Rapid development of nucleic acid diagnostics

Fitch, J. Patrick; Gardner, Shea N.; Kuczmarski, Tom; Kurtz, Stefan; Myers, Richard S.; Ott, L.; Slezak, Tom; Vitalis, Elizabeth; Zemła, Adam; McCready, Paula

doi:10.1109/jproc.2002.804680

Cited by 39 publications

(31 citation statements)

References 21 publications

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“…Analytical specificity of the END RRT-PCR, determined by a combination of computer-based and benchlevel screening of primers and probes, 6 demonstrated no false-positive reactions. Evaluation of clinical case material additionally indicated that the assay did not cross-react with Mycoplasma spp., avian influenza virus, avian infectious bronchitis virus, avian laryngotracheitis vaccine strain, or near neighbor APMV-1 or PPMV-1 viruses, including a unique PPMV-1 detected during the outbreak (GenBank accession AY428960).…”

Section: Resultsmentioning

confidence: 99%

High-Throughput Real-Time RT-PCR Assay to Detect the Exotic Newcastle Disease Virus during the California 2002–2003 Outbreak

Crossley¹,

Hietala²,

Shih³

et al. 2005

J VET Diagn Invest

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Abstract. During the 2002During the -2003 Exotic Newcastle Disease (END) outbreak in Southern California, a highthroughput real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) system was developed to respond to the large diagnostic and surveillance sample workload. A 96-well RNA extraction method, using magnetic bead technology, combined with a 96-well RRT-PCR assay, allowed 1 technician to process and test more than 400 samples per day. A 3-technician team could complete testing on approximately 1,900 samples per day. The diagnostic sensitivity of the high-throughput RRT-PCR assay was 0.9967 (95% CI 0.9937-0.9997) based on 926 virus isolation confirmed positive samples. Diagnostic specificity using an initial 434 virus isolation confirmed negative samples was 100%. A diagnostic specificity of 0.9999 (95% CI 0.9999, Ͼ0.9999) was subsequently calculated on the basis of 2 false-positive results among 65,343 surveillance samples collected after the final END-positive case was confirmed in May 2003. Assay performance over 500 replicates, including reproducibility of the combined extraction and RRT-PCR amplification steps yielded a standard deviation of 0.70 RRT-PCR cycle thresholds (Ct) and a standard deviation of 0.59 Ct for the RRT-PCR steps alone. The high-throughput RRT-PCR developed for END contributed significantly to the 2002-2003 END control effort, reducing the predicted timeline for eradication from 3 years to just 11 months, primarily because of the large number of samples that could be rapidly tested. The 96-well approach described for high-throughput END RRT-PCR could be adapted to other rapid, high-volume testing needs, as required for potential foreign animal disease responses or intensive surveillance efforts.

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Section: Resultsmentioning

confidence: 99%

High-Throughput Real-Time RT-PCR Assay to Detect the Exotic Newcastle Disease Virus during the California 2002–2003 Outbreak

Crossley¹,

Hietala²,

Shih³

et al. 2005

J VET Diagn Invest

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“…Multiple layers of in silico mining and in vitro selection processes can be combined using high throughput wet chemistry evaluation to create a discovery pipeline for microbial signature sequences. In this way, many of the same informational tools developed for use in the Human Genome Project can also be marshaled to feed a discovery pipeline leading to new molecular diagnostics for bacteria and viruses (94).…”

Section: High-throughput Methods For Reagent Discoverymentioning

confidence: 99%

Methods for Whole Cell Detection of Microorganisms

Brehm-Stecher

2008

ACS Symposium Series

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Microbes are ubiquitous, and can be found occupying nearly every imaginable niche on Earth. These include organic and inorganic surfaces, interfacial boundaries and within macroscopically solid matrices, such as the pore space of rocks. Because phylogenetically divergent microbes may be visually indistinguishable, understanding the species distribution and ecological significance of environmental microbes requires diagnostic tools that extend beyond simple phenotypic description. Methods for microbial diagnostics can be divided into two broad categories: cellular and acellular. Acellular techniques, such as the polymerase chain reaction or certain immunoassay formats may be effective at detecting molecular, structural or biochemical targets associated with specific cell types, but this information is provided out of its "natural", and arguably most meaningful context -that of the individual microbial cell. In contrast, cellular methods have the potential to preserve an abundance of valuable information. Apart from molecular identity, this includes information regarding cell morphology and other physiological characteristics, cell number and distribution within a sample, and physical or spatial associations with other cell types. The aim of this chapter is to provide an overview of whole cell methods for microbial detection, including both existing approaches and those still in development. The tools described here are expected to find wide application for the detection of microbes on surfaces or within complex matrices across a number of parallel or allied fields, including environmental, food and clinical microbiologies.

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“…PNNL's SWIR CRDS instrument is outfitted with a cavity that has a volume of 490 cm 3 . If it is assumed that a sampling apparatus could be designed such that all gas phase products from biological agent pyrolysis would be swept into a prior evacuated CRDS cavity, then the amount of pyrrole and pyridine that needs to come from pyrolysis in order to be detected is 1.47 x 10 15 and 7.35 x 10 15 molecules, respectively.…”

Section: Swir Crds Feasibility For Detection Biological Agent Pyrolysmentioning

confidence: 99%

Feasibility Study of Using Short Wave Infrared Cavity Ringdown Spectroscopy (SWIR-CRDS) for Biological Agent Detection

Aker¹,

Johnson²,

Williams³

et al. 2007

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Rapid development of nucleic acid diagnostics

Cited by 39 publications

References 21 publications

High-Throughput Real-Time RT-PCR Assay to Detect the Exotic Newcastle Disease Virus during the California 2002–2003 Outbreak

High-Throughput Real-Time RT-PCR Assay to Detect the Exotic Newcastle Disease Virus during the California 2002–2003 Outbreak

Methods for Whole Cell Detection of Microorganisms

Feasibility Study of Using Short Wave Infrared Cavity Ringdown Spectroscopy (SWIR-CRDS) for Biological Agent Detection

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