Direct hybridization and amplification applications for the diagnosis of infectious diseases

Wagar, Elizabeth A.

doi:10.1002/(sici)1098-2825(1996)10:6<312::aid-jcla2>3.0.co;2-8

Cited by 22 publications

(9 citation statements)

References 52 publications

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“…These technologies, however, like the determinations of phenotypic variables, are limited by microbial recovery and growth but then after few years, diagnostics using DNA-based tools, such as polymerase chain reaction (PCR), are increasingly popular due to their specificity and speed, as compared to culture-based methods (Louie et al, 2000). The amplified products, known as amplicons, may be characterized by various methods, including nucleic acid probe hybridization, analysis of fragments after restriction endonuclease digestion, or direct sequence analysis (Persing, 1991;Wagar, 2006). Further variations of PCR method like RT-PCR, ligase chain reaction (LCR), nested PCR, and multiplex PCR, etc have simplified and accelerated the process of nucleic acid amplification and easy detection of microbes (Wagar, 2006) but these all have drawbacks of less sensitivity, insufficient specificity, low amplification efficiency, not available for all species, high cost, use of special equipments etc.…”

Section: Why There Is Need Of Lampmentioning

confidence: 99%

Loop-mediated isothermal amplification (LAMP) based detection of bacteria: A Review

Saharan¹,

Dhingolia²,

Khatri³

et al. 2014

Afr. J. Biotechnol.

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Various diseases are caused by pathogenic bacteria and their diagnosis depends on accurate detection of pathogen from clinical samples. Several molecular methods have been developed including PCR, Real Time PCR or multiplex PCR which detects the pathogen accurately. However, every method has some limitations like low detection limit, whereas Loop-mediated isothermal amplification (LAMP) is a powerful and novel nucleic acid amplification method, which detects the DNA at very low level compared to other methods. This method amplifies very few copies of target DNA with high specificity, efficiency and rapidity under isothermal conditions by using a set of four specially designed primers and a DNA polymerase with strand displacement activity. This review presents detection of various bacteria by LAMP method and covers their detection limit in clinical specimens.

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Section: Why There Is Need Of Lampmentioning

confidence: 99%

Loop-mediated isothermal amplification (LAMP) based detection of bacteria: A Review

Saharan¹,

Dhingolia²,

Khatri³

et al. 2014

Afr. J. Biotechnol.

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“…Numerous modifications of the standard PCR procedure have been developed since its inception [4,5,41]. Some of these modifications effectively expand the diagnostic capabilities of PCR and have increased its utility in the clinical laboratory.…”

Section: Reverse Transcriptase (Rt)-pcrmentioning

confidence: 99%

“…Nucleic acid amplification technology has opened new avenues of microbial detection and characterization [1,5,41], such that growth is no longer required for microbial identification [42][43][44][45][46][47][48][49][50][51][52]. In this respect, molecular methods have surpassed traditional methods of detection for many fastidious organisms.…”

mentioning

confidence: 99%

Molecular Diagnostics of Infectious Diseases

Ohkusu

Ezaki²

2014

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In DNA-based diagnostics, the polymerase chain reaction (PCR) is the most widely used DNA amplification method. To enable both sensitive and specific detection of agents causing infectious diseases, the PCR needs to be combined with methods to prepare the clinical sample containing the genetic material of the pathogen. Furthermore, methods for detection and DNA sequence analysis of the PCR amplification products are needed. This thesis describes the development of integrated systems for detection, quantification and characterization of microorganisms.An immunomagnetic separation (IMS) technique has been used to isolate Bordetella pertussis from nasopharyngeal aspirate samples. The post-PCR detection and typing of Bordetella spp. was performed by a combination of restriction enzyme analysis of the amplified pertussis toxin (PT) promoter region and a solid-phase colorimetric detection system; detection of immobilized amplified nucleic acid (DIANA). To investigate whether this approach could be used for reliable discrimination between the three Bordetella spp. infecting humans, the PT promoter region used for diagnostics was sequenced in 33 strains. To determine the DNA sequence of this polymorphic and repetitive region, a new technique, bidirectional pyrosequencing, was utilized. This procedure was used to resolve the sequence of this DNA region, which is able to form stable secondary structures in conventional Sanger DNA sequencing. A quantitative assay using competitive PCR and the DIANA detection technique was also developed, for quantification of B. pertussis in clinical samples.By arbitrary PCR, a DNA sequence apparently specific for Vibrio cholerae O139 Bengal was isolated and characterized. A nested PCR assay was developed for sensitive and specific detection of V. cholerae O139 Bengal in clinical samples and in environmental water samples, where differentiation between V. cholerae O139 Bengal and V. cholera O1 is of epidemiological interest.The magnetic separation approach was also used to capture human immunodeficiency virus (HIV-1) RNA from patient plasma. A nested reverse transcription (RT)-PCR with four internal competitors was combined with electrophoretic separation and quantification of the PCR amplicons on an automated DNA sequencer. From the internal calibration curve, the amount of HIV-1 RNA in the sample could be determined. Furthermore, a primer extension assay was combined with detection and quantification of the competitive PCR products by the same biochemiluminescent detection technique that is used in pyrosequencing. Quantification of HIV-1 viral load has implications in monitoring of antiretroviral therapy and in assessment of disease progression into AIDS. LIST OF PUBLICATIONSThis thesis is based on the following papers, which in the text will be referred to by their Roman numerals:

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“…In addition this information does not reveal anything about the mechanisms behind particular characteristics. Many molecular tests used in microbiological diagnostics rely on DNA sequencing or nucleic acid hybridization to identify specific sequences or point mutations that vary between different clones (21)(22)(23)(24). An array format expands on these methods by enabling the simultaneous detection of thousands of genomic targets.…”

Section: Applications Of Oligonucleotide Arrays In Diagnostics and Sumentioning

confidence: 99%

Application of DNA Array Technology for Diagnostic Microbiology

Booth

Drebot

2000

Canadian Journal of Infectious Diseases and Medical Microbiolog

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Microarrays or DNA chips have been hailed as the ultimate experimental tool for research, drug discovery and diagnostics. They have the potential to perform a multitude of molecular tests simultaneously and to produce a wealth of information from a single clinical sample. Applications include genotyping, expression analysis and sequencing (1-4). The aim of this review is to provide a brief summary of current microarray technology and highlight the many ways in which it is being developed for use in clinical microbiology laboratories.

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Direct hybridization and amplification applications for the diagnosis of infectious diseases

Cited by 22 publications

References 52 publications

Loop-mediated isothermal amplification (LAMP) based detection of bacteria: A Review

Loop-mediated isothermal amplification (LAMP) based detection of bacteria: A Review

Molecular Diagnostics of Infectious Diseases

Application of DNA Array Technology for Diagnostic Microbiology

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