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Rapid Methods in Cosmetic Microbiology
Published in Philip A. Geis, Cosmetic Microbiology, 2020
Nucleic acid amplification-based rapid technologies utilize a number of gene amplification and detection platforms, including polymerase chain reaction (PCR), transcription-mediated amplification, 16S rRNA typing and gene sequencing. Most of these methods will detect the presence of a target microorganism or generate data that can be used to determine the identification of an isolate, from the genus level down to the sub-species and/or strain level (Table 7.5).
Bacterial Sexually Transmitted Diseases
Published in Attila Lorincz, Nucleic Acid Testing for Human Disease, 2016
Julius Schachter, Stephen A. Morse
The next NAAT to become commercially available was LCR. In fairly large, multicentered trials, sensitivities in the order of 90 to 95% were found for urethral swabs, male first-catch urine (FCU) specimens, and cervical swabs.9,16 In each case, a 30 to 50% increase was noted in the number of positive specimens detected by LCR compared to TC, which had a sensitivity ranging from 50 to 70%, depending on the specimen tested. Transcription-mediated amplification (TMA) and strand displacement amplification (SDA) are two other NAATs that arrived later and evaluations revealed they were at least as good as PCR and LCR.17,18 In general, the NAATs performed in a similar manner.
The Molecular Diagnosis of Pulmonary Infections
Published in Philip T. Cagle, Timothy C. Allen, Mary Beth Beasley, Diagnostic Pulmonary Pathology, 2008
A large number of nucleic acid amplification assays for the detection of M. tuberculosis have also been devised. The majority of these are suggested for the direct detection of M. tuberculosis from respiratory specimens, such as sputa or bronchoalveolar lavage (BAL). Two commercially available products are FDA approved, whereas third is not FDA approved, but commonly used in Europe and elsewhere outside the United States. These use three different types of nucleic acid amplification chemistry, namely, PCR, transcription-mediated amplification, and strand-displacement amplification. These products have not been cleared for use on pulmonary biopsies, but some of the laboratory-designed assays have been used in this manner. Commentaries regarding the most appropriate use of these assay are available for further review (42–14).
Diagnostic approaches for dengue infection
Published in Expert Review of Molecular Diagnostics, 2023
Gaythri Thergarajan, Shamala Devi Sekaran
DENV is a single-stranded positive-sense RNA virus of approximately 50 nm in length. The 11 kb genome of each virion encodes three structural proteins (capsid, C; precursor membrane, prM; and envelope, E) and seven non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) [60]. These non-structural proteins play roles in viral replication and assembly. Structurally, a virion consists of a nucleocapsid, enveloped by an outer glycoprotein shell and an inner lipid bilayer. Surface projections in the lipid membrane consist of E and membrane (M) glycoproteins [61]. Nucleic acid amplification tests and identification of virus antigen or antibody serve as the predominant means of detection of DENV, based on the molecular or immunological response to specified viral structural components. Commonly used methods are reverse transcription polymerase chain reaction (RT-PCR), nucleic acid sequence-based amplification (NASBA), and transcription-mediated amplification (TMA).
Critical insight into recombinase polymerase amplification technology
Published in Expert Review of Molecular Diagnostics, 2022
Since the development of PCR, several other nucleic acid amplification technologies (NAATs) have been developed, but PCR remains the most popular NAAT. Moreover, the NAATs developed following the PCR development are mostly isothermal nucleic acid amplification technologies (INAATs), meaning amplification of the target nucleic acid at a constant temperature. Being isothermal, INAATs exclude the requirement of heavy thermocyclers, and they can be done with simple, portable, and cost-effective instruments at the bedside of patients and field sites. The INAATs are becoming popular over time, and their global market size was estimated at 1.6 billion USD for the year 2016 [2]. The major technologies contributing to the market include transcription-mediated amplification (TMA) (16.84%), loop-mediated isothermal amplification of DNA (LAMP) (14.45%), helicase-dependent amplification (HDA) (12.08%), strand displacement amplification (SDA) (10.37%), nicking enzyme amplification reaction (NEAR) (9.11%), nucleic acid sequence-based amplification (NASBA) (7.87%), single primer isothermal amplification (SPIA) (7.40%), recombinase polymerase amplification (RPA) (7.08%), and rolling circle amplification (RCA) (6.52%) [2,3]. INAATs are mainly utilized for the detection of pathogen or contaminant nucleic acid from samples, and they are not commonly utilized for quantification, genotyping, relative quantification of genes expression, molecular cloning, sequencing, etc.
Molecular testing as a tool to combat the COVID-19 pandemic
Published in Expert Review of Molecular Diagnostics, 2021
Christina Liscynesky, Joan-Miquel Balada-Llasat
The use of NP collection that may have higher viral load was the specimen of choice at our institution, but hesitance focused on the use of rapid transcription mediated amplification testing versus traditional RT-PCR, since these tests may show lower sensitivity. For this reason, our institution implemented the Abbott ID NOW COVID-19 assay only for inpatients that were symptomatic because the rapid turnaround time benefited patient care. In order to evaluate the Abbott ID NOW COVID-19 assay (NP collected in dry swab), we performed a performance comparison with the Simplexa COVID-19 Direct Kit (NP collected in viral transport media), if results were discrepant the laboratory developed CDC RT-PCR was used. The Abbott ID NOW COVID-19 showed a similar performance to the Simplexa COVID-19 Direct Kit. COVID-19 is indistinguishable from other respiratory viral syndromes by symptoms alone. Symptoms consistent with COVID-19 include cough, shortness of breath, fever, chills, fatigue, muscle pain, headache, sore throat, new loss of taste or smell, congestion, nausea, vomiting or diarrhea[3]. Anti-viral therapy cannot be prescribed until the diagnosis is confirmed via testing, hence the need for a rapid result.