ArticleGenes2017
Gene-Based Pathogen Detection: Can We Use qPCR to Predict the Outcome of Diagnostic Metagenomics?
Article in Genes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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
9 citing papers in PubMed.
- Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.Microbial genomics · 2025Article
- Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.Foods (Basel, Switzerland) · 2025Review
- Defining a metagenomic threshold for detecting low abundances ofFrontiers in cellular and infection microbiology · 2024Article
- Advances and Challenges in Cytomegalovirus Detection Methods for Liver Transplant Donors.Diagnostics (Basel, Switzerland) · 2023Review
- Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries.Antibiotics (Basel, Switzerland) · 2021Article
- Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment.Microorganisms · 2020Article
- A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.Microorganisms · 2020Article
- Comparison of culture and broad-range polymerase chain reaction methods for diagnosing periprosthetic joint infection: analysis of joint fluid, periprosthetic tissue, and sonicated fluid.International orthopaedics · 2018Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus. This was used on human fecal samples spiked with 10³ or 10⁶ colony-forming units (CFU)/g
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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.