Multiplex strand displacement amplification (SDA) and detection of DNA sequences from<i>Mycobacterium tuberculosis</i>and other mycobacteria

Walker, G. Terrance; Nadeau, James G.; Spears, Patricia A.; Schram, James L.; Nycz, Colleen M.; Shank, D.

doi:10.1093/nar/22.13.2670

Cited by 75 publications

(34 citation statements)

References 18 publications

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“…Many commercial assays are now available; for instance, the COBAS AMPLICOR MTB system (Roche, Basel, Switzerland) uses PCR (4, 27), while the BDProbeTec ET system (14) from Becton Dickinson (Sparks, Md.) uses the "strand displacement amplification" technique for detecting M. tuberculosis (3,5,6,8,11,23,24,26).Amplification techniques have a good sensitivity for smearpositive specimens; however, for smear-negative samples, the reported sensitivity varies considerably (16,17,18,21).The objective of the present study was to compare the sensitivities and specificities of the BDProbeTec ET and the COBAS AMPLICOR MTB properly by evaluating the assays with the same set of processed specimens. Secondly, as the smear-negative specimens influence the overall sensitivities of the amplification methods, the accuracy of the two methods was studied in a considerable number of culture-positive and smear-positive specimens as well as in culture-positive but smear-negative specimens.…”

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Comparison of the COBAS AMPLICOR MTB and BDProbeTec ET Assays for Detection of Mycobacterium tuberculosis in Respiratory Specimens

et al. 2005

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The performances of the BDProbeTec ET (Becton Dickinson) and COBAS AMPLICOR MTB (Roche) were retrospectively evaluated for detecting Mycobacterium tuberculosis complex in various respiratory specimens. The BACTEC and MGIT liquid culture system (Becton Dickinson) was used as a reference method. A total of 824 respiratory specimens, comprised of sputa, bronchoalveolar lavage fluid, and bronchial and tracheal aspirates from 580 patients, were evaluated. Out of 824 clinical specimens, 109 specimens from 43 patients were culture positive for M. tuberculosis. Of these 109 specimens, 67 were smear positive, 85 were positive by the COBAS AMPLICOR MTB test, and 94 were positive by the BDProbeTec ET. Of the 715 culture-negative specimens, 17 were positive by the auramine staining, 11 were positive by the COBAS AMPLICOR MTB test, and 12 were positive by the BDProbeTec ET. After discrepancy analysis and review of the patients' clinical data, 130 specimens from 50 patients were considered "true-positive" specimens. This resulted in the following sensitivities: microscopy, 61.5%; COBAS AMPLICOR MTB test, 78.0%; and BDProbeTec ET, 86.2%. The specificities of each system, based on the clinical diagnosis, were 99.7% for microscopy, 99.9% for the COBAS AMPLICOR MTB test, and 99.9% for the BDProbeTec ET. The data presented represent a considerable number of specimens evaluated with a considerable number of culture-and auramine-positive and culturepositive and auramine-negative results and therefore give a realistic view of how the data should be interpreted in a daily routine situation. Specifically, the data with regard to the culture-positive and auramine-negative specimens are useful, because in a routine situation, auramine-negative specimens are sometimes accepted, on clinical indications, to be analyzed by an amplification method.In contrast to general expectations, the incidence of mycobacterial disease has significantly increased worldwide since 1990 (7). The technical developments in diagnosing infections caused by Mycobacterium tuberculosis have increased similarly, an important change being the replacement of traditional solid culture media by liquid media and the introduction of molecular amplification techniques, such as PCR, has decreased the turnaround time even further (1, 22). Many commercial assays are now available; for instance, the COBAS AMPLICOR MTB system (Roche, Basel, Switzerland) uses PCR (4, 27), while the BDProbeTec ET system (14) from Becton Dickinson (Sparks, Md.) uses the "strand displacement amplification" technique for detecting M. tuberculosis (3,5,6,8,11,23,24,26).Amplification techniques have a good sensitivity for smearpositive specimens; however, for smear-negative samples, the reported sensitivity varies considerably (16,17,18,21).The objective of the present study was to compare the sensitivities and specificities of the BDProbeTec ET and the COBAS AMPLICOR MTB properly by evaluating the assays with the same set of processed specimens. Secondly, as the smear-negative specimens influence the ...

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Comparison of the COBAS AMPLICOR MTB and BDProbeTec ET Assays for Detection of Mycobacterium tuberculosis in Respiratory Specimens

et al. 2005

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“…The need of an initial denaturation step and a longer processing time of two hours may be a reason. Additionally, some reports have shown a co-amplified background signal due to unspecific primer binding [125,127]. Due to the excess of human DNA in clinical samples [128,129], the large background nucleic acid can hamper the efficiency of the SDA considerably.…”

Section: Sda: Strand Displacement Amplificationmentioning

confidence: 99%

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

Tröger¹,

Niemann²,

Gärtig³

et al. 2015

J Nanomed Nanotechnol

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Nucleic acid amplification technologies (NAATs) offer the most sensitive tests in the clinical laboratory. These techniques are used as a powerful tool for screening and diagnosis of infectious diseases. Isothermal methods, as an alternative to polymerase chain reaction (PCR), require no thermocycling machine and can mostly be performed with reduced time, high throughput, and accurate and reliable results.However, current molecular diagnostic approaches generally need manual analysis by qualified and experienced personal which is a highly complex, time-consuming and labor-intensive task. Thus, the demand for simpler, miniaturized systems and assays for pathogen detection is steadily increasing. Microfluidic platforms and lab-on-a-chip devices have many advantages such as small sample volume, portability and rapid detection time and enable point-of-care diagnosis.In this article, we review several isothermal amplification methods and their implementation in microsystems in relation to quantification of nucleic acids. miniaturized systems can be diverse. The majority of publications are focussed on clinical diagnostics including foodborne organisms for environmental monitoring [10][11][12]. In case of an infectious disease, cultivation and phenotypic characterization are still the standard methods of microbiologists which need days up to weeks to obtain a diagnostic result. Hence, scientists started to make use of nucleic acid amplification methods to accelerate the analysis. The most widespread and well known technique for this purpose is the polymerase chain reaction (PCR) [10,13], which exploits the activity of the DNA polymerase. The method is based on a thermal cycling process consisting of repeated cycles of heating and cooling steps allowing for DNA melting, sequence specific primer binding and enzymatic amplification of the target nucleic acid. The quantitative assessment of target copies is possible by using a real-time PCR approach, where a concentration dependent signal (e.g. fluorescence) increases over time [14]. The latter enables the user to easily assess the pathogen load of patient samples [15][16][17][18]. Since the first example of a PCR on a miniaturized system in 1994 [19,20], numerous devices were presented, which integrate not just the amplification, but also sample preparation and detection steps [9,[21][22][23][24][25][26][27][28]. Just a few of those microsystems have reached the market so far, but some have shown a fascinating potential to replace the classical laboratory-oriented state-of-the art [29][30][31][32][33]. setups has been shown to obtain a similar result [34]. A smaller heat capacity allows for rapid changes in temperature beneficial for the PCR time as well as a higher parallelism of multiple genetic samples [34].However, a major drawback of the integration of PCR to microsystems is the necessity of sophisticated instrumentation. The reaction requires a thermal cycling instrumentation, space and considerable expertise [35]. Therefore, isothermal reactions for the ta...

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“…The isothermal single-strand displacement amplification (SDA) method, originally developed for the detection of DNA from pathogens of the Mycobacterium genus, is based on the resistance of phosphorothioates to the restriction endonuclease Hinc II (106). This methodology has been extended to mimic the rolling-circle replication of single-stranded phages (107 site-specific attachment of reporter groups, such as photoaffinty agents (108) and fluorescent dyes (109), to oligodeoxynucleotides via alkylation reactions.…”

Section: Phosphorothioatesmentioning

confidence: 99%

MODIFIED OLIGONUCLEOTIDES: Synthesis and Strategy for Users

Verma

Eckstein²

1998

Annu. Rev. Biochem.

303

190

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Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies.The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages. CONTENTS

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Multiplex strand displacement amplification (SDA) and detection of DNA sequences fromMycobacterium tuberculosisand other mycobacteria

Cited by 75 publications

References 18 publications

Comparison of the COBAS AMPLICOR MTB and BDProbeTec ET Assays for Detection of Mycobacterium tuberculosis in Respiratory Specimens

Comparison of the COBAS AMPLICOR MTB and BDProbeTec ET Assays for Detection of Mycobacterium tuberculosis in Respiratory Specimens

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

MODIFIED OLIGONUCLEOTIDES: Synthesis and Strategy for Users

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