Home About us Contact
|
Home About us Contact | ||
|
|
||
PCR Test (pcr + test)
Selected AbstractsEvaluation of a nested PCR test and bacterial culture of swabs from the nasal passages and from abscesses in relation to diagnosis of Streptococcus equi infection (strangles)EQUINE VETERINARY JOURNAL, Issue 1 2006L. MŲLLER GRŲNBĘK Summary Reasons for performing study: Streptococcus equi is the cause of strangles in horses. To improve diagnostic sensitivity, development and evaluation of DNA-based methods are necessary. Objectives: To evaluate diagnostic methods and observe the pattern of bacterial shedding during natural outbreaks. Methods: Two herds with natural outbreaks of strangles were visited over a period of 15 weeks and 323 samples originating from 35 horses investigated. The diagnostic use of a nested PCR test was evaluated using a collection of 165 isolates of Lancefield group C streptococci (species specificity) and swabs from nasal passages or from abscesses from horses infected with S. equi (diagnostic sensitivity). Results: All 45 S. equi isolates tested positive in the nested PCR, whereas no amplicon was formed when testing the other 120 Lancefield group C isolates. A total of 43 samples were collected from 11 horses showing clinical signs of strangles during the study period. The diagnostic sensitivity for PCR test was 45% and 80% for samples from the nasal passages and abscesses, respectively; the corresponding diagnostic sensitivity for cultivation was 18% and 20%. The diagnostic sensitivity was significantly higher for PCR than for bacterial cultivation. Furthermore, the shedding of S. equi in 2 infected horse populations was evaluated. An intermittent shedding period of S. equi of up to 15 weeks was recorded in this part of the study. It was also shown that shedding of S. equi occurred both from horses with and without clinical signs. Conclusions and potential relevance: The nested PCR test represents a species-specific and -sensitive method for diagnosis of S. equi from clinical samples. It may, however, be desirable in future to develop detection methods with high diagnostic sensitivity and specificity without the potential problems inherent in nested PCR. [source] High-resolution mapping of the Gli3 deletion in the mouse extra-toesH mutantGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 3 2007Matthieu Genestine Abstract Extra-toes is a semidominant mutation that affects the Gli3 gene and provokes limb and brain abnormalities. Among the different alleles of this mutation, XtH is due to a deletion that has not yet been fully characterized. Using a PCR-based strategy, we undertook a high-resolution mapping of this deletion and confirmed that XtH is a null allele of Gli3. We further designed a PCR test to identify unequivocally heterozygous and homozygous embryos from their wild-type littermates. Despite the length of the XtH deletion, available data on the mouse genome indicate that no genes other than Gli3 are deleted in XtH mutants. Thus, the XtH mutation can be used as a model for studying the effects that absence of Gli3 function has during development. genesis 45:107,112, 2007. © 2007 Wiley-Liss, Inc. [source] Validation of a real-time PCR for Haemophilus parasuisJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010C. Turni Abstract Aims:, To validate a real-time PCR test for the diagnosis of Glässer's disease, a major pig disease caused by Haemophilus parasuis. Methods and Results:, The specificity of a real-time PCR amplifying the inf,B gene was validated with 68 H. parasuis isolates and 36 strains of closely related species. As well, 239 samples of DNA from tissues and fluids of 16 experimentally challenged animals were tested with the real-time PCR, and the results were compared with culture and a conventional PCR. The real-time PCR produced significantly more positive results than the conventional PCR (165 vs 86). Conclusions:, The sensitivity of the real-time PCR combined with high specificity makes it a very valuable tool for the diagnosis of Glässer's disease. Significance and Impact of Study:, This new method will improve the ability of laboratories to diagnose Glässer's disease, especially in laboratories where the culture method for H. parasuis is not optimal. [source] Failure to confirm HIV infection in two end-stage HIV/AIDS patients using a popular commercial line immunoassayJOURNAL OF MEDICAL VIROLOGY, Issue 9 2008Julian W. Tang Abstract Immunoassays using either viral lysate (Western blot) or recombinant/synthetic antigen (immunoblot) for anti-HIV capture are still the preferred method to confirm HIV infection. Two cases of HIV-1-infected patients presented with acquired immunodeficiency syndrome (AIDS)-defining illnesses. Laboratory tests were performed using multiple commercial HIV test kits on multiple sera from both patients over several weeks. Both patients were strongly positive on the anti-HIV/p24 antigen combined screening assay. Yet, HIV-1 infection could not be confirmed using a popular commercial immunoassay. Eventually, HIV infection was confirmed using an alternative commercial Western blot assay as well as an HIV quantitative PCR test. In laboratories without nucleic acid testing (NAT) for HIV, indeterminate results may delay confirmation of HIV infection, if commercial line immunoassays alone are available. Some end-stage HIV/AIDS patients may not produce antibodies to specific HIV antigens and may therefore give indeterminant or negative results on some immunoassays, depending on the type of antigen used. This report highlights the utility of having NAT available when diagnosing difficult cases of HIV infection, especially in light of the recent Centers for Disease Control and Prevention move towards more universal, routine, HIV testing. J. Med. Virol. 80:1515,1522, 2008. © 2008 Wiley-Liss, Inc. [source] Rapid detection of Haemophilus influenzae by hel gene polymerase chain reactionLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2003M.C. Yadav Abstract Aims: To evaluate the efficiency of hel gene polymerase chain reaction (PCR) to detect Haemophilus influenzae in various clinical/non-clinical samples. Methods and Results: Seventy-four clinical samples (cerebrospinal fluid, blood, sputum, throat and nasal swabs) and throat swabs of 17 asymptomatic carriers were collected. Primers were used to amplify the hel gene of H. influenzae encoding P4 outer membrane protein directly from the processed samples. The samples were also examined by conventional culture methods and the results were compared with those of PCR. The culture methods showed positive results in 60 (65·9%) of 91 samples in contrast to 62 (68·12%) samples tested positive by PCR. None of the culture-positive samples were PCR-negative while two of the culture-negative samples were PCR-positive. The specificity of the products was confirmed by Southern hybridization and failure of various other organisms to amplify the hel gene product. The sensitivity of the PCR assay was found to be 50 pg of DNA. Conclusions: These findings suggest that the hel gene PCR is a rapid, sensitive and a specific new method for direct identification of H. influenzae. Significance and Impact of the study: Thus, this PCR test can improve the detection rate of H. influenzae in suspected clinical samples as compared with that of conventional culture methods. [source] Development of a PCR test to detect the downy mildew causal agent Plasmopara halstedii in sunflower seedsPLANT PATHOLOGY, Issue 2 2007R. Ioos Plasmopara halstedii, the causal agent of downy mildew of sunflower, is an obligate parasite but viable sporangia and oospores of the pathogen may be found in a quiescent state in seeds of sunflower and therefore may be transported with sunflower seeds in international commercial exchanges. In order to prevent the spread of this pathogen, especially the introduction of potentially new races, an efficient method to analyse sunflower seed samples is required. In this study, a P. halstedii -specific polymerase chain reaction (PCR) test was developed based on the ribosomal large sub unit (LSU) DNA. The forward (PHAL-F) and reverse (PHAL-R) PCR primers were designed from two polymorphic regions of LSU. After screening 22 isolates of P. halstedii corresponding to different races and countries and 32 other oomycete, deuteromycete and ascomycete isolates, the PHAL-F/R primers amplified only a single PCR band of c. 310 bp from P. halstedii. The PHAL-F/R PCR test could detect as little as 3 pg of P. halstedii genomic DNA per 20 µL reaction volume and enabled the direct detection of P. halstedii in 35 g sunflower seed samples without the need for any prior biological baiting step. An internal amplification control (IAC) was developed to help discriminate against false negative samples due to the potential presence of inhibitory compounds in DNA extracts. The test was successfully used on samples of naturally contaminated seeds. These new molecular tools should be of great interest for quarantine seed testing purposes. [source] A PCR test for mitochondrial heteroplasmy in sturgeonANIMAL GENETICS, Issue 2 2000A Ludwig [source] Real-time PCR with internal amplification control for detecting tuberculosis: method design and validationAPMIS, Issue 8 2009E. FLORES Flores E, Rodrķguez JC, Garcia-Pachón E, Soto JL, Ruiz M, Escribano I, Royo G. Real-time PCR with internal amplification control for detecting tuberculosis: method design and validation. APMIS 2009; 117: 592,7. Real-time PCR has been a major development in the diagnosis of tuberculosis. However, most tests do not include an internal amplification control (IAC), which therefore limits it clinical application. In this study a new, easy to perform real-time PCR test with IAC was designed and validated in clinical samples. The primers amplified a 163-bp fragment of IS6110 of Mycobacterium tuberculosis and the IAC was designed with a fragment of a different microorganism (Chlamydia trachomatis). The interassay and intraassay variation of this test were very low (0.45,1.65% and 0.18,1.80%, respectively). The detection accuracy was validated in 50 samples (25 urine, 25 sputum) with different concentrations of M. tuberculosis, 18 clinical isolates of non-tuberculous mycobacteria and 148 samples with clinical suspicion of pulmonary tuberculosis. The specificity was 100%. The detection limit of this PCR test without IAC was approximately 15 bacteria and with IAC approximately 32 bacteria. This real-time PCR with IAC assay can improve the detection of M. tuberculosis and contribute to standardization of this diagnostic technique. [source] Cost-effectiveness of different treatment strategies with intrapartum antibiotic prophylaxis to prevent early-onset group B streptococcal diseaseBJOG : AN INTERNATIONAL JOURNAL OF OBSTETRICS & GYNAECOLOGY, Issue 6 2005M.E. van den Akker-van Marle Objective To estimate the costs and effects of different treatment strategies with intrapartum antibiotic prophylaxis to prevent early-onset group B streptococcal (GBS) disease in the Netherlands. The treatment strategies include a risk-based strategy, a screening-based strategy, a combined screening/risk-based strategy and the current Dutch guideline. Design Cost-effectiveness analysis based on decision model. Setting Obstetric care system in the Netherlands. Population/Sample Hypothetical cohort of 200,000 neonates. Methods A decision analysis model was used to compare the costs and effects of different treatment strategies with no treatment. Baseline estimates were derived from literature and a survey among parents of children affected by GBS disease. The analysis was performed from a societal perspective, and costs and effects were discounted at a percentage of 3%. Main outcome measures Cost per quality adjusted of life-year (QALY). Result The risk-based strategy will prevent 352 cases of early-onset GBS for ,5.0 million, indicating a cost-effectiveness ratio of ,7600 per QALY gained. The combined screening risk-based strategy has comparable results. The current Dutch guideline resulted in lower effects for higher costs. The screening-based strategy shows the highest reduction in cases of early-onset GBS, however, at a cost-effectiveness ratio of ,59,300 per QALY gained. Introducing the polymerase chain reaction (PCR) test may lead to a more favourable cost-effectiveness ratio. Conclusion In the Dutch system, the combined screening/risk-based strategy and the risk-based strategy have reasonable cost-effectiveness ratios. If it becomes feasible to add the PCR test, the cost-effectiveness of the combined screening/risk-based strategy may even be more favourable. [source] Rapid assessment of the sex of codling moth Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) eggs and larvaeJOURNAL OF APPLIED ENTOMOLOGY, Issue 4 2009I. Fukovį Abstract Two different methods were tested to identify the sex of the early developmental stages of the codling moth Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) with a WZ/ZZ (female/male) sex chromosome system. First, it was shown that the sex of all larval stages can be easily determined by the presence or absence of sex chromatin, which is formed by the female-specific W chromosome in interphase nuclei. This trait can also be used to identify the sex of newly hatched larvae but it does require care and accuracy. Secondly, a new sexing technique was developed based on a molecular marker of the codling moth W chromosome. Flanking regions of an earlier described W-specific sequence (CpW2) were isolated and sequenced and a 2.74 kb sequence (CpW2- EcoRI), specific for the W chromosome, was obtained. Several PCR tests were conducted, which confirmed that the CpW2- EcoRI sequence is a reliable marker for the sex identification in codling moth samples of different geographical origin. In addition, a fragment of a codling moth gene, period (Cpper) was isolated and sequenced. Results of southern hybridization of the Cpper probe with female and male genomic DNA suggested that the Cpper gene is located on the Z chromosome. Then a multiplex PCR assay was developed, which co-amplified the CpW2- EcoRI sequence to identify the W chromosome and the Z-linked Cpper sequence, which served as a positive control of accurate processing of tested samples. The multiplex PCR provides an easy and rapid identification of the sex of embryos and early larval instars of the codling moth. [source] New molecular markers of early and progressive CJD brain infectionJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2004Zhi Yun Lu Abstract Transmissible spongiform encephalopathies (TSEs), including human Creutzfeldt,Jakob disease (CJD), are caused by a related group of infectious agents that can be transmitted to many mammalian species. Because the infectious component of TSE agents has not been identified, we examined myeloid cell linked inflammatory pathways to find if they were activated early in CJD infection. We here identify a specific set of transcripts in CJD infected mouse brains that define early and later stages of progressive disease. Serum amyloid A3 and L-selectin mRNAs were elevated as early as 20 days after intracerebral inoculation. Transcripts of myeloid cell recruitment factors such as MIP-1,, MIP-1,, and MCP1, as well as IL1, and TNF, were upregulated >10 fold between 30 and 40 days, well before prion protein (PrP) abnormalities that begin only after 80 days. At later stages of symptomatic neurodegenerative disease (100,110 days), a selected set of transcripts rose by as much as 100 fold. In contrast, normal brain inoculated controls showed no similar sequential changes. In sum, rapid and simple PCR tests defined progressive stages of CJD brain infection. These markers may also facilitate early diagnosis of CJD in accessible peripheral tissues such as spleen and blood. Because some TSE strains can differentially target particular cell types such as microglia, several of these molecular changes may also distinguish specific agent strains. The many host responses to the CJD agent challenge the assumption that the immune system does not recognize TSE infections because these agents are composed only of the host's own PrP. © 2004 Wiley-Liss, Inc. [source] Detection of Staphylococcus aureus and enterotoxin genotype diversity in Monte Veronese, a Protected Designation of Origin Italian cheeseLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2007A. Poli Abstract Aims:, To evaluate the risk associated with the load and enterotoxigenicity of Staphylococcus aureus in Monte Veronese, a PDO (Protected Designation of Origin) cheese of the Lessinia area (Verona, Italy). Methods and Results:,Staphylococcus aureus was quantified by a conventional culture method and by a nucA targeted real-time PCR assay developed in this study. Staphylococcus aureus numbers in cheese were higher than the limit tolerated by the Italian food legislation in 78% instances, according to both detection methods. Multiplex PCR tests for 17 Staph. aureus enterotoxin (SE) genes were applied to nucleic acids extracted from curds, cheeses and Staph. aureus isolates. The SE gene diversity appeared reduced after ripening. The gene encoding SED was found most frequently in dairy samples and the enterotoxin genes ser, sed, seg and sem predominated in the isolates. Conclusions:, The occurrence of enterotoxigenic Staph. aureus strains with complex SE genotypes in this PDO cheese at numbers often exceeding the Italian tolerance threshold represents an important risk factor. Significance and Impact of the Study:, The high frequency of contamination of Monte Veronese PDO cheese and, expectedly, similar typical productions from raw milk, by enterotoxigenic Staph. aureus imposes a tighter hygienic control in the earlier manufacturing phases. [source] Evaluation of Gossypium species for resistance to cotton leaf curl Burewala virusANNALS OF APPLIED BIOLOGY, Issue 1 2010K.P. Akhtar Cotton leaf curl disease (CLCuD), caused by cotton leaf curl Burewala virus (CLCuBV), has emerged as a major threat to cotton production in Pakistan. Resistance to CLCuBV was evaluated in cultivated and wild cotton genotypes representing six Gossypium species by visual symptom scoring and virus assessment using PCR tests. Considerable variation in responses was observed when using whitefly and graft transmission to inoculate Gossypium genotypes with CLCuBV in field and greenhouse experiments. Under field evaluation, all cultivated genotypes of Gossypium hirsutum and three genotypes of G. barbadense were susceptible. Eleven genotypes that represented six wild and cultivated Gossypium species were considered to be highly resistant as they were free from infection. Similar results were obtained when these genotypes were tested using whitefly transmission. To verify these findings, 132 cultivated and wild genotypes were tested by graft inoculation. All G. hirsutum genotypes (116 cultivated, 1 wild, 1 transgenic Coker-312 and 1 non-transgenic Coker-312), three G. barbadense genotypes and one G. thurberi genotype were highly susceptible and exhibited symptoms 9,12 days after grafting. Four genotypes of G. arboreum and one genotype of G. anomalum did not express symptoms but had a detectable level of virus. One genotype of G. herbaceum and three wild genotypes of G. hirsutum showed mild symptoms (severity indexes of 1,2) and exhibited delayed disease development. These genotypes were classified as moderately resistant to resistant. Resistant genotypes that were identified in this study will be useful sources for exploitation of breeding programmes aimed at developing CLCuBV-resistant varieties and increasing genetic diversity. [source] Australian surveillance for avian influenza viruses in wild birds between July 2005 and June 2007AUSTRALIAN VETERINARY JOURNAL, Issue 7 2009L Haynes Objective To identify and gain an understanding of the influenza viruses circulating in wild birds in Australia. Design A total of 16,303 swabs and 3782 blood samples were collected and analysed for avian influenza (AI) viruses from 16,420 wild birds in Australia between July 2005 and June 2007. Anseriformes and Charadriiformes were primarily targeted. Procedures Cloacal, oropharyngeal and faecal (environmental) swabs were tested using polymerase chain reaction (PCR) for the AI type A matrix gene. Positive samples underwent virus culture and subtyping. Serum samples were analysed using a blocking enzyme-linked immunosorbent assay for influenza A virus nucleoprotein. Results No highly pathogenic AI viruses were identified. However, 164 PCR tests were positive for the AI type A matrix gene, 46 of which were identified to subtype. A total of five viruses were isolated, three of which had a corresponding positive PCR and subtype identification (H3N8, H4N6, H7N6). Low pathogenic AI H5 and/or H7 was present in wild birds in New South Wales, Tasmania, Victoria and Western Australia. Antibodies to influenza A were also detected in 15.0% of the birds sampled. Conclusions Although low pathogenic AI virus subtypes are currently circulating in Australia, their prevalence is low (1.0% positive PCR). Surveillance activities for AI in wild birds should be continued to provide further epidemiological information about circulating viruses and to identify any changes in subtype prevalence. [source] | |||||||||||||||||||||||||