ArticleApplied and environmental microbiology2008
Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.Molecules (Basel, Switzerland) · 2019Pooled it
- The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.Antibiotics (Basel, Switzerland) · 2024Review
- The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health.MicrobiologyOpen · 2020Review
- High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR.Frontiers in cellular and infection microbiology · 2020Article
- Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology.Micromachines · 2019Review
- Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence.Science advances · 2019Article
- TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer.Frontiers in immunology · 2019Article
- Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.FEMS microbiology ecology · 2018Article
- Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent.FEMS microbiology ecology · 2018Article
- TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal.Applied microbiology and biotechnology · 2017Article
- Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers.Journal of environmental management · 2017Article
- Virulence factor activity relationships (VFARs): a bioinformatics perspective.Environmental science. Processes & impacts · 2017Review
- Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.Frontiers in microbiology · 2017Article
- Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens.FEMS microbiology ecology · 2016Article
- Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review.Asian-Australasian journal of animal sciences · 2015Article
- Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples.Applied and environmental microbiology · 2014Article
- Simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative PCR.Applied and environmental microbiology · 2013Article
- Detection of pathogens in water: from phylochips to qPCR to pyrosequencing.Current opinion in biotechnology · 2012Review
- In-feed antibiotic effects on the swine intestinal microbiome.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Digital PCR on a SlipChip.Lab on a chip · 2010Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (C(T)) equation was developed to calculate the number of starting copies based on an experimental C(T). The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (R(2) = 0.816) was observed between the predicted and experimental C(T)s based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3' end. The performance of the predictive C(T) equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive C(T) equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.