scholarly journals Genomics informed design of a suite of real‐time PCR assays for the specific detection of each Xylella fastidiosa subspecies

2020 ◽  
Author(s):  
Jennifer Hodgetts ◽  
Rachel Glover ◽  
Jennifer Cole ◽  
Jayne Hall ◽  
Neil Boonham
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Xylella Fastidiosa ◽  
Specific Detection ◽  
Pcr Assays

Development of real-time PCR assays for the specific detection of Francisella tularensis ssp. tularensis, holarctica and mediaasiatica

2010 ◽  
Vol 24 (2) ◽  
pp. 72-76 ◽  
Author(s):  
Jan L. Mitchell ◽  
Nicola Chatwell ◽  
Deanna Christensen ◽  
Helen Diaper ◽  
Timothy D. Minogue ◽  
...  
Keyword(s):  
Real Time ◽  
Francisella Tularensis ◽  
Real Time Pcr ◽  
Specific Detection ◽  
Pcr Assays

scholarly journals Intimin Gene (eae) Subtype-Based Real-Time PCR Strategy for Specific Detection of Shiga Toxin-Producing Escherichia coli Serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 in Cattle Feces

2013 ◽  
Vol 80 (3) ◽  
pp. 1177-1184 ◽  
Author(s):  
Delphine Bibbal ◽  
Estelle Loukiadis ◽  
Monique Kérourédan ◽  
Carine Peytavin de Garam ◽  
Franck Ferré ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Shiga Toxin ◽  
Real Time Pcr ◽  
Specific Detection ◽  
Content Type ◽  
E Coli ◽  
Cattle Feces ◽  
Pcr Assays

ABSTRACTShiga toxin-producingEscherichia coli(STEC) strains belonging to serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 are known to be associated with particular subtypes of the intimin gene (eae), namely, γ1, β1, ε, θ, and γ1, respectively. This study aimed at evaluating the usefulness of their detection for the specific detection of these five main pathogenic STEC serotypes in cattle feces. Using real-time PCR assays, 58.7% of 150 fecal samples were found positive for at least one of the four targetedeaesubtypes. The simultaneous presence ofstx,eae, and one of the five O group markers was found in 58.0% of the samples, and the five targetedstxpluseaeplus O genetic combinations were detected 143 times. However, taking into consideration the association betweeneaesubtypes and O group markers, the resultingstxpluseaesubtype plus O combinations were detected only 46 times. The 46 isolation assays performed allowed recovery of 22E. colistrains belonging to one of the five targeted STEC serogroups. In contrast, only 2 of 39 isolation assays performed on samples that were positive forstx,eaeand an O group marker, but that were negative for the correspondingeaesubtype, were successful. Characterization of the 24E. coliisolates showed that 6 were STEC, including 1 O157:H7, 3 O26:H11, and 2 O145:H28. The remaining 18 strains corresponded to atypical enteropathogenicE. coli(aEPEC). Finally, the more discriminatingeaesubtype-based PCR strategy described here may be helpful for the specific screening of the five major STEC in cattle feces.

Development and Application of Real-Time PCR Assays for Specific Detection of Contemporary Avian Influenza Virus Subtypes N5, N6, N7, N8, and N9

2018 ◽  
Vol 63 (sp1) ◽  
pp. 209 ◽  
Author(s):  
Joe James ◽  
Marek J. Slomka ◽  
Scott M. Reid ◽  
Saumya S. Thomas ◽  
Sahar Mahmood ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Avian Influenza ◽  
Avian Influenza Virus ◽  
Real Time ◽  
Real Time Pcr ◽  
Specific Detection ◽  
Pcr Assays

scholarly journals Novel real-time PCR assays for the specific detection of human infectiveCryptosporidiumspecies

Virulence ◽  
2016 ◽  
Vol 7 (4) ◽  
pp. 395-399 ◽  
Author(s):  
Maha Bouzid ◽  
Kristin Elwin ◽  
Johanna L. Nader ◽  
Rachel M. Chalmers ◽  
Paul R. Hunter ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Specific Detection ◽  
Pcr Assays

scholarly journals Development of a Real-Time PCR Probe for Quantification of the Heterotrophic Dinoflagellate Cryptoperidiniopsis brodyi (Dinophyceae) in Environmental Samples

2007 ◽  
Vol 73 (8) ◽  
pp. 2552-2560 ◽  
Author(s):  
Tae-Gyu Park ◽  
Miguel F. de Salas ◽  
Christopher J. S. Bolch ◽  
Gustaaf M. Hallegraeff
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Internal Transcribed Spacer ◽  
Environmental Samples ◽  
Field Survey ◽  
Temporal Variations ◽  
Heterotrophic Dinoflagellate ◽  
Specific Detection ◽  
Pcr Assays ◽  
Detection And Quantification

ABSTRACT A TaqMan format real-time PCR probe was developed against the internal transcribed spacer 2 ribosomal DNA region for the specific detection and quantification of Cryptoperidiniopsis brodyi in environmental samples. The assay specificity was confirmed by testing against related dinoflagellates and verified by sequencing PCR amplicons from natural water samples. Phylogenetic analysis of the sequenced environmental samples also showed that this assay is specific to C. brodyi. The C. brodyi-specific assay was used in conjunction with Pfiesteria piscicida- and Pfiesteria shumwayae-specific real-time PCR assays to investigate the temporal variations of C. brodyi, P. piscicida, and P. shumwayae abundance in the Derwent estuary, Tasmania. The 18-month field survey from November 2004 to April 2006 revealed that C. brodyi occurred in all seasons at very low densities, mostly below 25 cells liter−1, with higher abundance (maximum, 112 cells liter−1) in April and May. P. piscicida was detected only once, in May 2005 at 60 cells liter−1. P. shumwayae was not detected during the survey.

scholarly journals Real-Time PCR Assays for the Specific Detection of Field Balkan Strains of Lumpy Skin Disease Virus

2016 ◽  
Vol 66 (4) ◽  
pp. 444-454 ◽  
Author(s):  
Dejan Vidanović ◽  
Milanko Šekler ◽  
Tamaš Petrović ◽  
Zoran Debeljak ◽  
Nikola Vasković ◽  
...  
Keyword(s):  
Real Time ◽  
Disease Virus ◽  
Real Time Pcr ◽  
Skin Disease ◽  
Standard Procedure ◽  
Clinical Samples ◽  
Specific Detection ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Pcr Assays

Abstract Lumpy skin disease (LSD) is an important disease of cattle which is included in the OIE list of notifiable terrestrial animal diseases because of its great economic importance. The etiological agent is the Lumpy skin disease virus (LSDV). In the control of LSD attenuated strains of LSDV and SPPV are successfully used as vaccine strains in infected areas. In the case of vaccination policy, due to the possibility of mild or systemic post-vaccination reactions in vaccinated animals, the application of diagnostic procedures that will rapidly and specifically differentiate LSDV field strains from LSD vaccine virus strains are extremely important. Rapidity in diagnostics and disposal of infected animals is one of the key factors in the prevention of spreading the disease. In the presented study we have described the development and validation of two real-time TaqMan-PCR assays for a rapid, sensitive and specific detection of the virulent field LSDV strain currently circulating in the Balkan Peninsula. Specificity for the field strain and exclusivity for vaccine strains was tested on 171 samples from naturally infected and vaccinated animals. The results of this study show that both developed real-time PCR assays are more sensitive than the conventional nested PCR in detecting field LSDV strains thus enabling rapid and high-throughput detection of animals infected with field strains of LSDV. In conclusion, both KV-2 and FLI real-time PCR assays described in this study are simple, rapid, sensitive and suitable for routine use in a diagnostic laboratory and have the potential to replace conventional nested gel-based PCR assays as the standard procedure for the detection of field strains of LSDV in clinical samples.

scholarly journals Panel of 23S rRNA Gene-Based Real-Time PCR Assays for Improved Universal and Group-Specific Detection of Phytoplasmas

2009 ◽  
Vol 75 (9) ◽  
pp. 2945-2950 ◽  
Author(s):  
Jennifer Hodgetts ◽  
Neil Boonham ◽  
Rick Mumford ◽  
Matthew Dickinson
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Nested Pcr ◽  
Multiplex Assay ◽  
The Other ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Detection ◽  
23S Rrna Gene ◽  
Pcr Assays

ABSTRACT Primers and probes based on the 23S rRNA gene have been utilized to design a range of real-time PCR assays for routine phytoplasma diagnostics. These assays have been authenticated as phytoplasma specific and shown to be at least as sensitive as nested PCR. A universal assay to detect all phytoplasmas has been developed, along with a multiplex assay to discriminate 16SrI group phytoplasmas from members of all of the other 16Sr groups. Assays for the 16SrII, 16SrIV, and 16SrXII groups have also been developed to confirm that the 23S rRNA gene can be used to design group-specific assays.

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