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PubMed1996

Evaluation of the Gen-Probe amplified Mycobacterium tuberculosis direct detection test.

Mycobacterium tuberculosis direct (MTD) testing was performed on 423 specimens (from 293 patients) submitted for mycobacterial culture, including 121 from 47 patients with current or recent cultures positive for tuberculosis. Resolved sensitivity and specificity were 91.4% and 99.3%, respectively. The assay detected 12 of 14 patients with one specimen and 31 of 32 with > or = 2 specimens. The 10 missed specimens included 2 resembling blood clots and 6 smear negative or 1+ specimens; however, a 2+ and a 4+ specimen were missed, which implies inhibitors. Some smear positive/culture negative and smear negative/culture negative specimens from treated patients gave positive results. The number of smear negative, culture positive specimens from untreated patients was too low to evaluate rigorously. Consideration of these observations and of costs suggests that the assay is appropriate only for untreated patients with smear-positive, nonbloody specimens. They should not be reported as negative for tuberculosis until three smear positive specimens have given negative MTD results. Factors involved in the generation of false positive results, including amplicon contamination, are evaluated.

Bacteriological Techniques↗
PubMed2002

Performance assessment of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex from respiratory and extrapulmonary specimens.

The new BDProbeTec ET Mycobacterium tuberculosis Complex Direct Detection Assay (DTB) was compared with the enhanced M. tuberculosis Amplified Direct Test (AMTDII). The system is an automated walkaway system characterized by simultaneous DNA amplification (strand displacement amplification) and real-time fluorometric detection. It also contains an internal amplification control (IAC) designed to identify inhibition from the processed samples. The AMTDII assay amplifies rRNA by transcription-mediated amplification; it uses hybridization with a chemoluminescent probe as a detection system and is entirely manual. A total of 515 N-acetyl-L-cysteine-sodium hydroxide-decontaminated respiratory (n = 331) and extrapulmonary (n = 184) sediments (from 402 patients) were tested in parallel by both assays. The results were compared with those of acid-fast staining and culture (solid plus liquid media), setting the combination of culture and clinical diagnosis as the "gold standard." Culture results from the tested specimens were as follows: 121 Mycobacterium tuberculosis complex (MTB) (98 smear-positive), 46 nontuberculous mycobacteria (38 smear-positive), and 338 culture-negative results. After resolution of the discrepant results, the percent sensitivity, percent specificity, and positive and negative likelihood ratios for AMTDII were 88%, 99.2%, 110, and 0.11 for respiratory specimens and 74.3%, 100%, 740, and 0.26 for extrapulmonary specimens, respectively. The corresponding values for DTB were 94.5%, 99.6%, 235, and 0.05 for respiratory specimens and 92.3%, 100%, 920, and 0.07 for extrapulmonary specimens, respectively. The cumulative difference for all tuberculosis-positive extrapulmonary specimens was significant (P = 0.03). The overall inhibition rate for DTB was 5% (26 specimens). We conclude that both amplification assays proved to be rapid and specific for the detection of MTB in clinical samples and particularly feasible for a routine laboratory work flow. DTB combines a labor-intensive specimen preparation procedure with a completely automated amplification and detection. Finally, differences between AMTDII and DTB sensitivities were associated with the presence of inhibitory samples that the former assay, lacking IAC, could not detect.

Humans↗
PubMedDate not supplied

Direct detection of 8-oxo-deoxyguanosine using UV resonance Raman spectroscopy.

8-oxo-deoxyguanosine (8-oxo-dG) is a major oxidative lesion in DNA and is responsible for mutation and cancer. Current techniques for detecting 8-oxo-dG are indirect methods. Thus, development of new methodologies is needed to directly detect such oxidative lesions. In this article, we have used ultraviolet resonance Raman (UVRR) spectroscopy as a novel analytical technique for the detection of 8-oxo-dG. Here, the UVRR spectrum of 8-oxo-dG was acquired and compared to that of deoxyguanosine (dG) and deoxyadenosine (dA). Data analysis shows a distinct UVRR spectrum of 8-oxo-dG with characteristic peaks. Detection of 8-oxo-dG was easily achieved from a mixture with dG. These results reveal that UVRR spectroscopy shows promise as a direct method for detecting 8-oxo-dG.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1990

Multicenter clinical evaluation of the Du Pont Herpchek HSV ELISA, a new rapid diagnostic test for the direct detection of herpes simplex virus.

A new 4h rapid enzyme-immunoassay for direct detection of herpes simplex virus (HSV) antigen (Du Pont Herpchek) was evaluated with 743 clinical samples collected at obstetrics and gynecology (OB/GYN), sexually transmitted diseases (STD), and ophthalmology clinics. The sensitivity and specificity of Herpchek was 98.0% and 98.4% respectively compared to virus isolation in cell culture. Confirmatory blocking ELISA tests, clinical history and follow up indicate that the true specificity of the test is 100%.

Adult↗
PubMed2001

Development of an electrochemical immunosensor for direct detection of interferon-gamma at the attomolar level.

An electrochemical immunosensor for direct detection of the 15.5-kDa protein interferon-gamma (IFN-gamma) at attomolar level has been developed. Self-assembled monolayers (SAMs) of cysteine or acetylcysteine are formed on electropolished polycrystalline Au electrodes. IFN-gamma adsorbs physically to each of these SAMs. With injections of 100 mM KCl, IFN-gamma can be removed in the flow without damaging the acetylcysteine SAM. However, the cysteine SAM is affected by these KCl injections. In an on-line procedure in the flow, a specific antibody (MD-2) against IFN-gamma is covalently attached following carbodiimide/succinimide activation of the SAM. The activation of the carboxylic groups, attachment of MD-2, and deactivation of the remaining succinimide groups with ethanolamine are monitored impedimetrically at a frequency of 113 Hz, a potential of +0.2 V versus SCE, and an ac modulation amplitude of 10 mV. Plots of the real (Z') and imaginary (Z") component of the impedance versus time provide the information to control these processes. In the thermostated setup (23.0 degrees C), samples of unlabeled IFN-gamma (in phosphate buffer pH 7.4) are injected and the binding with immobilized MD-2 is monitored with ac impedance or potential-step methods. While the chronoamperometric results are rather poor, the ac impedance approach provides unsurpassed detection limits, as low as 0.02 fg mL-1 (approximately 1 aM) IFN-gamma. From a calibration curve (i.e. Z" versus the amount injected), recorded by multiple 50-microL injections of 2 pg mL(-1) of IFN-gamma, a dynamic range of 0-12 pg mL(-1) could be derived. However, when nonspecific adsorption is taken into account, which has been found to be largely reduced through injections of 100 mM KCl, a much smaller dynamic range of 0-0.14 fg mL(-1) remains. The immunosensor can be regenerated by using a sequence of potential pulses in the flow by which the SAM with attached MD-2 and bound IFN-gamma is completely removed. When the developed procedures described above are repeated, the response of the immunosensor is reproducible within 10%.

Acetylcysteine↗
PubMed2006

Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples.

AIMS: A rapid and sensitive method for Listeria monocytogenes direct detection from milk was developed. It is based on a magnetic capture hybridization procedure for selective DNA purification, followed by PCR identification. A comparison with two similar commercial systems from Dynal (Dynabeads) was carried out. METHODS AND RESULTS: The technique used previously developed nanoparticles modified with a 21-mer oligonucleotide. This sequence, sharing homology with all the L. monocytogenes strains, was selected on hlyA gene and located outside the desired specific PCR site to avoid cross-contaminations. Capture probe properties, in term of spacer length and purification, were determined to obtain the highest hybridization efficiency. Its specificity was tested in hybridization experiments with nontarget bacterial species. Any inhibitory effect of the nanoparticles on PCR was also examined. The amplification performed with the purified DNA could reliably identify a 10 CFU ml(-1) contamination rate. CONCLUSIONS: The optimized purification method showed a high specificity and sensitivity, with a detection level one log more sensitive than PCR carried out with nucleic acids obtained using commercial nanoparticles. SIGNIFICANCE AND IMPACT OF THE STUDY: The method, avoiding pre-enrichment, provides a rapid alternative to conventional microbiological detection methods. Furthermore, it is suitable for automation and can be proposed for the screening of a large number of samples.

Adsorption↗
PubMed2002

Two-channel direct-detection Doppler lidar employing a charge-coupled device as a detector.

A direct-detection Doppler lidar system is demonstrated that uses a CCD as a detector for the first time to our knowledge. The ability to use this linear device with the circular output from a Fabry-Perot etalon comes from use of a circle-to-line converter [Appl. Opt. 29, 1482 (1990)]. In addition to the gains in quantum efficiency obtained through use of this detector, the lidar system described in this paper also has the capability to measure winds from aerosol and molecular backscatter simultaneously in two separate channels by directing the light reflected from one channel into the other. Early measurements with this system are presented; it is shown that, although accurate aerosol wind measurements are easily obtained, molecular measurements require a carefully calibrated inverse model and special hardware to derive accurate wind measurements with this channel.

Journal Article↗
PubMed1997

Direct detection by PCR of Escherichia coli O157 and enteropathogens in patients with bloody diarrhea.

Direct detection of Escherichia coli O157 and foodborne pathogens associated with bloody diarrhea were achieved using polymerase chain reaction (PCR) after the preparation of DNA from stool specimens using the microspin technique. PCR was compared with cultivation and toxin production tests with respect to the efficiency of detection of each pathogen; E. coli O157, Vibrio parahaemolyticus, Salmonella serovar Enteritidis and Campylobacter jejuni. Detection of some or all of the above pathogens in clinical stool specimens was achieved using PCR. The minimum number of cells required for the detection of the above pathogens by PCR was 10(1) CFUs/0.5 g of stool sample. PCR was completed within 6 hr. The above pathogens were also detected in cultivation and toxin production tests. Partial purification of the template DNA using the microspin technique was essential for the elimination of PCR inhibitors from the DNA samples. This PCR method is an accurate, easy-to-read screening method for the detection of Shiga-like toxin producing E. coli O157 and enteropathogens associated with bloody diarrhea in stool specimens.

Bacteria↗
PubMed1990

Direct detection of Salmonella spp. in estuaries by using a DNA probe.

A method for direct detection of Salmonella spp. in water was developed by using a commercially available DNA probe. Particulate DNA was extracted from 500- to 1,500-ml water samples collected from New York Harbor and Chesapeake Bay and used as a substrate for a salmonella-specific DNA probe in dot blot assays. The method detected salmonellae in water samples from 12 of 16 sites, including 6 sites where salmonellae could not be cultured. The specificity of the probe was evaluated, and cross-hybridization, although negligible, was used to set detection limits for the assay. Salmonella DNA bound the probe quantitatively, and from these results Salmonella DNA in the total particulate DNA in environmental samples could be estimated. The data obtained in this study indicate that Salmonella spp. often are not detected in water samples by culture methods, even when they are present in significant numbers.

DNA Probes↗
PubMed1987

Dot immunoperoxidase assay using monoclonal antibody for direct detection of cytomegalovirus in urine samples.

A rapid, simple dot immunoperoxidase assay for the direct detection of cytomegalovirus in clinical urine samples was developed. The assay was performed on nitrocellulose paper dotted with urine pellets free of cellular debris. Cytomegalovirus was detected with a monoclonal antibody to the capsid antigen, and the complex was visualized by immunoperoxidase staining. Positive reactions appeared as well-defined dark blue spots. Of the 87 urine samples examined, 10 proved positive in the dot immunoperoxidase assay, and 77 proved negative. The results agreed completely with the detection of cytomegalovirus-induced antigens in cell cultures inoculated with clinical specimens.

Antibodies, Monoclonal↗
PubMed1990

Dot ELISA for direct detection of BK virus in urine samples.

The dot ELISA technique was applied for direct detection of BK virus in clinical urine samples. The assay was performed on nitrocellulose paper dotted with the polyethylene glycol precipitated urine samples free of cellular debris. BK virus was detected with an anti-BK virus monoclonal antibody, and the complex was visualized by immunoperoxidase staining. Positive reaction appeared as well-defined dark blue spots. Of the 110 urine samples examined, 31 were positive in the dot ELISA and 79 proved negative. Comparing with the IIF results, the dot ELISA had a 88.46% of sensibility and 90.4% of specificity, and the results agreed completely in 99 samples. The simple dot ELISA technique can be recommended for detection of BK virus excretion in routinary diagnostic.

Animals↗
PubMed2003

Use of PCR for direct detection of Campylobacter species in bovine feces.

This study reports on the use of PCR to directly detect and distinguish Campylobacter species in bovine feces without enrichment. Inhibitors present in feces are a major obstacle to using PCR to detect microorganisms. The QIAamp DNA stool minikit was found to be an efficacious extraction method, as determined by the positive amplification of internal control DNA added to bovine feces before extraction. With nested or seminested multiplex PCR, Campylobacter coli, C. fetus, C. hyointestinalis, and C. jejuni were detected in all fecal samples inoculated at approximately 10(4) CFU g(-1), and 50 to 83% of the samples inoculated at approximately 10(3) CFU g(-1) were positive. At approximately 10(2) CFU g(-1), C. fetus, C. hyointestinalis, and C. jejuni (17 to 50% of the samples) but not C. coli were detected by PCR. From uninoculated bovine feces, a total of 198 arbitrarily selected isolates of Campylobacter were recovered on four commonly used isolation media incubated at three temperatures. The most frequently isolated taxa were C. jejuni (152 isolates) and C. lanienae (42 isolates), but isolates of C. fetus subsp. fetus, Arcobacter butzleri, and A. skirrowii also were recovered (</=2 isolates per taxon). Considerable variability was observed in the frequency of isolation of campylobacters among the four media and three incubation temperatures tested. With genus-specific primers, Campylobacter DNA was detected in 75% of the fecal samples, representing an 8% increase in sensitivity relative to that obtained with microbiological isolation across the four media and three incubation temperatures tested. With nested primers, C. jejuni and C. lanienae were detected in 25 and 67% of the samples, respectively. In no instance was DNA from either C. coli, C. fetus, or C. hyointestinalis detected in uninoculated bovine feces. PCR was more sensitive than isolation on microbiological media for detecting C. lanienae (17%) but not C. jejuni. Campylobacters are a diverse and fastidious group of bacteria, and the development of direct PCR not only will increase the understanding of Campylobacter species diversity and their frequency of occurrence in feces but also will enhance the knowledge of their role in the gastrointestinal tract of livestock and of the factors that influence shedding.

Animals↗
PubMed2006

Prospects for direct detection of the circular polarization of the gravitational-wave background.

We discuss the prospects for directly detecting a circular polarization signal of the gravitational-wave background. We find it is generally difficult to probe the monopole mode of the signal due to the broad directivity of the gravitational-wave detectors. But the dipole (l=1) and octupole (l=3) modes of the signal can be measured in a simple manner by combining outputs of two unaligned detectors, and we can dig them deeply under confusion and detector noises. Around f approximately 0.1 mHz the Laser Interferometer Space Antenna will provide ideal data streams to detect these patterns whose magnitudes are as small as approximately 1 percent of the detector noise level in terms of the nondimensional energy density OmegaGW(f).

Journal Article↗
PubMed1991

Use of synthetic oligonucleotide DNA probes for identification and direct detection of Bacteroides forsythus in plaque samples.

Oligonucleotide DNA probes complementary to the hypervariable region of the 16S rRNA of Bacteroides forsythus were tested for their specificity and sensitivity against reference and clinical isolates of 73 different species of bacteria. The probes were used to detect the organism directly from nucleic acid extracts of subgingival plaque samples, and the results were compared with results of detection by culture methods. The data demonstrate that the probes are very specific (100%) and sensitive (100% when they are compared with those obtained by the culture method) and could reliably detect the organism in plaque samples. When a probe to a conserved region of the 16S rRNA (UP9A) was used to estimate the quantity of bacteria present in plaque samples, it gave results comparable to those of culture methods. The data suggest that total microbial load may be a parameter in periodontal disease.

Bacteroides↗
PubMed2002

Method for direct detection of quantum entanglement.

Basing on positive maps separability criterion we propose the experimentally viable, direct detection of quantum entanglement. It is efficient and does not require any a priori knowledge about the state. For two qubits it provides a sharp (i.e., "if and only if") separability test and estimation of amount of entanglement. We view this method as a new form of quantum computation, namely, as a decision problem with quantum data structure.

Journal Article↗
PubMed1997

Evaluation of the AMPLICOR CMV test for direct detection of cytomegalovirus in plasma specimens.

We evaluated the AMPLICOR CMV test (PCR) for the direct detection of cytomegalovirus in plasma. Sixty-eight specimens were involved for the comparison between the AMPLICOR test and the antigenemia assay. The sensitivities, specificities, and positive and negative predictive values were 97.1, 100, 100, and 97.1%, respectively, for the AMPLICOR test and 79.4, 100, 100, and 82.9%, respectively, for the antigenemia assay.

Antigens, Viral↗
PubMedDate not supplied

Evaluation of a commercial test based on ligase chain reaction for direct detection of Mycobacterium tuberculosis in respiratory specimens.

A ligase chain reaction DNA amplification method for direct detection of Mycobacterium tuberculosis (Abbott LCx MTB) in respiratory specimens was evaluated. Results from LCx MTB Assay were compared with those from acid fast bacilli smear, culture, and final clinical diagnosis for each patient. A total of 297 respiratory specimens (sputum and bronchial lavage) from 193 patients were tested. The sensitivity, specificity, positive predictive value and negative predictive value of LC vs culture were 92.7%, 93%, 67.8% and 98.7%, respectively. When compared to the clinical final diagnosis, the sensitivity, specificity, PPV and NPV for LCx were 88.9%, 96.8%, 86.5% and 97.4%, respectively. The sensitivity of LCx MTB assay was 75% for smear-negative, culture positive samples. The results indicate that LCx MTB assay is a rapid, simple and valuable technique as a complementary tool for the diagnosis of tuberculosis.

Bronchoalveolar Lavage Fluid↗
PubMed2004

Direct detection of bacterial pathogens in brain abscesses by polymerase chain reaction amplification and sequencing of partial 16S ribosomal deoxyribonucleic acid fragments.

OBJECTIVE: To evaluate the feasibility of detecting bacterial pathogens directly from the clinical brain abscess specimens by polymerase chain reaction (PCR) amplification and sequencing of bacterial 16S ribosomal deoxyribonucleic acid (rDNA). METHODS: A total of 14 specimens were tested by both culture and PCR amplification, targeting the full-length or a partial region of 16S rDNA. 16S rDNA is known to be conserved in bacteria. Sequencing of partial-length and full-length 16S rDNA was performed. The sequence data were compared with known sequences of 16S rDNA in the National Center for Biotechnology Information GenBank by using the Basic Local Alignment Search Tool (BLAST) algorithm. The species with the best match of similarity were regarded as the pathogenic species in the samples. We also developed a Streptococcus-specific multiplex PCR analysis for identifying members of the Streptococcus species, the most common pathogen of brain abscesses. RESULTS: The 10 culture-positive specimens were all PCR-positive for partial 16S rDNA, but only seven were positive for full-length 16S rDNA amplification. Bacterial DNA was not detected in the remaining four specimens with a negative culture. Species identification by phenotypes from culture was in agreement with that by sequencing results of partial-length (or full-length) 16S rDNA. The Streptococcus-specific PCR analysis could detect Streptococcus species correctly in one step. CONCLUSION: Bacterial 16S rDNA sequences provide reliable clues to the identification of unknown pathogens. PCR analysis of 16S rDNA and sequencing may identify pathogens to the species level directly from brain abscesses. This approach is rapid and is useful especially in the identification of slow-growing and fastidious organisms.

Adolescent↗