The Molecular Diagnosis of Pulmonary Infections
Philip T. Cagle, Timothy C. Allen, Mary Beth Beasley in 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).
Bacterial Sexually Transmitted Diseases
Attila Lorincz in Nucleic Acid Testing for Human Disease, 2016
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.
Rapid Methods in Cosmetic Microbiology
Philip A. Geis in 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).
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).
Screening, diagnosis and risks associated with Hepatitis E virus infection
Published in Expert Review of Anti-infective Therapy, 2019
Sébastien Lhomme, Florence Legrand-Abravanel, Nassim Kamar, Jacques Izopet
HEV RNA can also be detected using assays based on isothermal amplification such as the loop-mediated isothermal amplification (LAMP) assay [52]. This technique uses a set of six primers that recognize eight distinct regions of the target sequence and provides a one-step, single-tube, isothermal amplification of HEV RNA. The LAMP assay is quicker than real-time PCR and needs no special equipment, making it suitable for use in resource-limited areas. Another isothermal, single-tube nucleic acid amplification system, transcription-mediated amplification (TMA) uses two enzymes, RNA polymerase and reverse transcriptase. One which is completely automated, the Procleix assay, has a limit of detection of 24 IU/ml for HEV3a (WHO standard 6329/10), 34 IU/mL for HEV3c and 53 IU/mL for HEV3f [53]. This assay also appears to be suitable for detecting HEV in faeces. It detects all four major HEV genotypes (1, 2, 3, and 4) with a 95% LOD ranging from 7.9 copies/mL for HEV1 to 17.7 copies/mL for HEV4 using RNA transcripts for HEV 1, 2, 3a, 3b, 3f, and 4c [54]. The LOD was estimated to 5.5–10.5 IU/ml with the WHO standard (HEV3a) in other studies [54–56].
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.
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