PCR Method For Simultaneous Detection Research Articles

Development and application of a cycleave dual-probe fluorescence quantitative PCR method for simultaneous detection of Mycoplasma gallisepticum ts-11 vaccine strain and non-ts-11 strains

Development and application of a cycleave dual-probe fluorescence quantitative PCR method for simultaneous detection of Mycoplasma gallisepticum ts-11 vaccine strain and non-ts-11 strains

A duplex fluorescent quantitative PCR assay to distinguish the genotype I and II strains of African swine fever virus in Chinese epidemic strains.

African swine fever (ASF) is a highly contagious hemorrhagic disease that affects domestic and wild pigs. A recent study reported that both ASF virus (ASFV) genotypes I and II have invaded farm-raised pigs in China, causing chronic infection and morbidity. To develop a duplex fluorescent quantitative PCR method to distinguish the ASFV genotypes I and II in Chinese epidemic strains, the probes and primers were designed based on the B646L sequences of genotypes I and II listed in the GenBank database. After optimizing the system, a duplex fluorescent quantitative PCR method for simultaneous detection of ASFV genotypes I and II B646L genes was successfully established. This method had no cross-reaction with Porcine circovirus type 2 (PCV2), Pseudorabies virus (PRV), or Porcine Parvovirus (PPV), indicating that it has strong specificity. The sensitivity results indicated that the minimum detection limit of ASFV genotypes I and II B646L was 10 copies/Rxn. The inter- and intra-group coefficients of variation were both <3%, indicating that the method was highly reproducible. Therefore, the established duplex fluorescent quantitative PCR assay is important for the differential detection and epidemiological investigation of ASFV.

Specific quantitative detection of Streptococcus suis and Actinobacillus pleuropneumoniae in co-infection and mixed biofilms.

Respiratory infections seriously affect the swine industry worldwide. Co-infections of two vital pathogenic bacteria Streptococcus suis (S. suis) and Actinobacillus pleuropneumoniae (A. pleuropneumoniae), colonizing the respiratory tract often occurs in veterinary clinical practice. Moreover, our previous research found that S. suis and A. pleuropneumoniae can form biofilm in vitro. The formation of a mixed biofilm not only causes persistent infections, but also increases the multiple drug resistance of bacteria, which brings difficulties to disease prevention and control. However, the methods for detecting S. suis and A. pleuropneumoniae in co-infection and biofilm are immature. Therefore, in this study, primers and probes were designed based on the conservative sequence of S. suis gdh gene and A. pleuropneumoniae apxIVA gene. Then, a TaqMan duplex real-time PCR method for simultaneous detection of S. suis and A. pleuropneumoniae was successfully established via optimizing the reaction system and conditions. The specificity analysis results showed that this TaqMan real-time PCR method had strong specificity and high reliability. The sensitivity test results showed that the minimum detection concentration of S. suis and A. pleuropneumoniae recombinant plasmid was 10 copies/μL, which is 100 times more sensitive than conventional PCR methods. The amplification efficiencies of S. suis and A. pleuropneumoniae were 95.9% and 104.4% with R2 value greater than 0.995, respectively. The slopes of the calibration curves of absolute cell abundance of S. suis and A. pleuropneumoniae were 1.02 and 1.09, respectively. The assays were applied to cultivated mixed biofilms and approximately 108 CFUs per biofilm were quantified when 108 CFUs planktonic bacteria of either S. suis or A. pleuropneumoniae were added to biofilms. In summary, this study developed a TaqMan real-time PCR assay for specific, accurate quantification of S. suis or A. pleuropneumoniae in mixed biofilms, which may help for the detection, prevention and control of diseases caused by a bacterial mixed infection involving S. suis and A. pleuropneumoniae.

Development and application of a multiplex PCR method for simultaneous detection of waterfowl parvovirus, duck enteritis virus and goose astrovirus.

Waterfowl parvovirus, duck enteritis virus and goose astrovirus have become serious pathogens in waterfowl farming. Co-infections occasionally occur, and as a result, it ismuchharderto rapidlyandsimultaneously identify several pathogens using conventional PCR. According to the characteristics of the goose parvovirus (GPV) and muscovy duck parvovirus (MDPV) genome sequences, a universal PCR primer was designed using Rep1 as the target gene. The specific detection primers were designed based on the specific conserved regions of UL54 of the duck enteritis virus (DEV) gene and ORF1a of the goose astrovirus (GAstV) gene. The PCR reaction system and conditions were optimized, and the optimal annealing temperature was found to be 56.2℃. The volume ratio of the GPV-MDPV, GAstV and DEV primers (20μM) was 1:4:5. The established multiplex PCR detection method can simultaneously detect GPV, MDPV, DEV and GAstVwithin one reaction, and be negative for duck Tembusu virus, muscovy duck reovirus, duck hepatitis A virus type 3 and duck circovirus. The method with excellent sensitivity, specificity and repeatability was successfully applied to clinical samples, it is a useful platform for identifing co-infections of GPV, MDPV, DEV and GAstV in waterfowl.

Multiplex PCR method for simultaneous detection of five pathogenic bacteria closely related to foodborne diseases.

In this study, we describe a multiplex PCR method for the detection of five food-relevant virulence pathogenicity genes of intestinal pathogens. Five pairs of primers were designed based on nuc gene for Staphylococcus aureus, hlyA gene of Listeria monocytogenes, ipaH gene of Shigella flexneri, lysP gene of Yersinia enterocolitica and tpi gene of Clostridium difficile. Conditions were optimized to amplify fragments of those genes simultaneously in one PCR amplification. After developing and optimizing the multiplex PCR reaction system, the specificity and sensitivity of the multiple PCR assays were evaluated. The optimized program is also applied to retail meat for testing. The result indicated that when the annealing temperature was 54°C and the primer concentrations of S. aureus, L. monocytogenes, S. flexneri, Y. enterocolitica and C. difficile are 10, 10, 5, 3 and 2μM, the five strains could expand 484, 345, 204, 156, 88bp of clear fragments, respectively. So was the multiple PCR in artificially contaminated beef produce. All cultures were cultured and separated by traditional methods. The multiplex PCR method offers a rapid, simple, and accurate identification of pathogens and could be used in food safety investigations, clinical diagnosis as well as for the surveillance of the spreading determinants of pathogens in epidemiological studies.

Establishment of rapid detection method for multiple real-time fluorescent PCR of toxin-producing fungi

To establish a multiplex real-time fluorescent PCR rapid detection method for simultaneous detection of aflatoxin-producing fungi and three latent toxin-producing fungi in a single system. Primers and probes were designed based on the protein activation genes AflR, ITS sequence, β-tubulin coding region and LS rRNA of aflatoxin-producing fungi, Aspergillusochraceus, Penicillium and Fusarium, respectively. A real-time fluorescent PCR method for simultaneous detection of commontoxin-producing fungi was performed, and the sensitivity and specificity of the method were analyzed by optimizing the reaction components and reaction conditions. The detection limits of the optimized reaction system for aflatoxin-producing fungi, Aspergillusochraceus, Penicillium and Fusarium were 3. 37×10~4, 1. 91×10~4, 1. 53×10~4, 3. 95×10~4 copies/reaction, respectively. The multiplex real-time fluorescent PCR assay established in this study is highly specific and sensitive. It can detect toxin-producing fungi within 2 hours and provide technical support for fungal monitoring in food.

Dichelobacter nodosus in sheep, cattle, goats and South American camelids in Switzerland—Assessing prevalence in potential hosts in order to design targeted disease control measures

Footrot is a contagious foot disease caused by the bacterium Dichelobacter nodosus (D. nodosus) that affects sheep worldwide. Due to substantial economic and welfare impact, various countries have developed control programs against footrot. The aim of this cross-sectional study was to estimate the national prevalence of virulent and benign D. nodosus in Switzerland in the four domestic ruminant species sheep, cattle, goats and South American camelids (SAC) to detect potential host populations and to propose targeted disease control measures. Risk factors for infection with the virulent strain of D. nodosus, based on a survey carried out among farmers, were investigated on animal and herd level. Overall, 613 farms and 2920 animals were investigated during 2017–18 applying a two-stage cluster sampling strategy. A Real-Time PCR method for simultaneous detection of virulent and benign strains of D. nodosus was used for the first time in such a large study. On animal level, the true prevalence (TP) of virulent D. nodosus in sheep was estimated at 16.9% (95% confidence interval (CI95%): 9.5–24.3%). In cattle and goats no virulent D. nodosus was detected and in SAC an apparent prevalence (AP) of 0.2% (CI95%: 0.0–0.4%) was observed. On farm level, a TP of virulent D. nodosus of 16.2% (CI95%: 8.4–25.2%) for sheep and an AP of 1.5% (CI95%: 0.3–5.2%) for SAC herds was estimated. Since the Swiss control program only targets the virulent strains of D. nodosus, it was concluded that cattle, goats and SAC do not play a role in footrot epidemiology in Switzerland. Adult sheep were at higher risk of infection for virulent D. nodosus compared to lambs and yearlings. On herd level, risk factors for infection with virulent D. nodosus in sheep were earlier occurence of footrot, winter compared to summer and autumn, and goat contact on pasture. Liming pastures had a protective effect on D. nodosus infection. For benign D. nodosus, the TP in sheep was 6.3% (CI95%: 1.6–11.0%) and in cattle 88.4% (CI95%: 83.8–93.0%). The TP for benign D. nodosus in sheep farms was 2.8% (CI95%: 0.0–10.5%) and in cattle farms 95.9% (CI95%: 91.7–98.1%). In goat and SAC farms, the AP was 6.6% (CI95%: 3.4–11.5%) and 7.4% (CI95%: 3.8–13.1%), respectively. These findings could be relevant for wild ruminants such as Alpine ibex (Capra ibex ibex), which can develop clinical footrot after infection with benign D. nodosus. The findings of this study are crucial for assessing targeted disease control measures in Switzerland.

Development and application of multiplex PCR method for simultaneous detection of seven viruses in ducks

BackgroundMajor viruses, including duck-origin avian influenza virus, duck-origin Newcastle disease virus, novel duck parvovirus, duck hepatitis A virus, duck Tembusu virus, fowl adenovirus, and duck enteritis virus, pose great harm to ducks and cause enormous economic losses to duck industry. This study aims to establish a multiplex polymerase chain reaction (m-PCR) method for simultaneous detection of these seven viruses.ResultsSpecific primers were designed and synthesized according to the conserved region of seven viral gene sequences. Then, seven recombinant plasmids, as the positive controls, were reconstructed in this study. Within the study, D-optimal design was adopted to optimize PCR parameters. The optimum parameters for m-PCR were annealing temperature at 57 °C, Mg2+ concentration at 4 mM, Taq DNA polymerase concentration at 0.05 U/μL, and dNTP concentration at 0.32 mM. With these optimal parameters, the m-PCR method produced neither cross-reactions among these seven viruses nor nonspecific reactions with other common waterfowl pathogens. The detection limit of m-PCR for each virus was 1 × 104 viral DNA copies/μL. In addition, the m-PCR method could detect a combination of several random viruses in co-infection analysis. Finally, the m-PCR method was successfully applied to clinical samples, and the detection results were consistent with uniplex PCR.ConclusionGiven its rapidity, specificity, sensitivity, and convenience, the established m-PCR method is feasible for simultaneous detection of seven duck-infecting viruses and can be applied to clinical diagnosis of viral infection in ducks.

Establishment and Application of a Real-time, Duplex PCR Method for Simultaneous Detection of Mycoplasma hyopneumoniae and Mycoplasma hyorhinis

Establishment and Application of a Real-time, Duplex PCR Method for Simultaneous Detection of Mycoplasma hyopneumoniae and Mycoplasma hyorhinis

Duplex PCR assay and in situ hybridization for detection of Francisella spp. and Francisella noatunensis subsp. orientalis in red tilapia.

Conventional isolation and identification based on phenotypic characteristics is challenging with the highly fastidious, intracellular bacterium Francisella noatunensis subsp. orientalis (Fno). Here, we developed a duplex PCR method for simultaneous detection of the Francisella genus and Fno in one PCR reaction and an in situ hybridization method for paraffin section based diagnosis of Fno. The PCR results showed genus- and species-specific bands (1140 and 203 bp) from Fno but only one genus-specific band (1140 bp) from F. noatunensis subsp. noatunensis. Sensitivity of the duplex PCR assay revealed a detection limit of 20 to 200 fg genomic DNA (~10 to 100 genome equivalents) depending on DNA template extraction methods. The newly developed duplex PCR assay could be used to detect Fno from clinically sick fish exhibiting signs of visceral granulomas and would also be able to detect Fno infection in naturally diseased fish without symptoms of francisellosis, indicating potential application for diagnosis of field samples. The in situ hybridization assay using Fno species-specific probe revealed positive signals in multiple organs including the spleen, liver, kidney, gills and intestine of infected fish.

Development and application of a multiplex PCR assay for detection of the Clostridium perfringens enterotoxin-encoding genes cpe and becAB

Clostridium perfringens causes food-borne gastroenteritis following the consumption of contaminated food by producing C. perfringens enterotoxin (CPE) in the intestines. Recently, we reported a novel enterotoxin, binary enterotoxin of C. perfringens (BEC) in C. perfringens isolates, which caused two disease outbreaks in Japan. Consequently, in the event of food poisoning outbreaks caused by C. perfringens, it is now necessary to screen for both the cpe and becAB genes by diagnostic PCR. Here, we present a simple multiplex PCR method for simultaneous detection of cpe, becAB and a C. perfringens control locus, phospholipase C (plc). Applying this method, we investigated the prevalence of cpe- or becAB-carrying C. perfringens strains in human stool and bovine rectum swab samples. Using a total of 169 isolates, we found that the percentage of becAB-carrying strains was very small (0.59%), one-tenth that of cpe-carrying strains. The simple method presented in this study with high specificity and sensitivity to C. perfringens will be a useful tool to survey the global prevalence of becAB-carrying C. perfringens strains.

Simultaneous detection of pathogenic Listeria including atypical Listeria innocua in vegetables by a quadruplex PCR method

Listeria species are major foodborne pathogens that are the causative agents of listeriosis, a severe infection with high fatality rates. The development of rapid methods to detect the potential presence of pathogenic Listeria is important, particularly in the food industry. In this study, we developed a quadruplex PCR method for simultaneous detection and differentiation of Listeria monocytogenes, Listeria ivanovii, Listeria innocua, and atypical L. innocua. The specificity of this PCR method was tested with 28 strains, including 15 Listeria strains and 13 other bacterial strains. The developed PCR method could detect target sequences in 0.1 ng/μL of genomic DNA present in the reaction mixtures. By employing a combination of four primer pairs, all targeted Listeria species were successfully differentiated within a single reaction. Up to 1–10 CFU in 20 g green romaine vegetable samples could be detected after 24 h enrichment. The quadruplex PCR method developed in this study may be a useful alternative to culture-based methods for the routine detection of Listeria in the food industry.

Development of a multiplex real-time PCR method for simultaneous detection of Vibrio parahaemolyticus, Listeria monocytogenes and Salmonella spp. in raw shrimp

Vibrio parahaemolyticus, Listeria monocytogenes and Salmonella spp. are important pathogens contaminating seafood in China. In this study, we developed an efficient multiplex real-time PCR for the simultaneous detection of V. parahaemolyticus, L. monocytogenes and Salmonella spp. in raw shrimp without a prior enrichment step. In a test using 28 target and non-target strains only the targets were detected and two calibration curves, for pure cultures and artificially contaminated samples, were used to evaluate the efficiencies of this method. Amplification efficiencies of this multiplex real-time PCR were excellent in pure cultures and artificially contaminated shrimps. The limits of detection in artificially contaminated shrimps were 112 CFU/g for V. parahaemolyticus, 158 CFU/g for L. monocytogenes and 103 CFU/g for Salmonella spp. We validated this multiplex real-time PCR method on 48 commercial samples and the results were comparable to standard culture methods. This efficient multiplex real-time PCR, where each test takes only 50 min after DNA extraction, is a useful tool for high-throughput surveillance of V. parahaemolyticus, L. monocytogenes and Salmonella spp. in seafood products.

A novel quadruplex real-time PCR method for simultaneous detection of Cry2Ae and two genetically modified cotton events (GHB119 and T304-40).

BackgroundTo date, over 150 genetically modified (GM) crops are widely cultivated. To comply with regulations developed for genetically modified organisms (GMOs), including labeling policies, many detection methods for GMO identification and quantification have been developed.ResultsTo detect the entrance and exit of unauthorized GM crop events in China, we developed a novel quadruplex real-time PCR method for simultaneous detection and quantification of GM cotton events GHB119 and T304-40 in cotton-derived products (based on the 5′-flanking sequence) and the insect-resistance gene Cry2Ae. The limit of detection was 10 copies for GHB119 and Cry2Ae and 25 copies for T304-40. The limit of quantification was 25 copies for GHB119 and Cry2Ae and 50 copies for T304-40. Moreover, low bias and acceptable standard deviation and relative standard deviation values were obtained in quantification analysis of six blind samples containing different GHB119 and T304-40 ingredients.ConclusionsThe developed quadruplex quantitative method could be used for quantitative detection of two GM cotton events (GHB119 and T304-40) and Cry2Ae gene ingredient in cotton derived products.

Development and evaluation of a multiplex PCR for simultaneous detection of five foodborne pathogens

To develop a rapid multiplex PCR method for simultaneous detection of five major foodborne pathogens (Staphylococcus aureus, Listeria monocytogenes, Escherichia coli O157:H7, Salmonella Enteritidis and Shigella flexneri, respectively). Amplification by PCR was optimized to obtain high efficiency. Sensitivity and specificity assays were investigated by testing different strains. With a multipathogen enrichment, multiplex PCR assay was able to simultaneously detect all of the five organisms in artificially contaminated pork samples. The developed method was further applied to retail meat samples, of which 80% were found to be positive for one or more of these five organisms. All the samples were confirmed by traditional culture methods for each individual species. This study reported a rapid multiplex PCR assay using five primers sets for detection of multiple pathogens. Higher consistency was obtained between the results of multiplex PCR and traditional culture methods. This work has developed a reliable, useful and cost-effective multiplex PCR method. The assay performed equally as well as the traditional cultural method and facilitated the sensitive detection both in artificially contaminated and naturally contaminated samples.

Development of a multiplex real-time PCR method for simultaneous detection of Salmonella enterica, Shigella flexneri and Listeria monocytogenes in processed food samples

The present work is focused on the development of a TaqMan multiplex real-time PCR method for the detection of Salmonella, Shigella and L. monocytogenes in seafood, meat and ready-to-eat products. The aim of this study is to detect the three pathogens in one single test including an enrichment medium for the simultaneous growth of the bacteria of interest and an Internal Amplification Control (IAC) to monitor PCR inhibitors. For this purpose, three genes were selected, invA for Salmonella, ipaH for Shigella and hlyA for L. monocytogenes. Also, no. 17 broth without dextrose and further modified by adding Tween 80 was used for the enrichment step. Specificity of the method was checked against a panel of 24 non-target bacterial strains. RT-PCR efficiency obtained for the simultaneous amplification of all three pathogens was 102.5% for Salmonella, 108.9% for Shigella and 106.4% for L. monocytogenes. The limit of detection (LOD) was evaluated in seafood, meat and ready-to-eat products, being established within 3 and 22 cfu in 25 g of sample for the three bacteria analyzed. Seventy-eight samples were analyzed with multiplex RT-PCR including spiked and natural samples collected from different laboratories. Even though several RT-PCR methods have been developed for the detection of Salmonella, Shigella and L. monocytogenes, as far as we know this is the first method developed for the simultaneous detection of these three pathogens, coupling RT-PCR with an enrichment in the same broth and being tested in a wide range of different processed food samples with a low LOD. The application of this method can significantly reduce costs and time of analysis in laboratories, what would be reflected in a faster response in those risk situations when they are detected.

Development of a multiplex PCR method for simultaneous detection of diagnostic DNA markers of five disease and pest resistance genes in potato

Multiplex PCR is practically a reasonable choice for molecular marker-assisted selection in potato breeding. We had developed and were using a multiplex PCR method for selection of resistance genes to cyst nematode (H1), Potato virus X (Rx1) and late blight (R1 and R2). Since then, more reliable and tightly linked markers for H1 and R2, and a new marker for resistance to Potato virus Y (Ry chc ) were developed. In this article, all these superior markers, including a positive marker to eliminate PCR-failed samples, were incorporated into one multiplex PCR assay. Using the newly developed multiplex PCR technique, five plants potentially harboring all five resistance genes were selected from 96 hybrid plants approximately 5 h after DNA extraction, which is a third of the operation time compared with separate PCR reactions for each marker.

Simultaneous Detection of Four Food Borne Bacterial Pathogens by Metal Hydroxide Immobilised Multiplex PCR Method

Salmonella enterica, Vibrio parahaemolyticus, Escherichia coli and Listeria monocytogenes are human pathogenic bacteria which could be contaminated with many types of food, especially meat products. Testing of food for those pathogens has become routine practice all over the world. However, since the available traditional detection methods are time consuming and labor intensive, there is a need for rapid, sensitive, specific and cost effective detection technique. In this study, a rapid and sensitive single tube Multiplex PCR method for simultaneous detection of those four bacterial pathogens by amplification of target genes gyrB of V. parahaemolyticus, invA of S. enterica, eaeA of E.coli and hly of L. monocytogene was established . Concentration of bacterial cells from food samples for DNA extraction is another problem in testing of food pathogens by PCR techniques. Metal hydroxide immobilization was applied prior to DNA extraction and found to be effective step to overcome this problem. Key words : Food-borne Pathogens; Metal Hydroxide Immobilization; Multiplex PCR DOI: 10.4038/tare.v12i1.1983 Tropical Agricultural Research & Extension 12(1):2009 42-46

Development of Multiplex PCR Method for Simultaneous Detection of Four Events of Genetically Modified Maize: DAS-59122-7, MIR604, MON863 and MON88017

A novel multiplex PCR method was developed for simultaneous event-specific detection of four events of GM maize, i.e., DAS-59122-7, MIR604, MON88017, and MON863. The single laboratory examination of analytical performance using simulated DNA mixtures containing GM DNA at various concentrations in non-GM DNA suggested that the limits of detection (LOD) of the multiplex PCR method were 0.16% for MON863, MIR604, and MON88017, and 0.078% for DAS-59122-7. We previously developed a nonaplex (9plex) PCR method for eight events of GM maize, i.e., Bt11, Bt176, GA21, MON810, MON863, NK603, T25, and TC1507. Together with the nonaplex PCR method, the newly developed method enabled the detection and identification of eleven GM maize events that are frequently included in commercial GM seed used in Japan. In addition, this combinational analysis may be useful for the identification of combined event products of GM maize.

Simultaneous detection of Escherichia coli O175:H7, Salmonella spp., and Listeria monocytogenes by multiplex PCR

The wide application of nucleic acid amplification techniques and the increasing industrial interest toward rapid methods has led to the development and application of PCR based methods for the detection of microbial pathogens in food. In the present paper we describe the development of a multiplex PCR method for simultaneous detection of Salmonella enterica serovar Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7 in a complex food matrix (liquid whole egg). Four different DNA extraction procedures were evaluated for their application on food and, among these, Chelex resin combined with a DNA purification step were found to better perform on the food system considered. A multiplex PCR system was developed, based on the evaluation and combination of published primer sets, and applied to the simultaneous detection of the target pathogens plus an internal amplification control, both in culture media and in a model food system. The overall system proposed, based on an overnight enrichment step followed by DNA isolation and multiplex PCR, was satisfactorily tested for its specificity and sensitivity and allowed the detection of the presence of bacterial DNA and the identification of the target pathogens down to 10 cells/25 g liquid whole egg.