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At least 19 recordsLinked to original sources
PubMed1995

[Prior enrichment of HIV-DNA with probe-DNA particles for an efficient PCR diagnosis].

PCR mediated detection of HIV-DNA has been widely used. However, compared with traditional immunological diagnoses, the extraction of DNA is a laborious and time consuming step. We have developed a procedure for the efficient isolation and concentration of HIV-DNA from cell lysates. We report here a novel method by one can recover HIV-DNA in a small volume (approximately 50 microliters) of solution from a large volume of crude cell lysate which contains as few as several copies. The method uses the specific hybridization of HIV-DNA to HIV probe-DNA particles. This prior enrichment augmented the sensitivity in the detection of HIV-DNA by PCR, and allows us to make a diagnosis even if the specimen contained an extremely low copy number of HIV-DNA molecules in a large volume, which would have otherwise resulted in false-negative data with the conventional extraction method. The method also enables the examination of 100 individual blood specimens in a combined form. Thus, the application of the present enrichment procedure with HIV probe-DNA particles should reduce the labor and cost of HIV diagnosis, since the HIV positive samples represent a very minor group of people among specimens subjected to clinical laboratory tests, and particularly, among blood samples voluntarily donated to be used for transfusions.

Base Sequence↗
PubMed2000

Characterisation of a novel interspersed Toxoplasma gondii DNA repeat with potential uses for PCR diagnosis and PCR-RFLP analysis.

A novel Toxoplasma gondii interspersed repeat element (TgIRE), present in most of the tachyzoite chromosomes, was characterised. Two regions on the TgIRE sequence showed high identity to two different T. gondii expressed sequence tag cDNAs of unknown function, which seems to be TgIRE pseudogenes. Two set of primers were designed, 2-2' and 2-3, that amplify products of 1.02 and 0.62 kb, respectively. T. gondii DNA from RH and Me49 strains was amplified with TgIRE 2-2' primers, and the respective 1.02 kb products were digested with several endonucleases. Different fragment patterns by gel electrophoresis were found only with MboI. Sensitivity analysis revealed that the set 2-3 was more sensitive than 2-2', detecting by gel visualisation the amount of DNA equivalent to 1 and 10 parasites, respectively.

Amino Acid Sequence↗
PubMed2001

Comparison of various sample preparation methods for PCR diagnosis of visceral leishmaniasis using peripheral blood.

We have compared various sample preparation methods for the PCR diagnosis of visceral leishmaniasis (VL) using peripheral blood samples and tested the influence of these protocols upon sensitivity. Four methods of lysis-DNA extraction were used with two types of blood samples: whole blood (WB) and buffy coat (BC). Comparisons were first carried out with seeded samples at various parasite concentrations. At high concentrations (> or = 1,000 parasites/ml), there were no significant differences in PCR sensitivity among the methods tested. At concentrations of < or = 100 parasites/ml, proteinase K (PK)-based methods proved clearly superior to guanidine-EDTA-based methods. Moreover, a 10-fold increase in sensitivity was observed for BC over that for WB. Thus, the best sensitivity was obtained with the BC prepared with PK-based methods. With this combination, the PCR reliably detected 10 parasites/ml but was inconsistent when the sample contained 1 parasite/ml of blood. The methods that yielded the highest sensitivities were evaluated with seven dogs and four human VL patients. Again, the utilization of the BC prepared with PK-based methods gave the best results. The optimization of each step of the assay (sample preparation, DNA extraction, and PCR conditions) yielded a highly sensitive tool for the diagnosis of VL using patient blood, thus avoiding more invasive diagnostic procedures and allowing the detection of low parasitemia during posttherapeutic follow-up.

Animals↗
PubMed2002

Usefulness of sampling with cotton swab for PCR-diagnosis of cutaneous leishmaniasis in the New World.

In this study, we tested the polymerase chain reaction (PCR)-method to diagnose cutaneous leishmaniasis (CL) by taking exudate materials from lesions with cotton swabs, using our previously tested (PCR) panel comprised of Leishmania (Viannia) panamensis, L. (V.) braziliensis, L. (V.) guyanensis, L. (Leishmania) mexicana and L. (L.) amazonensis. The objectives of the present study were to improve the sampling method convenient for the patients and to test the usefulness of samples taken with cotton swabs. Sixteen patients were clinically diagnosed to have CL including one case of diffuse cutaneous leishmaniasis (DCL) in Ecuador and the causative Leishmania parasites were identified by PCR. All the 12 samples from CL patients of La Mana, positive for Leishmania DNA, were identified as L. (V.) panamensis, while two from CL of Huigra and one from DCL of San Ignacio were L. (L.) mexicana. In the field condition, taking biopsy material is not only painful but sometimes causes iatrogenic bacterial infections. Considering the sensitivity of the test, and convenient sampling procedure, it may be suggested that collection of exudates using cotton swabs may be a better alternative to biopsy sample for PCR-diagnosis of CL.

Adult↗
PubMed1995

Use of a semi-nested PCR diagnosis test to evaluate antifolate resistance of Plasmodium falciparum isolates.

The antifols, inhibitors of the dihydrofolate reductase (DHFR), such as pyrimethamine and proguanil, have been used against Plasmodium falciparum in the areas where chloroquine resistance is widespread. This use has selected resistant strains in Southeast Asia and South America. The resistance is correlated with point mutations in precise positions of the DHFR gene. A reliable semi-nested PCR diagnosis test was established and used to determine the genotypic features of 29 isolates of P. falciparum originating from Africa. The results obtained by the PCR technique were compared with those of the in vitro drug sensitivity test. Some isolates were found to be polyclonal. Among the mutations tested, only mutations on codon 108 which generate an asparagine induce a decrease in sensitivity to pyrimethamine and cycloguanil, whereas mutation on codon 59 strengthens resistance to both antifols. No mutation on codon 16 or codon 164 was found.

Animals↗
PubMed1998

PCR diagnosis on formalin-fixed, paraffin-embedded tissues with acid-fast stain and culture negativity in chronic dialysis patients of cervico-mediastinal tuberculous lymphadenitis.

BACKGROUND: Bacteriologic studies often provide negative results in tuberculous infection, and do not favour early diagnosis. Polymerase chain reaction (PCR) is known to diagnose tuberculosis quickly. With this in mind, we used PCR to detect mycobacterial DNA on formalin-fixed, paraffin-embedded tissues with acid-fast stain and culture negativity in two dialysis patients with cervico-mediastinal lymphadenopathy. METHODS: Sections of neck lymph nodes were cut at two different levels. At each level, two semi-adjacent sections with a thickness of 5 microm each were cut using standard microtomes with disposable blades. The first section mounted on a glass slide was stained by Ziehl-Neelsen, and the second section was examined by PCR based on a 123 bp fragment of IS6110 that is specific for the Mycobacterium tuberculosis complex. RESULTS: The histology of lymph nodes disclosed inflammatory necrotizing granulomas, but acid-fast stain for M. tuberculosis was negative in the two patients. DNA of M. tuberculosis was detected in lymph node samples from each patient by PCR on the IS6110 element and by dot-blot hybridization. CONCLUSIONS: PCR assay is a potentially useful approach for early and rapid diagnosis of tuberculous lymphadenitis in chronic dialysis patients, since mycobacterial staining and culture often provide negative results.

Adult↗
PubMed1998

Molecular characterization and PCR diagnosis of Thailand deletion of alpha-globin gene cluster.

Thailand deletion of alpha-Thalassemia (thal) 1 involves the zeta2-, phi zeta1-, alpha2-, alpha1-, and theta1-globin genes. In Southeast Asians and Taiwanese, this mutation is the second most common long-segment deletion of two alpha-globin genes, after the Southeast Asian deletion. To define the Thailand deletion breakpoints, we used polymerase chain reaction (PCR) to amplify the normal-sequence DNA fragments across the breakpoints. The amplified products were sequenced directly or after cloning into pGem-3Z or pCR2.1 vectors. Comparison of the normal and mutant sequences revealed that the 5' breakpoint lies between nucleotides 1,269 and 1,290 upstream of the initiator codon adenine of the zeta2-globin gene, and the 3' breakpoint lies between nucleotides 29,387 and 29,408 downstream of it. A total of 30,677 nucleotides were deleted. Both breakpoints mentioned above lie within the Alu repetitive sequences and an extensive sequence homology is present around the two breakpoints. These findings suggest that homologous recombination is the mechanism by which the deletion occurs. Based on our data, we used three oligonucleotide primers to amplify the regions across the deletion and its corresponding normal sequence. The feasibility of PCR diagnosis was confirmed in 20 carriers with this deletion.

Base Sequence↗
PubMed2006

The consanguinity effect on QF-PCR diagnosis of autosomal anomalies.

OBJECTIVES: Quantitative Fluorescent PCR (QF-PCR) is a simpler and faster method of detecting common chromosomal abnormalities when compared to cytogenetic analysis. The aim of our study is to investigate the applicability of this methodology in a population where consanguineous marriages are common and to estimate the heterozygous frequency of the PCR markers used. METHODS: Four hundred and twenty-three DNA samples were extracted from uncultured amniocytes and amplified with 18 short tandem repeats (STR) markers specific to chromosomes 13, 18 and 21. Amplification products were analyzed using the GeneScan software. RESULTS: QF-PCR correctly identified all the numerical abnormalities related to chromosomes 13, 18 and 21. A total of 24 autosomal trisomies (5.7%) were detected. The markers D21S1432 and D21S11 were the most consistent in providing unequivocal positive results for chromosome 21 and the heterozygosity percentages of the markers used were lower than the values reported in Western populations. CONCLUSION: QF-PCR is reliable for the prenatal diagnosis of numerical anomalies of the chromosomes 13, 18 and 21 in our study population. The absence of STR heterozygosity data from Lebanon and surrounding countries makes our study very useful for the development of a reliable QF-PCR trisomy detection test.

Adult↗
PubMed1999

[Analysis of PCR-diagnosis of brucellosis in human].

Polymerase chain reaction (PCR) was used for the diagnosis of brucellosis in humans with different forms of this disease. A high incidence (77.6%) of Brucella infection was revealed in the staff of cattle breeding centers with unfavorable situation with regard to brucellosis. Such a conclusion was made after PCR testing of native human sera. In acute brucellosis of humans amplification of the specific site of brucella DNA in PCR is possible only after extraction of DNA by a procedure adapted for DNA extraction from intact brucella cells. In chronic infection weak amplification of brucella genome DNA fragment was observed in investigation of native sera by the PCR. More expressed amplification product was recorded in PCR with a DNA precipitate from this serum obtained by ethanol precipitation. A still higher level of brucella DNA fragment amplification was observed after DNA extraction from sediment obtained by ethanol precipitation from this serum. These data confirmed the incomplete phagocytosis phenomenon at the early stage of infection, known in brucellosis pathogenesis, and allowed some hypotheses on the pathogenesis of chronic phase of brucellosis infection.

Animals↗
PubMed2002

[Significance and limits of PCR diagnosis in orofacial and genital herpes simplex virus infection in the pregnant woman and neonate].

The availability of methods of detection of DNA by PCR amplification has deeply modified the knowledge on herpes simplex virus infections. These methods have allowed a better understanding of the physiopathogeny of the disease. In particular, PCR has revealed the importance of asymptomatic viral shedding in infected patients. PCR helps diagnosis in many situations where viral isolation by culture proves difficult or impossible, i.e. in treated or atypical lesions, or in newborn central nervous system infections. In addition, PCR has underlined the existence of prolonged viremia in infected newborns. PCR helps sequencing of the viral genome for further epidemiological studies or analysis of resistance to antiviral drugs. Recent PCR-derived techniques have been developed to quantify viral load in real time, and allow to obtain a diagnosis in a few hours. Despite these major advances, the use of PCR in several clinical situations still needs to be further validated.

Female↗
PubMedDate not supplied

PCR diagnosis of HPV in cervical biopsies of CIN and invasive neoplasia formerly diagnosed as HPV negative.

OBJECTIVE: To evaluate whether the polymerase chain reaction (PCR) enhances the diagnosis of human papillomavirus (HPV) in biopsies of the uterine cervix with cervical intraepithelial neoplasia (CIN) or invasive neoplasia. STUDY DESIGN: Samples of 71 paraffin-embedded cervical tissue blocks from patients seen in the period 1997-1998 were analyzed. Samples were selected according to age (18-60 years old) and an active sexual life and divided in to 3 groups: test (samples with CIN or invasive neoplasia and a negative HPV diagnosis), positive controls (samples with CIN or invasive neoplasia and a positive HPV diagnosis) and negative controls (samples without CIN or invasive neoplasia and a negative HPV diagnosis). Samples were subjected to DNA extraction and PCR for HPV detection. RESULTS: PCR analysis matched the colposcopic and cytopathologic diagnoses in the positive and negative controls. However, 77% of samples in test group were HPV positive. CONCLUSION: CIN, an invasive neoplasm, is associated with the presence of HPV. Colposcopy and cytopathology are efficient but not sufficient to identify HPV. Thus, despite the high cost, PCR can be used as an additional examination, in women with cervical lesions.

Adolescent↗
PubMed2005

Aspergillus polymerase chain reaction (PCR) diagnosis.

In recent years novel molecular methods, notably polymerase chain reaction (PCR) assays, have been developed to improve the diagnosis of life-threatening invasive aspergillosis in patients at high risk, especially patients with malignant hematological disease. Early diagnosis and treatment are essential for adequate therapeutic management. Management, however, often remains difficult since most of the diagnostic tools used clinically at present either lack specificity or acceptable sensitivity. The clinical value, advantages and remaining problems of PCR approaches to detect the emerging fungal pathogen are reviewed.

Aspergillosis↗
PubMed2006

Fecal specimens preparation methods for PCR diagnosis of human taeniosis.

Sample preparation and DNA extraction protocols for DNA amplification by PCR, which can be applied in human fecal samples for taeniasis diagnosis, are described. DNA extracted from fecal specimens with phenol/chloroform/isoamilic alcohol and DNAzol reagent had to be first purified to generate fragments of 170 pb and 600 pb by HDP2-PCR. This purification step was not necessary with the use of QIAmp DNA stool mini kit. Best DNA extraction results were achieved after eggs disruption with glass beads, either with phenol/chloroform/isoamilic alcohol, DNAzol reagent or QIAmp DNA stool mini kit.

Animals↗
PubMed2006

PCR diagnosis of Fasciola hepatica in field-collected Lymnaea columella and Lymnaea viatrix snails.

Fasciolosis, caused by the trematode Fasciola hepatica, is a zoonosis of economic importance in livestock that is emerging as a chronic disease in humans. The intermediate hosts are lymnaeid snails, in which diagnosis of infection is traditionally based on cercarial shedding, tissue sectioning and crushing. We developed a PCR assay for the sensitive and specific detection of F. hepatica in field-collected Lymnaea sp. snails. A primer pair was designed to amplify a 405 bp fragment of the cytochrome c oxidase subunit 1 gene of F. hepatica. The PCR assay showed a limit of detection of 10 pg of genomic F. hepatica DNA. No cross-reactions were observed with samples from other related trematode species or from the snail hosts Lymnaea columella and Lymnaea viatrix. DNA sequencing of the amplicon showed 100% homology with F. hepatica, and 75-89% homology with other trematodes on regions that did not include the entire set of primers. Two samples from Argentina were analysed. For snails in sample 1 (n = 240), identified as L. columella, the infection rate was 17.5 and 51.3% by direct examination and PCR, respectively. For snails in sample 2 (n = 34), identified as L. viatrix, the infection rate was 2.9 and 61.8% by direct examination and PCR, respectively. Differences in infection rates between these diagnosis methods were significant for both samples. Our PCR technique showed to be effective for detecting specific F. hepatica infections of low intensity in the intermediate host, and hence it could be used to study the epidemiological situation in a given area, as well as to assess host suitability for the parasite.

Animals↗
PubMed2006

[Outsourced real-time PCR diagnosis of cutaneous leishmaniasis in the outbreak region of Constatine, Algeria].

Taking into account the re-emergence of leishmaniasis in the world, the geographic variability of its epidemiology and the growing numbers of travellers, a pilot study on the diagnosis of cutaneous leishmaniasis was undertaken in Constatine, one of the outbreak regions in eastern Algeria. A total of 143 specimens were collected on blotters and tested by real-time PCR. Results were compared with those of direct examination. Diagnosis was positive for leishmaniasis in 81% of cases using PCR versus 48% of cases using microscopy. Real-time PCR showed a significant quantitative difference between patients for whom microscopic diagnosis was positive and those for whom direct examination was negative. The results presented in this study demonstrated the effectiveness and sensitivity of PCR in the diagnosis of cutaneous leishmaniasis from blotter specimens. This technique enabled in-field collection of specimens from each patient and provided prompt results. North-South cooperation based on the use of simple means for transmission of specimens for molecular diagnosis allowed creation of an effective partnership for daily diagnosis and promoted exchange between investigators in preparation for technology transfer.

Adolescent↗
PubMed2001

Integrated RT-PCR/nested PCR diagnosis for differentiating between subgroups of plum pox virus.

An RT-PCR/nested PCR technique was developed for the simultaneous detection and typing of plum pox virus (PPV) and its major types--Dideron (D), Marcus (M), El-Amar (EA) and Cherry (C). Degenerated oligonucleotides were synthesized for the general detection of PPV, flanking the coding sequence for the N-terminal portion of the coat protein (CP), within which strain-specific differences were identified. On the basis of these characteristic differences, degenerated primer pairs were designed to differentiate between the four major subgroups of the virus in nested PCR reactions. The validity of the technique was tested on viral strains and cloned cDNAs overlapping the CP region. High specificity was observed with no detectable cross-reactions. The results of general PPV detection with the new primers and those of the PCR-based detection of the 3' non-coding region of the viral genome correlated with complete coincidence. The PCR typing results correlated well with those of the RsaI-RFLP and serological typing and revealed a surprisingly high incidence of PPV-D in Hungary.

Amino Acid Sequence↗
PubMed2002

Comparison of different DNA preparation protocols for PCR diagnosis of Human African Trypanosomosis in Côte d'Ivoire.

During a medical survey the sleeping sickness focus in Bonon, Ivory Coast, PCR with Trypanosoma brucei specific primers (TBR 1-2 from Parasitology 99 (1989) 57) was tested on DNA derived from blood samples. DNA purification using a chelating resin was performed either on whole blood or on the buffy coat prepared in two different ways. The preparation based on whole blood performed better than those using the buffy-coat. Using this first method, the sensitivity was 100% on parasitologically confirmed patients, and the specificity was 92%. However, problems of reproducibility of the technique were pointed out, particularly on samples from serologically positive but apparently aparasitemic individuals. It is suggested that the PCR could help in the diagnosis of Human African Trypanosomosis, but the use of other primers should be investigated.

Animals↗
PubMed2006

Quality control assessment for the PCR diagnosis of tick-borne encephalitis virus infections.

BACKGROUND: Reverse transcriptase-polymerase chain reaction (RT-PCR) is an efficient method for the early detection of tick-borne encephalitis virus (TBEV) RNA in blood and serum samples taken prior to the appearance of antibodies. Improved diagnostics are critical for optimally detecting and managing TBE infections and quality control measures are therefore essential. OBJECTIVE: To assess the diagnostic quality of laboratories by performing an external quality assurance (EQA) programme for the molecular detection of TBE infections. STUDY DESIGN: A panel of 12 prepared human plasma samples were distributed and tested for the presence of TBEV-specific RNA. The panel comprised eight samples spiked with different TBEV strains of European, Siberian and Far Eastern subtypes, and included a 10-fold dilution series. Two specificity controls consisted of a sample with Louping ill virus (LIV) and a sample with a pool of four other flaviviruses, and two negative control samples were further included. RESULTS: Twenty-three laboratories from 16 European and 2 non-European countries participated in this EQA programme. Only two participants correctly identified all samples. Nine laboratories correctly identified 75.0-91.7% of the samples; seven laboratories correctly identified 54.5-66.7% and five laboratories correctly identified < or =50%. CONCLUSIONS: The EQA programme provides information on the quality of the RT-PCR methods used by the participating laboratories and indicates that most of these need to improve sensitivity and specificity of their molecular assays for TBEV.

Encephalitis Viruses, Tick-Borne↗