Development Of Polymerase Chain Reaction Assay Research Articles

EPIDEMIOLOGY STUDY OF VIRAL NERVOUS NECROSIS (VNN) IN MALAYSIAN GROUPERS: SEQUENCE ANALYSIS STRATEGIES AND QUASISPECIES DETERMINANT’S

EPIDEMIOLOGY STUDY OF VIRAL NERVOUS NECROSIS (VNN) IN MALAYSIAN GROUPERS: SEQUENCE ANALYSIS STRATEGIES AND QUASISPECIES DETERMINANT’S

Development of Polymerase Chain Reaction assays with host-specific internal controls for Chlamydophila abortus

Chlamydophila abortus (C. abortus) is one of the most important infectious agents causing abortion in ruminants. The bacterium is obligately intracellular, cannot grow on agar, but it needs cell culture or embryo - nated eggs for growth. Therefore, culture-independent detection methods such as the polymerase chain reaction are increasingly important and needed. The aim of this study was to develop a polymerase chain reaction assay with an internal control for detection of C. abortus in clinical samples . Using newly-designed two primer sets specific for C. abortus, the polymerase chain reaction assay was first tested with positive and negative control DNA and its sensitivity and specificity were determined. A new polymerase chain reaction protocol was developed by combining the new primer pair sets with bovine (12SM-FW and 12SBT-REV2) and ruminant host-specific primer sets (12S-FW and 12S-REV). In conclusion, the developed polymerase chain reaction assays can potentially be used for direct detection of Chlamydophila abortus in bovine and ruminant samples.

Development of real-time PCR assays to detect cashew (Anacardium occidentale) and macadamia (Macadamia intergrifolia) residues in market analysis of processed food products

Real-time polymerase chain reaction (PCR)-based assays for detection of cashew (Anacardium occidentale) and macadamia nut (Macadamia intergrifolia) traces in food products are described here. The real time PCR technique proposed herein were developed based on the design of macadamia and cashew-specific primers from the ITS region and a TaqMan fluorescent probe. The methods were positive for cashew and macadamia respectively, and negative for all other heterologous plant and animal species tested. Using a series of model samples with defined levels of raw and heat-treated cashew and macadamia nut, respectively, within a range of concentrations of 0.1–100 000 mg kg−1, practical detection limits of 0.1 mg kg−1 for cashew and macadamia nut were estimated. Practical applicability of the PCR methods was tested by the analysis of a total of 214 commercial foodstuffs. These PCR methods, are useful for highly selective, and sensitive detection of traces of macadamia and cashew nuts in commercial food products and is therefore proposed as a ready-to-use analytical tool to trace these target allergens in foods.

Development of multiplex real-time PCR assay for the detection of Brucella spp., Leptospira spp. and Campylobacter foetus.

Abortion among dairy cattle is one of the major causes of economic losses in the livestock industry. This study describes a 1-step multiplex real-time polymerase chain reaction (PCR) to detect Brucella spp., Leptospira spp. and Campylobacter foetus, these are significant bacteria commonly implicated in bovine abortion. ß-actin was added to the same PCR reaction as an internal control to detect any extraction failure or PCR inhibition. The detection limit of multiplex real-time PCR using purified DNA from cultured organisms was set to 5 fg for Leptospira spp. and C. foetus and to 50 fg for Brucella spp. The multiplex real-time PCR did not produce any non-specific amplification when tested with different strains of the 3 pathogens. This multiplex real-time PCR provides a valuable tool for diagnosis, simultaneous and rapid detection for the 3 pathogens causing abortion in bovine.

Development and verification of real-time PCR assay for identification of viral agents causing acute respiratory infections in human beings.

A multiplex polymerase chain reaction (PCR) for identification of four viruses causing acute respiratory diseases in human beings was developed. The analytical sensitivity of developed RT-PCR for identification of adenovirus, respiratory-syncytial virus, flu viruses types A and B, and actual subtypes of type A flu virus (seasonal and pandemic variants H1N1, seasonal H3N2, and viruses of bird flu that are pathogenic to human beings H5 and H7) was 1 × 103 genome equivalents per milliliter. Diagnostic sensitivity for flu virus type A and B, and also subtypes H1 (seasonal H1N1, pandemic variant of H1N1 of year 2009), H3, H5 was 1 × 103–104 viral particles per milliliter. The method developed has high specificity and does not have positive signal in experiments with DNA/cDNA of human beings and viral DNA. We have studied 50 samples using the developed set. Etiology was defined in 33 samples.

Development and evaluation of specific PCR and LAMP assays for the rapid detection of Phytophthora melonis

Phytophthora melonis is a widespread and devastating pathogen for the Cucurbitaceae family. Early and accurate detection of P. melonis is essential to control the disease in the field. To establish a simple, visual, and rapid detection system for P. melonis, we developed nested polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) systems based on the Ras-related protein (Ypt1) gene. All 36 isolates of P. melonis, from geographically distinct counties in China, yielded positive detection results on LAMP or nested PCR assays. No cross reaction was observed with other oomycetes or fungal pathogens. A sensitivity assay showed that both methods had a detection limit of 10 fg genomic DNA. We also detected P. melonis in diseased cucumber tissues and soils, and evaluated positive detection rates using LAMP, nested PCR, and conventional isolation methods. The results suggest that the LAMP assay has the greatest potential for active detection of P. melonis in regions that are at risk of contracting the disease, and for use in resource-poor settings.

Development and evaluation of a 28S rRNA gene-based nested PCR assay for P. falciparum and P. vivax

The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase chain reaction (PCR) primers were designed from the 3R region of the 28SrRNA gene and evaluated on field isolates. This is the first report demonstrating the utility of this gene for species-specific diagnosis of malaria for these two species, prevalent in India. The initial evaluation on 363 clinical isolates indicated that, in comparison with microscopy, which showed sensitivity and specificity of 85·39% and 100% respectively, the sensitivity and specificity of the nested PCR assay was found to be 99·08% and 100% respectively. This assay was also successful in detecting mixed infections that are undetected by microscopy. Our results demonstrate the utility of the 28S rRNA gene as a diagnostic target for the detection of the major plasmodial species infecting humans.

PCR based diagnosis of trypanosomiasis exploring invariant surface glycoprotein (ISG) 75 gene

The invariant surface glycoprotein (ISG-75) gene of Trypanosoma evansi buffalo isolate from Karnataka state in India was sequenced and analyzed to elucidate its relationship with other isolates/species. The sequenced ISG-75 gene was also explored to device a polymerase chain reaction (PCR) strategy for the diagnosis of trypanosomiasis in carrier animals. The six cloned ISG gene sequences revealed the open reading frame (ORF) of 1572 and 1527 nucleotide (nt) encoding a polypeptide of 523 and 508 amino acids (aa) respectively and belongs ISG-75 gene family. Sequence analysis revealed 91–100% and 65–99% similarity at nt and aa levels, respectively with other isolates/species and belongs to the RoTat 1.2 strain. The diagnostic PCR based on ISG-75 sequence amplifies a 407bp product specifically from the different T. evansi isolates and could detect 0.04pg and 1.2ng of DNA from purified trypanosomes and T. evansi infected rat blood samples respectively. Subsequently the PCR detected 0.02 and 0.27trypanosomesml−1 respectively, from purified trypanosomes and T. evansi (buffalo isolate) infected rat blood. By the developed PCR assay trypanosomal nucleic acid was detected in experimental rats and buffalo on 24h post infection (p.i.) and 3rd day post infection (d.p.i.), respectively. The developed ISG-75 gene based PCR assay could be useful in detection of carrier status of trypanosomiasis in animals.

Development and application of highly specific PCR for detection of chicken (Gallus gallus) meat adulteration

In order to prevent fraud in the sale and strengthen quality assurance, authentic identification of chicken meat is essential. In the present investigation, a chicken (Gallus gallus)-specific polymerase chain reaction (PCR) was developed for the unambiguous identification of chicken meat. The PCR assay employs pair of primers designed against chicken nuclear 5-aminolevulinate (ALA) synthase gene. Highly chicken-specific diagnostic amplicon of 288 bp was established upon PCR and was evident in all the nine breeds/strains of chicken species. Sensitivity of PCR in detecting chicken meat adulteration was established to be at 0.1 % in the foreign meat matrix, while limit of detection (LOD) of chicken DNA was 10 pg. Suitability of the developed chicken-specific PCR was validated and confirmed in raw, cooked/heat treated (60, 80, 100, and 121 °C), and micro-oven cooked meat samples. Possibility of cross-amplification of adulterating DNA was excluded by cross-checking the developed PCR assay with several animal and avian species. The PCR assay developed in this study is highly promising for applications involving circumstances that require authentic identification of chicken meat.

Identification and molecular discrimination of toxigenic and nontoxigenic diphtheria Corynebacterium strains by combined real-time polymerase chain reaction assays

With the recognition of several diphtheria outbreaks and the emergence of nontoxigenic corynebacteria strains, there has been renewed interest in the development of laboratory diagnostic methods. Previously reported polymerase chain reaction (PCR) assays can have low diagnostic sensitivity or give species misidentifications among clinical isolates. The aim of the present study was the development of combined real-time PCR assays, based on the tox and rpoB genes, for the detection and differentiation of toxigenic and nontoxigenic corynebacteria. By the PCR tox assay, it was possible to perform the direct identification of DT tox gene of Corynebacterium diphtheriae and Corynebacterium ulcerans, while the PCR rpoB assay differentiated C. diphtheriae from C. ulcerans, irrespective of their toxigenic status. In addition, we detected the DT toxin of Corynebacterium pseudotuberculosis for the first time. These assays revealed high sensitivity, specificity, and reproducibility, and the availability of plasmid controls will facilitate further research into the diagnostics of diphtheria corynebacteria.

Establishment and Application of Event-Specific Polymerase Chain Reaction Methods for Two Genetically Modified Soybean Events, A2704-12 and A5547-127

For implementation of the issued regulations and labeling policies for genetically modified organism (GMO) supervision, the polymerase chain reaction (PCR) method has been widely used due to its high specificity and sensitivity. In particular, use of the event-specific PCR method based on the flanking sequence of transgenes has become the primary trend. In this study, both qualitative and quantitative PCR methods were established on the basis of the 5' flanking sequence of transgenic soybean A2704-12 and the 3' flanking sequence of transgenic soybean A5547-127, respectively. In qualitative PCR assays, the limits of detection (LODs) were 10 copies of haploid soybean genomic DNA for both A2704-12 and A5547-127. In quantitative real-time PCR assays, the LODs were 5 copies of haploid soybean genomic DNA for both A2704-12 and A5547-127, and the limits of quantification (LOQs) were 10 copies for both. Low bias and acceptable SD and RSD values were also achieved in quantification of four blind samples using the developed real-time PCR assays. In addition, the developed PCR assays for the two transgenic soybean events were used for routine analysis of soybean samples imported to Shanghai in a 6 month period from October 2010 to March 2011. A total of 27 lots of soybean from the United States and Argentina were analyzed: 8 lots from the Unites States were found to have the GM soybean A2704-12 event, and the GM contents were <1.5% in all eight analyzed lots. On the contrary, no GM soybean A5547-127 content was found in any of the eight lots. These results demonstrated that the established event-specific qualitative and quantitative PCR methods could be used effectively in routine identification and quantification of GM soybeans A2704-12 and A5547-127 and their derived products.

Detection of Adulteration of Meat and Meat Products with Buffalo Meat Employing Polymerase Chain Reaction Assay

The primer pair was designed based on mitochondrial d-loop gene for detection of adulteration of buffalo meat in admixed meat and meat products by polymerase chain reaction (PCR) assay. Amplification of 537-bp DNA fragments was observed from buffalo, without any cross-reaction with cattle, sheep, goat, pig, and chicken. The amplification was further confirmed by BamHI restriction enzymes. No adverse effect of processing was found on PCR amplification of buffalo meat DNA extracted from processed meat and meat products, even from meat emulsion autoclaved at 121 °C, 20 psi for 15–20 min. The detection limit for buffalo meat was found to be 1% in the admixed meat and meat products; however, very faint and inconsistent results were obtained in autoclaved meat emulsion at 1% level. The developed PCR assay was found to be specific for buffalo and could be a useful tool for detection of meat adulteration.

Development of PCR assays for detection of Escherichia coli O157:H7 in meat products

A multiplex polymerase chain reaction (PCR) procedure based on fliC h7 and rfbE genes was developed for the detection of Escherichia coli O157:H7 in raw pork meat and ready-to-eat (RTE) meat products. Two different DNA extraction procedures were evaluated for application on meat products. MasterPure™ DNA Purification kit in combination with immunomagnetic separation was found to be the best method in a meat system. The optimized PCR included an enrichment step in brilliant green bile 2% broth at 37 °C. This method was applied to artificially inoculated meat and RTE meat products with different concentrations of E. coli O157:H7. The results indicate that the PCR assay developed could sensitively and specifically detect E. coli O157:H7 in raw pork meat and RTE meat products in approximately 10 h, including a 6 h enrichment step. Thus, this method could be proposed for screening E. coli O157:H7 in raw pork and RTE meat products.

Development of multiplex PCR assays to identify Escherichia coli pathogenic genes in food

In order to rapidly screen for the virulence factor that produces pathogenic Escherichia coli in food, we have developed multiplex polymerase chain reaction (PCR) assays. The multiplex PCR assays detect 4 pathogenic genes of enterohaemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), and enteroinvasive E. coli (EIEC). This allows for the generation of specific fragments 150, 179, 218, 401, 465, 584, and 881 bp for VT1, ST, LT, 16S rRNA, inV, VT2, and eaeA genes, respectively. The detection limit of 3 log CFU/mL for eaeA, LT, VT1, VT2, 4 log CFU/mL for inV, 6 log CFU/mL for ST by single PCR, while 5 log CFU/mL for VT1, VT2, 6 log CFU/mL for eaeA, LT, 7 log CFU/mL for ST, inV by multiplex PCR. This optimized detection method of pathogenic E. coli can be used as supportive data to revise the microbiological analytical manuals for the Korean Food Code.

Development of a duplex real-time TaqMan PCR assay with an internal control for the detection of Mycoplasma gallisepticum and Mycoplasma synoviae in clinical samples from commercial and backyard poultry

In this study, we report the development and validation of a duplex real-time polymerase chain reaction (PCR) assay with an internal control using TaqMan-labelled probes for the detection of Mycoplasma gallisepticum and Mycoplasma synoviae (duplex MGMS PCR). The MGMS PCR was highly specific with a sensitivity of 7 and 1 colony-forming units/ml for M. gallisepticum and M. synoviae, respectively, using dilution of pure culture that corresponds to 34 and 29 DNA copies per reaction. Validation of the assay was completed with 260 and 27 pooled samples (tracheal swabs) from commercial chickens and turkeys, respectively, with potential M. gallisepticum and M. synoviae involvement and 42 samples (palatine cleft swabs) from backyard geese and ducks. Using isolation as the gold standard, the MGMS PCR was more sensitive than isolation and the analytical sensitivity was 0.944 and 0.958 for M. gallisepticum and M. synoviae, respectively. In comparison with a gapA-based assay (gapA PCR) and a 16S rRNA-based assay (16S PCR) for M. gallisepticum and M. synoviae, respectively, the results agreed for 94.5% and 96.6%, respectively. The use of the internal control allowed monitoring of proper extraction and inhibition of amplification that was detected in 12 samples. The duplex MGMS PCR was shown to be superior to the presently reported real-time PCR assays in terms of combination of sensitivity, specificity and capacity of detection of more than one target in a single tube. In conclusion, the duplex MGMS PCR was highly specific, sensitive, and reproducible and could be used on clinical samples from commercial chickens, turkeys and backyard poultry including ducks and geese.

The Effect of Primer-Template Mismatches on the Detection and Quantification of Nucleic Acids Using the 5′ Nuclease Assay

Real-time polymerase chain reaction (PCR) is the current method of choice for detection and quantification of nucleic acids, especially for molecular diagnostics. Complementarity between primers and template is often crucial for PCR applications, as mismatches can severely reduce priming efficiency. However, little quantitative data on the effect of these mismatches is available. We quantitatively investigated the effects of primer-template mismatches within the 3'-end primer region on real-time PCR using the 5'-nuclease assay. Our results show that single mismatches instigate a broad variety of effects, ranging from minor (<1.5 cycle threshold, eg, A-C, C-A, T-G, G-T) to severe impact (>7.0 cycle threshold, eg, A-A, G-A, A-G, C-C) on PCR amplification. A clear relationship between specific mismatch types, position, and impact was found, which remained consistent for DNA versus RNA amplifications and Taq/Moloney murine leukemia virus versus rTth based amplifications. The overall size of the impact among the various master mixes used differed substantially (up to sevenfold), and for certain master mixes a reverse or forward primer-specific impact was observed, emphasizing the importance of the experimental conditions used. Taken together these data suggest that mismatch impact follows a consistent pattern and enabled us to formulate several guidelines for predicting primer-template mismatch behavior when using specific 5-nuclease assay master mixes. Our study provides novel insight into mismatch behavior and should allow for more optimized development of real-time PCR assays involving primer-template mismatches.

Development of real-time PCR assays for the detection of lupin residues in food products

Lupin is a legume from the Leguminosae family that is used, amongst other, for human nutrition. In Europe, lupin is used as a substitute for soy in bakery and dietary products and recently its consumption has increased significantly. Unfortunately lupin is known to trigger allergic reactions in sensitised individuals and therefore its use in food products requires a mandatory declaration on the label in accordance with Directive 2007/68/EC. To protect the allergic consumer the availability of detection methods for the identification of lupin in food products is required. Here we present the development of two real-time polymerase chain reaction (PCR) methods that allow the detection of lupin-specific DNA as a marker for the presence of this allergenic ingredient in food products. Genomic DNA sequences coding for conglutin genes were chosen as targets for the detection of lupin. One primer set and probe was designed for the amplification of a 153 bp fragment of α-conglutin; another primer set and probe was designed for the detection of a 150 bp δ-conglutin amplicon. Lupin at a level of 10 mg/kg food matrix could be detected in cookies baked from a lupin containing dough using the α-conglutin method. Since lupin is used in bakery products the effects exerted by heat treatments on lupin detection by real-time PCR have been investigated. Enzyme-linked immunosorbent assay (ELISA) analyses were performed in parallel to compare the detection of lupin DNA with that of lupin protein in market products. Qualitative ELISA results confirm results obtained by the real-time PCR methods targeting α- and δ-conglutin.

Development and in‐house validation of the event‐specific qualitative and quantitative PCR detection methods for genetically modified cotton MON15985

To implement genetically modified organism (GMO) labeling regulations, an event-specific analysis method based on the junction sequence between exogenous integration and host genomic DNA has become the preferential approach for GMO identification and quantification. In this study, specific primers and TaqMan probes based on the revealed 5'-end junction sequence of GM cotton MON15985 were designed, and qualitative and quantitative polymerase chain reaction (PCR) assays were established employing the designed primers and probes. In the qualitative PCR assay, the limit of detection (LOD) was 0.5 g kg(-1) in 100 ng total cotton genomic DNA, corresponding to about 17 copies of haploid cotton genomic DNA, and the LOD and limit of quantification (LOQ) for quantitative PCR assay were 10 and 17 copies of haploid cotton genomic DNA, respectively. Furthermore, the developed quantitative PCR assays were validated in-house by five different researchers. Also, five practical samples with known GM contents were quantified using the developed PCR assay in in-house validation, and the bias between the true and quantification values ranged from 2.06% to 12.59%. This study shows that the developed qualitative and quantitative PCR methods are applicable for the identification and quantification of GM cotton MON15985 and its derivates.

Development of a real-time TaqMan PCR assay for the detection of porcine and bovine Torque teno virus

The goal of this study was to develop and to optimize molecular tools to detect the presence of Torque teno virus (TTV) in swine and cattle. A novel real-time polymerase chain reaction (PCR) using a TaqMan probe was developed to detect both genogroups of TTV strains. Oligonucleotide primers and hybridization probes were designed based on sequence analysis of the noncoding region, a highly conserved part of the genome. The real-time PCR assay specifically detected bovine and porcine TTV DNA without cross-amplification of other common pathogens. The assay was compared with conventional PCR and nested-PCR assays for the detection of porcine genogroups 1 and 2 and bovine TTV on plasma and faecal samples, and the assay was found faster, more reliable and reduced the risk of false positive results. The real-time PCR assay provided better detection results for the two TTV genogroups in both swine and cattle compared to the conventional PCR assays. This new TaqMan PCR assay will be a useful tool for the detection of animal TTV strains, to evaluate the viral load from animal host and finally to identify the presence of these viruses in the agri-food continuum.

Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohnʼs disease

Campylobacter concisus and other members of the Campylobacter genus have recently been suggested as possible etiological agents of Crohn's disease (CD). To further investigate this issue we determined the prevalence of these organisms in pediatric patients newly diagnosed with CD. DNA was extracted from fecal specimens collected from 54 children with CD, 27 noninflammatory bowel disease (non-IBD), and 33 healthy controls and subjected to polymerase chain reaction (PCR) sequencing. Detection of C. concisus DNA using a newly developed PCR assay targeting the 16S rRNA gene of C. concisus showed that 65% (35/54) of fecal samples from CD children were positive, a prevalence significantly higher than that in the healthy (33%, 11/33, P = 0.008) and non-IBD controls (37%, 10/27, P = 0.03). The prevalence of all Campylobacter DNA using genus-specific primers in children with CD was 72% (39/54), which was significantly higher than the 30% (10/33, P = 0.0002) and 30% (8/27, P = 0.0003) observed in healthy and non-IBD controls, respectively. Given the strengthening evidence for a significantly higher prevalence of C. concisus and other non-jejuni Campylobacter species in pediatric CD, investigation into the role of these non-jejuni Campylobacter species in the initiation of human IBD is clearly a priority.