ArticleScientific reports2019
Plasmid DNA contaminant in molecular reagents.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 2 of them syntheses that pooled it.
What it found
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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
17 citing papers in PubMed, 2 syntheses or guidelines pooled it, 26 citations in OpenAlex.
- Incidental Bystander or Essential Culprit: A Systematic Review of Bacterial Significance in the Pathogenesis of Breast Implant-Associated Anaplastic Large Cell Lymphoma.International journal of molecular sciences · 2023Pooled it
- Towards an understanding of the avian virome.The Journal of general virology · 2020Pooled it
- Towards a Comprehensive Screening Approach for Detecting Gene Doping in Racehorses and Sport Horses by Targeting Common and Intrinsic Plasmid Sequences.Drug testing and analysis · 2026Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples.ISME communications · 2025Article
- Comparative genomic assessment of members of genus Tenacibaculum: an exploratory study.Molecular genetics and genomics : MGG · 2023Review
- Efficient plasmid transfer via natural competence in a microbial co-culture.Molecular systems biology · 2023Article
- Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections.Open forum infectious diseases · 2022Article
- Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Genetic determinants of antimicrobial resistance in three multi-drug resistant strains ofAccess microbiology · 2022Article
- The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance.Sensors (Basel, Switzerland) · 2021Article
- An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer.Microbiome · 2021Article
- Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies.Microorganisms · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study.BMC pediatrics · 2020Article
- Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes.Antimicrobial agents and chemotherapy · 2019Article
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 3 countries.
Funding
Abstract
Background noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.
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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.