scholarly journals Multiplex Fast Real-Time PCR for Quantitative Detection and Identification of cos- and pac-Type Streptococcus thermophilus Bacteriophages

2008 ◽  
Vol 74 (15) ◽  
pp. 4779-4781 ◽  
Author(s):  
Beatriz del Rio ◽  
María Cruz Martín ◽  
Noelia Martínez ◽  
Alfonso H. Magadán ◽  
Miguel A. Alvarez
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Industrial Process ◽  
Streptococcus Thermophilus ◽  
Quantitative Detection ◽  
Detection And Identification ◽  
Pcr Method

ABSTRACT The fermentation of milk by Streptococcus thermophilus is a widespread industrial process that is susceptible to bacteriophage attack. In this work, a preventive fast real-time PCR method for the detection, quantification, and identification of types of S. thermophilus phages in 30 min is described.

Quantitative Real-Time Polymerase Chain Reaction Detection of BK Virus Using Labeled Primers

2010 ◽  
Vol 134 (3) ◽  
pp. 444-448 ◽  
Author(s):  
Zhengming Gu ◽  
Jianmin Pan ◽  
Matthew J. Bankowski ◽  
Randall T. Hayden
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Real Time Pcr ◽  
Quantitative Polymerase Chain Reaction ◽  
Bk Virus ◽  
Clinical Samples ◽  
Quantitative Detection ◽  
Chain Reaction ◽  
Pcr Method ◽  
Polymerase Chain

Abstract Context.—BK virus infections among immunocompromised patients are associated with disease of the kidney or urinary bladder. High viral loads, determined by quantitative polymerase chain reaction (PCR), have been correlated with clinical disease. Objective.—To develop and evaluate a novel method for real-time PCR detection and quantification of BK virus using labeled primers. Design.—Patient specimens (n = 54) included 17 plasma, 12 whole blood, and 25 urine samples. DNA was extracted using the MagNA Pure LC Total Nucleic Acid Isolation Kit (Roche Applied Science, Indianapolis, Indiana); sample eluate was PCR-amplified using the labeled primer PCR method. Results were compared with those of a user-developed quantitative real-time PCR method (fluorescence resonance energy transfer probe hybridization). Results.—Labeled primer PCR detected less than 10 copies per reaction and showed quantitative linearity from 101 to 107 copies per reaction. Analytical specificity of labeled primer PCR was 100%. With clinical samples, labeled primer PCR demonstrated a trend toward improved sensitivity compared with the reference method. Quantitative assay comparison showed an R2 value of 0.96 between the 2 assays. Conclusions.—Real-time PCR using labeled primers is highly sensitive and specific for the quantitative detection of BK virus from a variety of clinical specimens. These data demonstrate the applicability of labeled primer PCR for quantitative viral detection and offer a simplified method that removes the need for separate oligonucleotide probes.

Quantitative Detection of Campylobacter jejuni on Fresh Chicken Carcasses by Real-Time PCR

2007 ◽  
Vol 70 (6) ◽  
pp. 1373-1378 ◽  
Author(s):  
ANNA-CLARA RÖNNER ◽  
HANS LINDMARK
Keyword(s):  
Detection Limit ◽  
Real Time ◽  
Dna Extraction ◽  
Campylobacter Jejuni ◽  
Real Time Pcr ◽  
Close Correlation ◽  
Quantitative Detection ◽  
Quantitative Real Time Pcr ◽  
Direct Plating ◽  
Pcr Method

Campylobacter jejuni infection is a significant cause of foodborne gastroenteritis worldwide. Consumption and handling of poultry products is believed to be the primary risk factor for campylobacteriosis. Risk assessments require quantitative data, and C. jejuni is enumerated usually by direct plating, which sometimes allows growth of non-Campylobacter bacteria. The objective of the present study was to develop a quantitative real-time PCR method (q-PCR) for enumerating C. jejuni in chicken rinse without a culturing step. The procedure to obtain the template for the PCR assay involved (i) filtration of 10 ml of chicken rinse, (ii) centrifugation of the sample, and (iii) total DNA extraction from the pellet obtained using a commercial DNA extraction kit. The detection limit of the method was comparable to that for plating 100 μl of chicken rinse on modified charcoal cefoperazone deoxycholate agar, and the detection limit could be further improved 10-fold by concentrating the DNA eluate by ethanol precipitation. A close correlation for spiked chicken rinse was obtained for the results of the quantitative real-time PCR method and direct plating (r = 0.99). The coefficient of correlation for the methods was 0.87 when samples from chicken carcasses on the slaughter line were analyzed, whereas a lower correlation (r = 0.76) was obtained when samples from retail carcasses were analyzed. Greater variation in the proportion of dead and/or viable but not culturable Campylobacter types in the retail samples may explain the decreased correlation between the methods. Overall, the new method is simple and fast and the results obtained are closely correlated with those for direct plating for samples containing a low proportion of dead Campylobacter cells.

scholarly journals An improved rapid quantitative detection and identification method for a wide range of fungi

2009 ◽  
Vol 58 (8) ◽  
pp. 1037-1044 ◽  
Author(s):  
Nobutoshi Soeta ◽  
Masanori Terashima ◽  
Mitsukazu Gotoh ◽  
Shuichi Mori ◽  
Kyoko Nishiyama ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Diagnostic Technique ◽  
Fungal Species ◽  
Quantitative Detection ◽  
Its2 Region ◽  
The Real ◽  
Detection And Identification ◽  
Wide Range ◽  
Pcr Products

To develop a rapid and quantitative diagnostic technique for the detection and identification of a wide range of fungi, an improved molecular method based on real-time PCR and the analysis of its products that targets the internal transcribed spacer (ITS) 2 region was established. The real-time PCR could quantitatively and specifically detect the ITS2 region from all 24 tested pathogenic fungal species at between 101 and 107 copies per test without amplification of bacterial or human DNA. The sequences of the primer-binding sites are conserved in the registered sequences of 34 other pathogenic fungal species, suggesting that the PCR would also detect these species. The hyperpolymorphic nature of the ITS2 region between fungal species in terms of length and nucleotide sequence provided valuable information for the determination of species. By labelling the 5′ end of the reverse primer with NED fluorescent dye, the fragment lengths of the real-time PCR products and their 3′-terminal fragments, derived using restriction enzyme ScrFI digestion, were easily evaluated by capillary electrophoresis. Using this analysis, the number and species of fungi present in samples could be estimated. Moreover, sequence analysis of the real-time PCR products could accurately determine species in samples containing a single species. This diagnostic technique can estimate a wide range of fungi from various clinical samples within 1 day and accurately identify them in 2 days. Quantitative results for fungal titre in samples can also provide useful information for understanding the progression of disease and the efficacy of antifungal chemotherapy.

scholarly journals Development of a mreB-targeted real-time PCR method for the quantitative detection of Vibrio harveyi in seawater and biofilm from aquaculture systems

Aquaculture ◽  
2020 ◽  
Vol 525 ◽  
pp. 735337 ◽  
Author(s):  
Julia Mougin ◽  
Roxane Roquigny ◽  
Marie-Agnès Travers ◽  
Thierry Grard ◽  
Maryse Bonnin-Jusserand ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Vibrio Harveyi ◽  
Quantitative Detection ◽  
Pcr Method

scholarly journals Direct Quantitative Detection and Identification of Lactococcal Bacteriophages from Milk and Whey by Real-Time PCR: Application for the Detection of Lactococcal Bacteriophages in Goat's Raw Milk Whey in France

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Mai Huong Ly-Chatain ◽  
Loïc Durand ◽  
Véronique Rigobello ◽  
Annabelle Vera ◽  
Yann Demarigny
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Direct Detection ◽  
Raw Milk ◽  
Quantitative Detection ◽  
Amplification Efficiency ◽  
The Real ◽  
Milk Whey ◽  
Detection And Identification ◽  
Milk Fermentation

The presence ofLactococcusbacteriophages in milk can partly or completely inhibit milk fermentation. To prevent the problems associated with the bacteriophages, the real-time PCR was developed in this study for direct detection from whey and milk of three main groups ofLactococcusbacteriophages, c2, 936, and P335. The optimization of DNA extraction protocol from complex matrices such as whey and milk was optimized allowed the amplification of PCR without any matrix and nontarget contaminant interference. The real-time PCR program was specific and with the detection limit of 102PFU/mL. The curve slopes were −3.49, −3.69, and −3.45 with the amplification efficiency estimated at 94%, 94%, and 98% and the correlation coefficient () of 0.999, 0.999, and 0.998 for c2, 936 and P335 group, respectively. This method was then used to detect the bacteriophages in whey and goat's raw milk coming from three farms located in the Rhône-Alpes region (France).

Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy

2017 ◽  
Vol 63 (4) ◽  
pp. 296-302 ◽  
Author(s):  
Massimiliano Bergallo ◽  
Ilaria Galliano ◽  
Paola Montanari ◽  
Martina Rosa Brusin ◽  
Serena Finotti ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Acute Gastroenteritis ◽  
Taqman Assay ◽  
Quantitative Detection ◽  
Common Disease ◽  
Median Viral Load ◽  
Significant Difference ◽  
Pcr Method ◽  
Children Under 5

Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.

scholarly journals Optimisation of protocol for Clostridium botulinum detection in mink feed

2015 ◽  
Vol 59 (3) ◽  
pp. 377-382
Author(s):  
Tomasz Grenda ◽  
Elżbieta Kukier ◽  
Magdalena Goldsztejn ◽  
Krzysztof Kwiatek ◽  
Nina Kozieł
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Anaerobic Bacteria ◽  
National Standards ◽  
Test Material ◽  
Gene Detection ◽  
Detection And Identification ◽  
Natural Microflora ◽  
Agar Media ◽  
Pcr Method

Abstract As the test material mink feed with natural microflora was used. The analyses were conducted using Wrzosek and TPGY broth media, and Willis–Hobbs and Zeissler differential agar media. Wrzosek, Willis–Hobbs, and Zeissler media are described in Polish Standards approved by the National Standards Body in Poland and routinely used in detection of anaerobic bacteria in Poland. Detection and identification of C. botulinum was performed with a previously validated real-time PCR method based on ntnh gene detection, which is common in all C. botulinum toxotypes. The use of Wrzosek broth and Zeissler agar in routine analyses for detection and identification of C. botulinum was ineffective and limited. The obtained results showed the highest culturing process effectiveness in TPGY broth with 72 h incubation at 30°C and isolation on Willis–Hobbs agar. The real-time PCR method based on ntnh gene detection used in this study could be utilised as a supplementary tool to the mouse lethality assay.

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