Multiplex real-time PCR detection of fumonisin-producing and trichothecene-producing groups of Fusarium species

Some species of Fusarium can produce mycotoxins during food processing procedures that facilitate fungal growth, such as the malting of barley. The objectives of this study were to develop a 5' fluorogenic (Taqman) real-time PCR assay for group-specific detection of trichothecene- and fumonisin-producing Fusarium spp. and to identify Fusarium graminearum and Fusarium verticillioides in field-collected barley and corn samples. Primers and probes were designed from genes involved in mycotoxin biosynthesis (TRI6 and FUM1), and for a genus-specific internal positive control, primers and a probe were designed from Fusarium rDNA sequences. Real-time PCR conditions were optimized for amplification of the three products in a single reaction format. The specificity of the assay was confirmed by testing 9 Fusarium spp. and 33 non-Fusarium fungal species. With serial dilutions of purified genomic DNA from F. verticillioides, F. graminearum, or both as the template, the detection limit of the assay was 5 pg of genomic DNA per reaction. The three products were detectable over four orders of magnitude of template concentration (5 pg to 5 ng of genomic DNA per reaction); at 50 ng template per reaction, only the TRI6 and FUM1 PCR products were detected. Barley and corn samples were evaluated for the presence of Fusarium spp. with traditional microbiological methods and with the real-time PCR assay. The 20 barley samples and 1 corn sample that contained F. graminearum by traditional methods of analysis tested positive for the TRI6 and internal transcribed spacer (ITS) PCR products. The five corn samples that tested positive for F. verticillioides by traditional methods also were positive for the FUMI and ITS PCR products. These results indicate that the described multiplex real-time PCR assay provides sensitive and accurate differential detection of fumonisin- and trichothecene-producing groups of Fusarium spp. in complex matrices.     

Immunological detection of Fusarium species in cornmeal

An indirect enzyme-linked immunosorbent assay (ELISA) was developed to detect Fusarium species in foods. Antibodies to proteins extracted from the mycelia of Fusarium graminearum and Fusarium moniliforme (verticillioides) were produced in New Zealand white rabbits. These antibodies detected 13 Fusarium species in addition to the producer strains. Levels of Fusarium semitectum and Fusarium tricinctum strains were below the detection threshold. The specificity of the assay was tested against 70 molds and yeasts belonging to 23 genera. One strain of Monascus species and one strain of Phoma exigua were detected; however, these two molds are not common contaminants of cereal grains or foods and should not interfere with the assay. The indirect ELISA's detection limits for F. graminearum and F. moniliforme were 0.1 and 1 microg of mold mycelium per ml of a cornmeal mixture, respectively. When spores of each mold were added individually to cornmeal mixtures (at ca. 10 spores per g) and incubated at 25 degrees C, these spores were detected by the indirect ELISA when they reached levels of 10(2) to 10(3) CFU/ml after 24 to 36 h. The indirect ELISA developed here shows promise for the detection of Fusarium species in grains or foods.     

PCR detection assay of fumonisin-producing Fusarium verticillioides strains

Fusarium verticillioides is considered to be the main source of fumonisins, a group of toxins that contaminate commodities and result in chronic and acute diseases affecting humans and animals. The detection and control of this species is crucial to prevent fumonisins from entering the food chain. The objective of the present research was to develop a specific, sensitive, and robust PCR assay to detect F. verticillioides strains using two pairs of specific primers for F. verticillioides, which have been designed on the basis of the intergenic spacer region of the rDNA units. The first pair of primers was F. verticillioides species specific, whereas the second pair of primers detected fumonisin-producing F. verticillioides strains. This second pair of primers allowed for the discrimination between the major group of F. verticillioides strains, fumonisin-producing strains that are mainly associated with crops, and a minor group of strains, non-fumonisin-producing strains that are associated with bananas. Fifty-four strains of F. verticillioides from different geographical regions and hosts were tested using both sets of primers. Sixteen additional Fusarium species were examined. The specificity of the primer sequences provides the basis for a simple, rapid, accurate, and sensitive detection and identification method of this fungal species that represents a risk for human and animal health.     

Multiplex polymerase chain reaction assay for simultaneous detection of Staphylococcus aureus and streptococcal causes of bovine mastitis

To improve diagnosis of mastitis in dairy cattle, a multiplex polymerase chain reaction (PCR) assay was developed for the simultaneous detection of the four major bacterial causes of bovine mastitis, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis. The target sequence was the 16S to 23S rRNA spacer regions. The performance of the assay was examined with 117 milk samples collected from a subclinically infected herd, and the diagnostic specificities and sensitivities of the multiplex PCR were compared with conventional culture. PCR was significantly more sensitive than culture for detection of S. aureus and S. uberis, but there were no significant differences in sensitivities between PCR and culture for the detection of S. agalactiae and S. dysgalactiae. The results suggest that this multiplex PCR assay could be used as an alternative method in routine diagnosis for rapid, sensitive, and specific simultaneous detection of S. aureus, S. agalactiae, S. dysgalactiae, and S. uberis in milk samples.     

多重PCR法同时检测黄酒酒曲中多种生物胺产生菌

该研究建立了检测多种生物胺产生菌的多重聚合酶链反应（PCR）方法,首先检测了已报道的针对酪胺、腐胺产生菌和革兰氏阴性组胺产生菌的多对引物的特异性,针对革兰氏阴性菌的组氨酸脱羧酶基因的引物特异性差,重新设计了该引物,在此基础上,建立了可同时检测酪胺、腐胺和组胺产生菌的多重PCR方法,并优化了多重PCR反应条件为退火温度50 ℃,Mg2+浓度1.0 mmol/L,引物浓度配比为Tdc-F/R 0.2 μmol/L,Hdc1/2 0.4 μmol/L和Odc3/4 0.4 μmol/L。该方法特异性强,对酪胺、腐胺和组胺产生菌的灵敏度分别为1.2 ng/μL、1.5 ng/μL和1.5 ng/μL,可用于黄酒酒曲中生物胺产生菌的快速检测。     

应用gyrA基因聚合酶链反应检测食品中弓形菌

建立了一种快速、敏感、特异检测弓形菌的PCR方法。选取弓形菌gyrA基因序列作为靶序列设计特异性引物Arco/gyrAF和Arco/gyrAR,进行PCR扩增实验。结果弓形菌呈现出一条298 bp的特异性条带,其余非弓形菌均无阳性扩增。灵敏度实验结果表明,该法可以检测到82.6 pg的DNA。经过对16份生鲜鸡肉样品的检测,9份样品中检测到弓形菌,样品阳性率为56.25%。该PCR方法可以高效、灵敏地检测食品中弓形菌,具有很强的实际应用价值。     

聚合酶链式反应技术快速检测原料乳中荧光假单胞菌

目的 利用PCR（polymerase chain reaction）技术建立一种快速、准确检测原料乳中最常见有害嗜冷微生物——荧光假单胞菌的方法。方法 以荧光假单胞菌蛋白酶基因aprX为检测靶标,设计特异性PCR简并引物,建立原料乳中荧光假单胞菌PCR检测体系,对该体系的特异性及检测限进行评价。结果 筛选到特异性引物F3：5’-WSNGGNGGNGAYTTYCAYATGAC-3’;R3：5’-RTCRTTNCCNCCNCCRTCCC-3’,建立了最佳PCR检测体系：引物浓度0.5 μmol/L、Taq DNA聚合酶添加量0.4 μL、dNTPs浓度0.16 mmol/L、Mg²⁺浓度1.6 mmol/L,退火温度56.4 ℃,扩增35个循环。此检测方法对荧光假单胞菌具有特异性,检测限为2.57×10³ CFU/mL。结论 本方法操作简便,特异性强,检测限低,对快速检测原料乳中嗜冷菌,保障原料乳品质与安全具有一定参考意义。     

Assessment of Fusarium infection in wheat heads using a quantitative polymerase chain reaction (qPCR) assay

The accuracy of a quantitative polymerase chain reaction assay in quantifying the DNA of trichothecene-producing F. culmorum and F. graminearum within harvested wheat grains and head tissue was evaluated in comparison with incidences of infected kernels and deoxynivalenol levels. In a first experiment, six durum and bread wheat varieties were grown in randomized plots for a 2-year period, and inoculated with Fusarium macroconidia at six growth stages between heading and dough ripening, to obtain a wide range of Fusarium head blight incidences. There was a close relationship between fungal DNA and the amount of deoxynivalenol, and this relationship was consistent over Fusarium species, wheat species and varieties, and over a wide range of Fusarium head blight infection. In a second experiment potted wheat plants were grown under environmentally controlled conditions and inoculated with the two Fusarium species at full flowering; head samples were collected before inoculation and after 6 h to 12 days, and processed by the quantitative polymerase chain reaction assay. This assay made it possible to detect the dynamic of fungal invasion in planta after infection had occurred, and to single out the presence of infection before the onset of the disease symptoms: A robust detection of the infection occurred within 18-24 h for F. culmorum, and within 2-9 days for F. graminearum.     

Rapid polymerase chain reaction/DNA probe membrane-based assay for the detection of Listeria and Listeria monocytogenes in food

We describe the development of polymerase chain reaction (PCR)/DNA probe membrane-based colorimetric assays for the detection and identification of Listeria and L. monocytogenes. PCR primers designed from the 16S to 23S rRNA intergenic spacer region amplified products that were reverse hybridized to membrane-bound oligonucleotide probes specific for Listeria and L. monocytogenes with a detection limit of 1 to 10 CFU/25 ml in inoculated raw and pasteurized milk samples. These qualitative assays have the potential to be integrated into testing laboratories for monitoring the microbiological quality of foods.     

Development of a multiplex polymerase chain reaction assay for detection and differentiation of Staphylococcus aureus in dairy products

A multiplex polymerase chain reaction (PCR) assay was developed for the detection and differentiation of enterotoxigenic Staphylococcus aureus in dairy products. A solvent extraction procedure was successfully modified for extraction of S. aureus DNA from 10 ml of artificially contaminated skim milk or 20 g cheddar cheese. Primers targeting the enterotoxin C gene (entC) and thermostable nuclease gene (nuc) were used in the multiplex PCR. PCR products were confirmed using restriction fragment length polymorphism analysis. DNA was consistently quantified and amplified by uniplex PCR from 10 CFU/ml of S. aureus in skim milk or 10 CFU/20 g cheddar cheese. The sensitivity of the multiplex PCR was 100 CFU/ml of skim milk or 100 CFU/20 g cheddar cheese. The developed methodology allows presumptive identification and differentiation of enterotoxigenic S. aureus in less than 6 h.     

Development of a polymerase chain reaction assay for species identification of goose and mule duck in foie gras products

Polymerase chain reaction amplification of a conserved region of the -actin gene has been used for the specific identification of goose (Anser anser) and mule duck (Anas platyrhynchos×Cairina moschata) foie gras. Universal primers were used for the amplification of a DNA fragment containing three introns and four exons of the -actin gene in goose and mule duck. Sequence analysis of the amplified fragments was necessary for the design of forward species-specific primers in the goose and mule duck -actin genes. The use of species-specific forward primers, together with a reverse universal primer, produced amplicons of different length, allowing clear identification of goose and mule duck foie gras samples. Analysis of experimental mixtures demonstrated that 1% of duck can be easily detected in goose foie gras using the PCR method developed here. This genetic marker can be very useful for the accurate identification of these two species in foie gras products.     

The polymerase chain reaction: Applications for the detection of foodborne pathogens

Faster methods for the detection of foodborne microbial pathogens are needed. The polymerase chain reaction (PCR) can amplify specific segments of DNA and is used to detect and identify bacterial genes responsible for causing diseases in humans. The major features and requirements for the PCR are described along with a number of important variations. A considerable number of PCR‐based assays have been developed, but they have been applied most often to clinical and environmental samples and more rarely for the detection of foodborne microorganisms. Much of the difficulty in implementing PCR for the analysis of food samples lies in the problems encountered during the preparation of template DNAs from food matrices; a variety of approaches and considerations are examined. PCR methods developed for the detection and identification of particular bacteria, viruses, and parasites found in foods are described and discussed, and the major features of these reactions are summarized.     

Polymerase chain reaction assay for detection of sheep and goat meats

Polymerase Chain Reaction (PCR) was applied to a qualitative differentiation between sheep, goat and bovine meats. Oligonucleotide primers were designed for the amplification of sheep satellite I DNA sequence. The PCR amplified 374 bp fragments from sheep and goat DNA, but no fragment from bovine, water buffalo, sika deer, pig, horse, rabbit and chicken DNA. Sheep DNA (10 pg) was detected by 4% agarose gel electrophoresis following PCR amplification. Althoug cooking of the sample meats reduced the PCR products, sheep DNA was detected in the meat heated at 120°C. In order to differentiate between sheep and goat meats, nucleotide sequences of the PCR products were determined directly by cycle sequencing. The sequence of PCR products showed 92% of homology between sheep and goat. They were differentiated by ApaI digestion of the PCR products because sheep had one ApaI site and goat had no site in the PCR products.     

牛奶中志贺氏菌PCR检测方法的建立

根据Genbank志贺氏菌侵袭性质粒抗原H (ipaH)基因序列, 自行设计引物, 扩增特异的326 bp核酸片段, 经过优化PCR扩增条件, 建立了志贺氏菌特异、敏感、快速的PCR检测方法, 并对牛奶中的志贺氏菌进行了检测.特异性试验结果表明, 志贺氏菌参考菌株均能扩增出特异的核酸片段, 大肠杆菌、巴氏杆菌、金黄色葡萄球菌、沙门氏菌、蜡样芽孢杆菌、变形杆菌、绿脓杆菌的扩增结果均为阴性.敏感性试验结果表明, 采用试剂盒提取基因组, 该方法的敏感性可达到1.75×102 cfu/mL.人工污染牛奶的模拟检测结果表明, PCR方法的检测限为1.75×103 cfu/mL.     

Vancomycin-modified poly-l-lysine magnetic separation combined with multiplex polymerase chain reaction assay for efficient detection of Bacillus cereus in milk

In this study, a new vancomycin (Van)-modified poly-l-lysine (PLL) magnetic bead (MB) technique was developed for isolation of gram-positive bacteria. The method combines magnetic separation with a multiplex PCR (mPCR) assay and gel electrophoresis for easy and rapid detection of Bacillus cereus. Vancomycin was used as a molecular ligand between the MB and the d-alanyl-d-alanine moieties on the cell wall surface of B. cereus. The PLL served as a flexible molecular tether between the MB and Van that reduced steric hindrance maintaining the biological activity of Van. The MB-PLL-Van capture nanoprobes exhibited excellent capture and isolation efficiency for B. cereus in spiked milk matrix samples without interference from the complex food matrix. The subsequent mPCR assay showed high specificity for the 4 target genes in B. cereus, the entFM, cesB, cer, and 16S rRNA genes, that were used to achieve efficient genotyping and detection. Under optimum conditions, the limit of detection reached 10³ cfu/mL, with a dynamic range of detection at 10³ to 10⁷ cfu/mL in pure culture. Application of the MB-PLL-Van mediated mPCR assay for B. cereus in milk matrix samples achieved results similar to those of the pure culture. In addition, with a 6-h pre-enrichment of B. cereus that was spiked in milk matrix samples, the limit of detection reached 10¹ cfu/mL. The MB-PLL-Van mediated mPCR assay developed in this study could be used as a universal technology platform for the efficient enrichment and genotyping of gram-positive bacteria.     

Methods for the detection of beef and pork in foods using real-time polymerase chain reaction

Summary Two TaqMan?‐polymerase chain reaction (PCR) systems have been developed which permit the detection of even minute amounts of beef and pork in processed foods. In these methods cattle‐specific primers amplified a fragment from the phosphodiesterase gene having a length of 104 base pairs (bp), and the swine‐specific primers amplified a fragment from the ryanodin gene having a length of 108 bp. Beyond this, a third TaqMan?‐PCR system, developed on the basis of the detection of the myostatin gene, permits a reliable exclusion of false‐negative results by detecting meat from a variety of mammals or poultry in the material to be tested.     

副溶血弧菌PCR检测方法研究进展

副溶血弧菌是引起包括我国在内的世界各地沿海地区食物中毒的重要食源性致病菌,患者有典型的肠胃炎症状。及时准确地对食品中的副溶血弧菌进行检测是预防该菌引起的食物中毒的关键。分子生物学检测方法在副溶血弧菌检测中具有许多优势,现已得到广泛的应用。本文对PCR检测方法中的多重PCR、有扩增内标的PCR、实时荧光PCR(包括荧光染料法和荧光探针法)、基于DNA染料叠氮溴化乙锭和叠氮溴化丙锭的PCR、纳米粒子PCR、免疫捕获PCR、PCR-变性高效液相色谱、PCR-酶联免疫吸附等方法的国内外研究情况进行了综述,并对其检测效率、灵敏度、优点和缺点等进行了分析比较,环介导等温扩增(loop-mediated isothermal amplification,LAMP)——包括常规LAMP和原位LAMP因与PCR方法有相似之处,故一并进行了综述,为副溶血弧菌PCR检测方法的应用与开发提供参考。     

Development of a quantitative polymerase chain reaction assay for detection of Kudoa septempunctata in olive flounder (Paralichthys olivaceus)

Kudoa septempunctata is a newly identified myxosporean parasite that infects the trunk muscles of olive flounder (Paralichthys olivaceus) and a causative agent of the increasing number of foodborne gastroenteritis outbreaks with unknown etiology which have occurred in Japan over the last few years. Here, we developed a quantitative polymerase chain reaction (QPCR) assay for the detection of K. septempunctata 18S rDNA in olive flounder muscle tissue samples. Additionally, we compared the relative efficacy of four DNA extraction methods, including two commercial kits, and assessed intrafish variability in the distribution of K. septempunctata spores in flounder using this QPCR method in order to establish a more accurate quantitative measurement. Our QPCR assay displayed high sensitivity, specificity, and reproducibility, and had good correlation with a microscopic detection method. Our data also indicated that the DNeasy? Blood & Tissue Kit was more efficient method for the extraction of K. septempunctata DNA than the three other methods (heating, alkaline lysis, and FastDNA? SPIN Kit method). We believe that our method would be useful for investigating foodborne outbreaks caused by K. septempunctata and for the monitoring and quantification of this parasite in retail or aquacultured olive flounders to prevent such outbreaks.     

Application of a multiplex polymerase chain reaction assay for the simultaneous confirmation of Listeria monocytogenes and other Listeria species in turkey sample surveillance

A multiplex polymerase chain reaction was developed to simultaneously identify Listeria monocytogenes and species of the genus Listeria. Two sets of primers were used, with the first amplifying a 938-bp region of the 16S rRNA gene that is highly conserved in all Listeria species and the second amplifying a 174-bp region of the listeriolysin (hlyA) gene of L. monocytogenes. Thus, isolates of Listeria spp. yield a single 938-bp product, whereas L. monocytogenes isolates yield both the 938-bp product and a 174-bp product. The specificity of the assay was verified with all six Listeria species and 11 serotypes of L. monocytogenes, as well as nonrelated bacteria. The multiplex PCR assay was used to determine the incidence of Listeria spp., especially L. monocytogenes, in mechanically separated turkey samples (n = 150 samples). L. monocytogenes strains were selected by using the University of Vermont two-step enrichment protocol and plating to selective Palcam agar. The multiplex PCR assay was used for verification of presumptive Listeria colonies. Approximately 38% of mechanically separated turkey samples (57 of 150) yielded L. monocytogenes; an additional 18% of these samples (27 of 150) harbored other Listeria spp. Fifty-one percent (29 of 57) of the L. monocytogenes isolates were of serogroup 1, 44% (25 of 57) were of serogroup 4, and 2% (1 of 57) were assigned to serogroups other than 1 and 4.     

真鲷虹彩病毒聚合酶链式反应检测方法的建立

目的:真鲷虹彩病毒一直都被列入在世界卫生组织（OIE）水生动物疫病病原的名录中,故需要对其检测方法进行深入研究,建立操作简单,普遍适用的检测技术手段。方法:本文针对RSIV片段设计了一对特异性引物,对反应体系和反应程序进行筛选和优化,建立了检测RSIV聚合酶链式反应的方法。并且用优化好的反应体系和反应程序对重组质粒p MD18-T-RSIV进行扩增。结果:研究发现该方法特异性强,与IHNV、IPNV、SVCV和VHSV无交叉反应,并且灵敏度高,可以达到0.2pg。结论:成功的建立了真鲷虹彩病毒常规PCR检测方法,可以为真鲷虹彩病毒病的诊断提供理论依据。