNA gene fragments were used to investigate bacterial numbers, antivity, and community composition, respectively. Our results showed that bacterial numbers and activity significantly increased in the presence of bacterial-feeding nematodes, which indicated that bacterial-feeding nematodes had a significant positive effect on soil bacteria. The different nematode species had different effects on bacterial numbers and activity. C. persegnis and P. filiformis, isolated from native soil, increased the bacterial number and activity more than C. elegans. The DGGE analysis results showed that dominant bacterial species significantly differed among the treatments, which suggested that bacterial-feeding nematode species modified the bacterial community composition in soil. Further gene sequence analysis results showed that the dominant bacterial species in this study were gram-negative bacteria. Given the completely same conditions except nematode species, the varied selective feeding behavior of different nematode species was the most likely reason for the altered bacterial community composition. Overall, the alteration of bacterial numbers, activity and community composition resulting from the bacterial-feeding nematodes may ult!mately affect soil ecological functioning and processes.     

Identification of goose (Anser anser) and mule duck (Anasplatyrhynchos x Cairina moschata) foie gras by multiplex polymerase chain reaction amplification of the 5S RDNA gene.

Polymerase chain reaction (PCR) amplification of the nuclear 5S rDNA gene has been used for the identification of goose and mule duck foie gras. Two species-specific reverse primers were designed and used in a multiplex reaction, together with a forward universal primer, to amplify specific fragments of the 5S rDNA in each species. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose and mule duck foie gras samples. This genetic marker can be useful for detecting fraudulent substitution of the duck liver for the more expensive goose liver.     

Analysis of polyphenols using capillary zone electrophoresis and HPLC: detection of soy, lupin, and pea protein in meat products

The analysis of polyphenols, which are characteristic of certain legumes, enables a rapid and sensitive detection of legume proteins in meat products. Separation of specific isoflavones can be achieved by capillary zone electrophoresis (CZE) or high-performance liquid chromatography (HPLC), both coupled with a photodiode array detector (DAD). The use of CZE in the identification process is an appropriate means of rapid screening; the HPLC is less dependent on matrix effects and clearly more sensitive. Additives of soy protein isolates up to 0.1% could be detected in meat products, even in sausages heated to a high temperature or with hydrolyzed soy proteins. A solid-phase extraction procedure with polyamide cartridges has been developed to concentrate polyphenols. A similar detection of lupin protein is possible in principle. In the case of pea protein, a reliable detection was not possible depending on the coincidental appearance of polyphenols as indicating substances.     

Multiplex PCR method for use in real-time PCR for identification of fish fillets from grouper (Epinephelus and Mycteroperca species) and common substitute species

Mitochondrial 16S rRNA sequences from morphological validated grouper (Epinephelus aeneus, E. caninus, E. costae, and E. marginatus; Mycteroperca fusca and M. rubra), Nile perch (Lates niloticus), and wreck fish (Polyprion americanus) were used to develop an analytical system for group diagnosis based on two alternative Polymerase Chain Reaction (PCR) approaches. The first includes conventional multiplex PCR in which electrophoretic migration of different sizes of bands allowed identification of the fish species. The second approach, involving real-time PCR, produced a single amplicon from each species that showed different Tm values allowing the fish groups to be directly identified. Real-time PCR allows the quick differential diagnosis of the three groups of species and high-throughput screening of multiple samples. Neither PCR system cross-reacted with DNA samples from 41 common marketed fish species, thus conforming to standards for species validation. The use of these two PCR-based methods makes it now possible to discriminate grouper from substitute fish species.     

Simultaneous detection of eight genetically modified maize lines using a combination of event- and construct-specific multiplex-PCR technique

To fulfill labeling and traceability requirement of genetically modified (GM) maize for trade and regulation, it is essential to develop an event-specific detection method for monitoring the presence of transgenes. In pursuit of this purpose, we systematically optimized and established a combined event- and construct-specific multiplex polymerase chain reaction (mPCR) technique for simultaneous detection of 8 GM maize lines. Altogether 9 sets of primers were designed, including six that were event-specific for Event176, Bt11, TC1507, NK603, MON863, and Mon810; two that were construct-specific for T25 and GA21, and one for an endogenous zein gene. The transgene in each GM maize line and the endogenous zein gene could be clearly detected and distinguished according to the different sizes of PCR amplicons. The limit of detection (LOD) was approximately 0.25% (v/v), although the detection can be as sensitive as 0.1% as demonstrated by the International Seed Testing Association (ISTA) proficiency test. This study further improves the current PCR-based detection method for GM maize. The method can be used in an easy, sensitive, and cost and time effective way for the identification and quality screening of a specific GM maize line.     

Detection of land animal remains in fish meals by the polymerase chain reaction-restriction fragment length polymorphism technique

In the present study a technique was developed with the aim of guaranteeing the composition and security of fish meals, since it allows verification of whether these meals contain land animal remains. The method is based on polymerase chain reaction (PCR) and length polymorphism, followed by a restriction fragment length polymorphism (RFLP). Specific primers for every species were designed and calibrated, generating exclusively a PCR product with a specific size when DNA for each species was present in the sample. This technique allows the detection of land animal remains in fish meals, specifically cow, chicken, pig, horse, sheep, and goat. The identity of the PCR products can be confirmed by RFLP analysis using only one restriction enzyme. The selected restrictase generated one characteristic restriction profile for every species included in this study. The detection limit of this method was calculated by using mixtures of fish meals in different proportions and meal that exclusively contained remains of one of these land species studied. The analytical strategy herein proposed was applied to fish and meat meals, giving good results, both in the analyzed standards and in commercial samples.     

来自海南等地的17个Bt分离株质粒多样性分析

本研究采用琼脂糖凝胶电泳对分离白海南岛的12个反菌株与分离自广西、黑龙江的5株＆菌株及2株胁模式菌株进行质粒数量、大小等特征分析。19个供试菌株可区分为16种独特的质粒电泳图谱,充分显示出不同来源肪菌株的质粒多样性。进一步选择了其中的10个菌株,利用包埋法制备琼脂块进行脉冲场凝胶电泳（PFGE）,结果表明苏云金芽孢杆菌大质粒组成特征也具有丰富多样性。但是供试菌株的质粒电泳图谱并未体现与地理和生态特征相关联的特征差异。研究结果初步证实海南分离株S3078—1是一株无内生质粒的助菌株,而S3031-1和S3073—1两个分离株仅有一个大质粒存在,这三个分离株将为进一步研究质粒功能提供初始菌株。本研究进一步暗示将琼脂糖凝胶电泳和脉冲场凝胶电泳结合起来研究质粒特征提高了结果的可靠性。     

Fast and efficient discrimination of the Isotoma viridis group (Insecta: Collembola) by PCR-RFLP

Identification of collembolan species is generally based on specific morphological characters, such as chaetotaxy and pigmentation pattern. However, some specimens do not match to described characters because these refer to adult specimens, often of one specific sex, or the characters are highly variable in adults (e.g. pigmentation, setae or furcal teeth). Isozymes have frequently assisted species discrimination, and also these may vary with developmental stage or environmental conditions. For identification of single species of the Isotoma viridis group, we present both direct sequencing of the cytochrome oxidase subunit II (COII) gene and a simple DNA-based molecular method.

Five PCR primers amplifying the COII region (717 bp) of the mitochondrial DNA were used. The sequences clearly separated the species I. viridis, I. riparia and I. anglicana, irrespective of colour varieties within the first species. DNA amplification products of different species can also be distinguished by digestion with restriction endonucleases, followed by gel electrophoresis for separation of fragments. This restriction fragment length polymorphism (RFLP), obtained after digestion with the endonucleases TaqI, VspI, MvaI and Bsp143I, revealed specific fragments that separated the three species from each other. Since restriction enzymes are sensitive to single base mutations, we suggest to use a combination of enzymes with at least two species-specific restriction sites when using the RFLP technique. For the I. viridis complex, VspI and Bsp143I appear to be an appropriate combination.     

两轮多重反转录巢式PCR方法扩增全长GalUR基因

研究了两轮多重反转录巢式PCR扩增全长基因的方法.先用多重巢式引物和cDNA进行第1轮PCR扩增;再用纯化的第1轮PCR产物和相同的引物进行第2轮扩增;最后通过改变Mg^2＋浓度、退火时间和退火温度进行PCR条件的优化,以增加PCR扩增的产量,用于克隆.结果显示该方法方便和快速地扩增出了草莓（Fragaria ananassa cv.SweatCharlie）高产量和高质量的全长GalUR基因,也非常快速地扩增出了用于基因构建的带有酶切位点的全长GalUR基因.该方法也可以用于其它全长基因的克隆.     

Real-time polymerase chain reaction based assays for quantitative detection of barley, rice, sunflower, and wheat

Quality assurance is a major issue in the food industry. The authenticity of food ingredients and their traceability are required by consumers and authorities. Plant species such as barley (Hordeum vulgare), rice (Oryza sativa), sunflower (Helianthus annuus), and wheat (Triticum aestivum) are very common among the ingredients of many processed food products; therefore the development of specific assays for their specific detection and quantification are needed. Furthermore, the production and trade of genetically modified lines from an increasing number of plant species brings about the need for control within research, environmental risk assessment, labeling/legal, and consumers' information purposes. We report here the development of four independent real-time polymerase chain reaction (PCR) assays suitable for identification and quantification of four plant species (barley, rice, sunflower, and wheat). These assays target gamma-hordein, gos9, helianthinin, and acetyl-CoA carboxylase sequences, respectively, and were able to specifically detect and quantify DNA from the target plant species. In addition, the simultaneous amplification of RALyase allowed bread from durum wheat to be distinguished. Limits of detection were 1 genome copy for barley, sunflower, and wheat and 3.3 copies for rice real-time PCR systems, whereas limits of quantification were 10 genome copies for barley, sunflower, or wheat and approximately 100 haploid genomes for rice real-time PCR systems. Real-time PCR cycling conditions of the four assays were stated as standard to facilitate their use in routine laboratory analyses. The assays were finally adapted to conventional PCR for detection purposes, with the exception of the wheat assay, which detects rye simultaneously with similar sensitivity in an agarose gel.     

Development of a multiplex polymerase chain reaction method for simultaneous detection of eight events of genetically modified maize

In this study, we developed a novel multiplex polymerase chain reaction (PCR) method for simultaneous detection of up to eight events of genetically modified (GM) maize within a single reaction. The eight detection primer pairs designed to be construct specific for eight respective GM events (i.e., Bt11, Event176, GA21, MON810, MON863, NK603, T25, and TC1507) and a primer pair for an endogenous reference gene, ssIIb, were included in the nonaplex(9plex) PCR system, and its amplified products could be distinguished by agarose gel and capillary electrophoreses based on their different lengths. The optimal condition enabled us to reliably amplify two fragments corresponding to a construct specific sequence and a taxon specific ssIIb in each of the eight events of GM maize and all of nine fragments in a simulated GM mixture containing as little as 0.25% (w/w) each of eight events of GM maize. These results indicate that this multiplex PCR method could be an effective qualitative detection method for screening GM maize.     

Quantitative Determination of Gluten Protein Types in Wheat Flour by Reversed-Phase High-Performance Liquid Chromatography

A combined extraction-HPLC procedure was developed on a microscale to determine the amounts of the different gluten protein types (ω5-, ω1,2-, α- and γ-gliadins; high molecular weight [HMW] and low molecular weight [LMW] glutenin subunits) in wheat flour. After preextraction of albumins and globulins from flour (100 mg) with a salt solution (2 × 1.0 mL), extraction of gliadins was achieved with 60% aqueous ethanol (3 × 0.5 mL). Subsequently, the glutenin subunits were extracted under nitrogen and at 60°C with 50% aqueous 1-propanol containing Tris-HCl (0.05 mol/L, pH 7.5), urea (2 mol/L) and dithioerythritol (1%). The separation and quantitative determination of gliadins and glutenin subunits was then performed by reversed-phase HPLC on C₈ silica gel at 50°C using a gradient of increasing acetonitrile concentration in the presence of 0.1% trifluoroacetic acid. The flow rate was 1.0 mL/min, and the detection wavelength was 210 nm. Temperature and flow rate were modified for the quantitation of single underivatized HMW subunits. To determine the absolute amounts of protein types, different protein standards (gliadin, LMW and HMW subunits, bovine serum albumin) with known protein contents were compared to HPLC absorbance areas. The calibration curves were almost identical and linear over a broad range (20–220 μg). This extraction-HPLC procedure allows an accurate, reproducible, sensitive, and relatively fast quantitative determination of all gluten protein types in wheat flour, and can be applied to quality evaluation of cereals as raw materials or in processed products.     

Liquid chromatographic determination of rotenone in fish, crayfish, mussels, and sediments

An analytical procedure is described for determining residues of rotenone in fish muscle, fish offal, crayfish, freshwater mussels, and bottom sediments. Tissue samples were extracted with ethyl ether and extracts were cleaned up by gel permeation chromatography and silica gel chromatography. Sediment samples were extracted with methanol, acidified, partitioned into hexane, and cleaned up on a silica gel column. Rotenone residues were quantitated by liquid chromatography, using ultraviolet (295 nm) detection. Recoveries from sediment samples fortified with rotenone at 0.3 microgram/g were 80.8%, whereas recoveries from tissue samples fortified with 0.1 microgram/g ranged from 87.7 to 96.8%. Samples fortified with 0.3 microgram/g and stored at -10 degrees C for 6 months before analysis had recoveries ranging from 83.2 to 90.5%. Limits of detection were 0.025 microgram/g for sediments and 0.005 microgram/g for tissue samples.     

三种对虾病毒多重实时荧光PCR检测方法的建立

根据基因库中白斑综合征病毒（WSSV）、传染性皮下及造血器官坏死病毒（IHHNV）和桃拉综合征病毒（TSV）的基因序列,设计了WSSV 、IHHNV和TSV的三对特异性引物和三条用不同荧光基团标记的TaqMan探针。对反应条件和试剂浓度进行优化,建立了能够同时检测WSSV 、IHHNV和TSV的三重实时荧光PCR方法。该方法特异性好,对WSSV 、IHHNV和TSV的检测敏感性分别达到20000、20和20000个模板拷贝数;此外抗干扰能力强,对WSSV 、IHHNV和TSV不同模板浓度进行组合,仍可有效地同时检测这三个病毒。对保存的45份经常规PCR检测仅为WSSV 、IHHNV和TSV阳性的样品进行二重实时荧光PCR检测,结果都为阳性,其中2份为WSSV和IHHNV混合感染。本研究建立的三重实时荧光PCR方法用于WSSV、IHHNV和TSV的检测具有特异、敏感、快速、定量等优点。     

Detection of ruminant meat and bone meals in animal feed by real-time polymerase chain reaction: result of an interlaboratory study

The commercialization of animal feeds infected by prions proved to be the main cause of transmission of bovine spongiform encephalopathy (BSE). Therefore, feed bans were enforced, initially for ruminant feeds, and later for all feeds for farmed animals. The development and validation of analytical methods for the species-specific detection of animal proteins in animal feed has been indicated in the TSE (Transmissible Spongiform Encephalopathies) Roadmap (European Commission. The TSE (Transmissible Spongiform Encephalopathy) roadmap. URL: http://europa.eu.int/comm/food/food/biosafety/bse/roadmap_en.pdf, 2005) as the main condition for lifting the extended feed ban. Methods based on polymerase chain reaction (PCR) seem to be a promising solution for this aim. The main objective of this study was to determine the applicability of four different real-time PCR methods, developed by three National expert laboratories from the European Union (EU), for the detection and identification of cattle or ruminant species in typical compound feeds, fortified with meat and bone meals (MBM) from different animal species at different concentration levels. The MBM samples utilized in this study have been treated using the sterilization condition mandatory within the European Union (steam pressure sterilization at 133 degrees C, 3 bar, and 20 min), which is an additional challenge to the PCR methods evaluated in this study. The results indicate that the three labs applying their PCR methods were able to detect 0.1% of cattle MBM, either alone or in mixtures with different materials such as fishmeal, which demonstrates the improvement made by this technique, especially when compared with results from former interlaboratory studies.