scholarly journals A Multiplex PCR Assay to Detect and Differentiate Select Agent Strains of Ralstonia solanacearum

Plant Disease ◽  
2015 ◽  
Vol 99 (3) ◽  
pp. 333-341 ◽  
Author(s):  
Michael J. Stulberg ◽  
Jonathan Shao ◽  
Qi Huang
Keyword(s):  
United States ◽  
Multiplex Pcr ◽  
Ralstonia Solanacearum ◽  
Species Complex ◽  
Bacterial Species ◽  
The United States ◽  
Pcr Assay ◽  
Plant Dna ◽  
Multiplex Pcr Assay ◽  
Verification Methods

Ralstonia solanacearum race 3 biovar 2 strains are considered select agents by the U.S. government because they are not endemic to the United States and have the potential to cause brown rot in our potato production fields. Simple and accurate methods are needed for quick identification prior to more discriminating but time-consuming verification methods. We developed a multiplex PCR assay that identifies R. solanacearum species complex strains, signals whether the strain detected is a select agent, and controls for false negatives associated with PCR inhibition or unsuccessful DNA extractions in one reaction. We identified unique sequences of non-phage-related DNA for the R. solanacearum species complex strains, and for select agent strains, using in silico genome subtraction. We also designed and included an internal plant DNA control assay. Our multiplex PCR assay correctly identified 90 R. solanacearum species complex strains and 34 select agent strains, while not recognizing five out-group bacterial species. Additionally, the multiplex PCR assay facilitated the detection of plant DNA and R. solanacearum from infected tomato, potato, geranium, and tobacco plants. Our rapid, accurate, and reliable detection assay can help government officials make timely and appropriate recommendations to exclude this bacterium from the United States.

scholarly journals Developing a One-Step Multiplex PCR Assay for Rapid Detection of Four Stubby-Root Nematode Species, Paratrichodorus allius, P. minor, P. porosus, and Trichodorus obtusus

Plant Disease ◽  
2019 ◽  
Vol 103 (3) ◽  
pp. 404-410 ◽  
Author(s):  
Danqiong Huang ◽  
Guiping Yan ◽  
Neil Gudmestad ◽  
Weimin Ye ◽  
Jonathan Whitworth ◽  
...  
Keyword(s):  
United States ◽  
Multiplex Pcr ◽  
The United States ◽  
Parasitic Nematodes ◽  
Diagnostic Efficiency ◽  
Pcr Assay ◽  
Its1 Region ◽  
Multiplex Pcr Assay ◽  
One Step ◽  
Plant Parasitic

Four trichodorid species, Paratrichodorus allius, P. minor, P. porosus, and Trichodorus obtusus, were found in multiple states in the United States. Traditional diagnosis based on morphology and morphometrics is laborious and requires an experienced taxonomist. Additionally, end-point diagnosis using PCR was only available for P. allius. To increase diagnostic efficiency and reduce costs, a one-step multiplex PCR assay was developed to simultaneously identify these four species using one PCR reaction. Available sequences of 18S ribosomal DNA and internal transcribed spacer 1 (ITS1) region of these species were aligned and five primers were designed. The conserved forward primer located in the 18S region, in combination with the species-specific antisense primer in the ITS1 region, amplified a single distinctive PCR fragment for each species (421/425 bp for P. allius, 190 bp for P. minor, 513 bp for P. porosus, and 353 bp for T. obtusus). In silico analysis with 10 other trichodorid species and experimental analysis using samples with these four species, 20 other plant-parasitic and three non-plant-parasitic nematodes demonstrated high specificity with the primers designed. The multiplex PCR amplified desirable fragments using a set of artificially mixed templates containing one, two, three, or four targeted species. The reliability of multiplex PCR results was demonstrated by using nematode populations isolated from infested fields from diverse geographic regions in eight states. The multiplex PCR-based tool developed in this study for the first time provides a simple, rapid, and cost-friendly assay for accurate diagnosis of the four major trichodorid nematodes in the United States.

scholarly journals Multiplex PCR Assay for Detection and Identification of Clostridium botulinum Types A, B, E, and F in Food and Fecal Material

2001 ◽  
Vol 67 (12) ◽  
pp. 5694-5699 ◽  
Author(s):  
Miia Lindström ◽  
Riikka Keto ◽  
Annukka Markkula ◽  
Mari Nevas ◽  
Sebastian Hielm ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Clostridium Botulinum ◽  
Botulinum Neurotoxin ◽  
Bacterial Species ◽  
Type A ◽  
Food Samples ◽  
Type B ◽  
Fecal Material ◽  
Pcr Assay ◽  
Multiplex Pcr Assay

ABSTRACT Botulism is diagnosed by detecting botulinum neurotoxin andClostridium botulinum cells in the patient and in suspected food samples. In this study, a multiplex PCR assay for the detection of Clostridium botulinum types A, B, E, and F in food and fecal material was developed. The method employs four new primer pairs with equal melting temperatures, each being specific to botulinum neurotoxin gene type A, B, E, or F, and enables a simultaneous detection of the four serotypes. A total of 43 C. botulinum strains and 18 strains of other bacterial species were tested. DNA amplification fragments of 782 bp for C. botulinum type A alone, 205 bp for type B alone, 389 bp for type E alone, and 543 bp for type F alone were obtained. Other bacterial species, including C. sporogenes and the nontoxigenic nonproteolytic C. botulinum-like organisms, did not yield a PCR product. Sensitivity of the PCR for types A, E, and F was 102 cells and for type B was 10 cells per reaction mixture. With a two-step enrichment, the detection limit in food and fecal samples varied from 10−2 spore/g for types A, B, and F to 10−1 spore/g of sample material for type E. Of 72 natural food samples investigated, two were shown to contain C. botulinum type A, two contained type B, and one contained type E. The assay is sensitive and specific and provides a marked improvement in the PCR diagnostics of C. botulinum.

Evaluation of a Multiplex PCR Assay for the Identification of Salmonella Serovars Enteritidis and Typhimurium Using Retail and Abattoir Samples

2017 ◽  
Vol 80 (2) ◽  
pp. 295-301 ◽  
Author(s):  
Dele Ogunremi ◽  
Susan Nadin-Davis ◽  
Andrée Ann Dupras ◽  
Imelda Gálvan Márquez ◽  
Katayoun Omidi ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Multiplex Pcr ◽  
Internal Control ◽  
Broiler Chickens ◽  
Salmonella Enteritidis ◽  
Bacterial Species ◽  
Pcr Assay ◽  
Multiplex Pcr Assay ◽  
Retail Outlets ◽  
Dna Fragment

ABSTRACT A multiplex PCR was developed to identify the two most common serovars of Salmonella causing foodborne illness in Canada, namely, serovars Enteritidis and Typhimurium. The PCR was designed to amplify DNA fragments from four Salmonella genes, namely, invA gene (211-bp fragment), iroB gene (309-bp fragment), Typhimurium STM 4497 (523-bp fragment), and Enteritidis SE147228 (612-bp fragment). In addition, a 1,026-bp ribosomal DNA (rDNA) fragment universally present in bacterial species was included in the assay as an internal control fragment. The detection rate of the PCR was 100% among Salmonella Enteritidis (n = 92) and Salmonella Typhimurium (n = 33) isolates. All tested Salmonella isolates (n = 194) were successfully identified based on the amplification of at least one Salmonella-specific DNA fragment. None of the four Salmonella DNA amplicons were detected in any of the non-Salmonella isolates (n = 126), indicating an exclusivity rate of 100%. When applied to crude extracts of 2,001 field isolates of Salmonella obtained during the course of a national microbiological baseline study in broiler chickens and chicken products sampled from abattoir and retail outlets, 163 isolates, or 8.1%, tested positive for Salmonella Enteritidis and another 80 isolates, or 4.0%, tested as Salmonella Typhimurium. All isolates identified by serological testing as Salmonella Enteritidis in the microbiological study were also identified by using the multiplex PCR. The new test can be used to identify or confirm pure isolates of the two serovars and is also amenable for integration into existing culture procedures for accurate detection of Salmonella colonies.

scholarly journals Multiplex PCR Analysis for Rapid Detection of Klebsiella pneumoniae Carbapenem-Resistant (Sequence Type 258 [ST258] and ST11) and Hypervirulent (ST23, ST65, ST86, and ST375) Strains

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Fangyou Yu ◽  
Jingnan Lv ◽  
Siqiang Niu ◽  
Hong Du ◽  
Yi-Wei Tang ◽  
...  
Keyword(s):  
United States ◽  
Klebsiella Pneumoniae ◽  
Multiplex Pcr ◽  
Virulence Genes ◽  
The United States ◽  
Sequence Type ◽  
Pcr Assay ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Resistant Strains

ABSTRACT Carbapenem-resistant and hypervirulent Klebsiella pneumoniae strains have emerged recently. These strains are both hypervirulent and multidrug resistant and may also be highly transmissible and able to cause severe infections in both the hospital and the community. Clinical and public health needs require a rapid and comprehensive molecular detection assay to identify and track the spread of these strains and provide timely infection control information. Here, we develop a rapid multiplex PCR assay capable of distinguishing K. pneumoniae carbapenem-resistant isolates of sequence type 258 (ST258) and ST11, and hypervirulent ST23, ST65/ST375, and ST86 clones, as well as capsular types K1, K2, K locus type 47 (KL47), and KL64, and virulence genes rmpA, rmpA2, iutA, and iroN. The assay demonstrated 100% concordance with 118 previously genotyped K. pneumoniae isolates and revealed different populations of carbapenem-resistant and hypervirulent strains in two collections in China and the United States. The results showed that carbapenem-resistant and hypervirulent K. pneumoniae strains are still rare in the United States, whereas in China, ∼50% of carbapenem-resistant strains carry rmpA/rmpA2 and iutA virulence genes, which are largely associated with the epidemic ST11 strains. Similarly, a high prevalence of hypervirulent strains was found in carbapenem-susceptible isolates in two Chinese hospitals, but these primarily belong to ST23, ST65/ST375, and ST86, which are distinct from the carbapenem-resistant strains. Taken together, our results demonstrated that this PCR assay can be a useful tool for molecular surveillance of carbapenem-resistant and hypervirulent K. pneumoniae strains.

scholarly journals “Pathotyping” Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence

2017 ◽  
Vol 55 (9) ◽  
pp. 2617-2628 ◽  
Author(s):  
Kate J. Howell ◽  
Lucy A. Weinert ◽  
Sarah E. Peters ◽  
Jinhong Wang ◽  
Juan Hernandez-Garcia ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Generalized Linear Model ◽  
Bacterial Species ◽  
Haemophilus Parasuis ◽  
Pcr Assay ◽  
Current Standard ◽  
Content Type ◽  
The United Kingdom ◽  
Multiplex Pcr Assay ◽  
Upper Respiratory

ABSTRACTHaemophilus parasuisis a diverse bacterial species that is found in the upper respiratory tracts of pigs and can also cause Glässer's disease and pneumonia. A previous pangenome study ofH. parasuisidentified 48 genes that were associated with clinical disease. Here, we describe the development of a generalized linear model (termed a pathotyping model) to predict the potential virulence of isolates ofH. parasuisbased on a subset of 10 genes from the pangenome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence. This new diagnostic mPCR was tested on 143 field isolates ofH. parasuisthat had previously been whole-genome sequenced and a further 84 isolates from the United Kingdom from cases ofH. parasuis-related disease in pigs collected between 2013 and 2014. The combination of the mPCR and the pathotyping model predicted the virulence of an isolate with 78% accuracy for the original isolate collection and 90% for the additional isolate collection, providing an overall accuracy of 83% (81% sensitivity and 93% specificity) compared with that of the “current standard” of detailed clinical metadata. This new pathotyping assay has the potential to aid surveillance and disease control in addition to serotyping data.

scholarly journals Confirmation of psaA in All 90 Serotypes of Streptococcus pneumoniae by PCR and Potential of This Assay for Identification and Diagnosis

2000 ◽  
Vol 38 (1) ◽  
pp. 434-437
Author(s):  
Katherine E. Morrison ◽  
Derrick Lake ◽  
Jennifer Crook ◽  
George M. Carlone ◽  
Edwin Ades ◽  
...  
Keyword(s):  
United States ◽  
Streptococcus Pneumoniae ◽  
Bacterial Species ◽  
The United States ◽  
Culture Collection ◽  
Pcr Assay ◽  
Gene Encoding ◽  
Atcc Strain ◽  
Viridans Group Streptococci ◽  
Culture Positive

ABSTRACT The gene encoding the pneumococcal surface adhesin A (PsaA) protein, psaA , was confirmed in all Streptococcus pneumoniae serotypes by a newly developed PCR ( psaA PCR) assay. Eighty-nine of the 90 serotypes amplified produced an 838-bp fragment; the exception was a serotype 16F strain acquired from the American Type Culture Collection (ATCC). Analysis of 20 additional 16F strains from the United States and Brazil showed that the gene was amplified in all 16F strains, implying that the serotype 16F ATCC strain must be a variant. The specificity of the assay was verified by the lack of signal from analysis of heterologous bacterial species ( n = 30) and genera ( n = 14), including viridans group streptococci. The potential of the assay for clinical application was shown by its ability to detect pneumococci in culture-positive nasopharyngeal specimens. Demonstration of psaA in all 90 serotypes and lack of amplification of heterologous organisms suggest that this assay could be a useful tool for detection of pneumococci and diagnosis of disease.

Development of a Multiplex Real-Time PCR Assay with Internal Amplification Control for the Detection of Shigella Species and Enteroinvasive Escherichia coli

2010 ◽  
Vol 73 (9) ◽  
pp. 1618-1625 ◽  
Author(s):  
DEANNE M. DEER ◽  
KEITH A. LAMPEL
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Real Time ◽  
Real Time Pcr ◽  
The United States ◽  
Internal Amplification Control ◽  
Control Strain ◽  
Pcr Assay ◽  
Multiplex Pcr Assay ◽  
Shigella Species

Shigella species, particularly S. sonnei and S. flexneri, remain some of the leading bacterial etiological agents of gastrointestinal diseases in the United States and globally. The isolation and detection of these foodborne pathogens are critical for preventing the spread of disease and facilitating epidemiological investigations aimed at determining the source of a Shigella infection outbreak. A multiplex real-time PCR-based assay was developed that targets all four species of Shigella plus enteroinvasive Escherichia coli. The assay incorporates primers directed to the ipaH genes located on both the virulence plasmid and chromosome, the plasmid-encoded virulence gene mxiC, a mutated mxiC gene (mxiC::kan) that differentiates wild-type strains from a laboratory control strain, and an internal amplification control. More than 50 isolates of all four Shigella species were tested for inclusivity and specificity of the multiplex PCR assay, and more than 30 non-Shigella isolates were tested for exclusivity of the assay. The sensitivity of the assay was 1 to 3 CFU and 5 to 50 fg of target (total) DNA for the ipaH, mxiC, and mxiC::kan gene targets. The assay performed equally well and with no measurable inhibition in the Shigella target reactions when rinsates of several high-risk produce commodities (parsley, cilantro, alfalfa sprouts, and lettuce) were added to the reactions. This multiplex PCR assay is sensitive and specific and has the added dimension of discriminating all Shigella species from the positive control strain so that in any sample analysis other strains can be excluded as a source of contamination.

Usefulness of a Multiplex PCR for Detection of Diarrheagenic Escherichia coli in a Diagnostic Microbiology Laboratory Setting

2016 ◽  
Vol 1 (2) ◽  
pp. 38-42 ◽  
Author(s):  
Khairun Nessa ◽  
Dilruba Ahmed ◽  
Johirul Islam ◽  
FM Lutful Kabir ◽  
M Anowar Hossain
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Clinical Laboratory ◽  
Proteinase K ◽  
Microbiology Laboratory ◽  
Pcr Assay ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Multiplex Pcr Assay ◽  
Diagnostic Microbiology

A multiplex PCR assay was evaluated for diagnosis of diarrheagenic Escherichia coli in stool samples of patients with diarrhoea submitted to a diagnostic microbiology laboratory. Two procedures of DNA template preparationproteinase K buffer method and the boiling method were evaluated to examine isolates of E. coli from 150 selected diarrhoeal cases. By proteinase K buffer method, 119 strains (79.3%) of E. coli were characterized to various categories by their genes that included 55.5% enteroaggregative E. coli (EAEC), 18.5% enterotoxigenic E. coli (ETEC), 1.7% enteropathogenic E. coli (EPEC), and 0.8% Shiga toxin-producing E. coli (STEC). Although boiling method was less time consuming (<24 hrs) and less costly (<8.0 US $/ per test) but was less efficient in typing E. coli compared to proteinase K method (41.3% vs. 79.3% ; p<0.001). The sensitivity and specificity of boiling method compared to proteinase K method was 48.7% and 87.1% while the positive and negative predictive value was 93.5% and 30.7%, respectively. The majority of pathogenic E. coli were detected in children (78.0%) under five years age with 53.3% under one year, and 68.7% of the children were male. Children under 5 years age were frequently infected with EAEC (71.6%) compared to ETEC (24.3%), EPEC (2.7%) and STEC (1.4%). The multiplex PCR assay could be effectively used as a rapid diagnostic tool for characterization of diarrheagenic E. coli using a single reaction tube in the clinical laboratory setting.Bangladesh J Med Microbiol 2007; 01 (02): 38-42

Sign in / Sign up

Export Citation Format

Share Document