ArticleMolecular biotechnology2002
Comparison of different decontamination methods for reagents to detect low concentrations of bacterial 16S DNA by real-time-PCR.
Article in Molecular biotechnology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 69 citations in OpenAlex.
- Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples.ISME communications · 2025Article
- Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics.Frontiers in microbiology · 2022Review
- Increasing Reproducibility in Oral Microbiome Research.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.Clinical microbiology reviews · 2020Review
- A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum.PloS one · 2020Article
- PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens.Scientific reports · 2019Article
- New Microbiological Techniques in the Diagnosis of Bloodstream Infections.Deutsches Arzteblatt international · 2018Review
- Amplification of bacterial genomic DNA from all ascitic fluids with a highly sensitive polymerase chain reaction.Molecular medicine reports · 2018Article
- The Madness of Microbiome: Attempting To Find Consensus "Best Practice" for 16S Microbiome Studies.Applied and environmental microbiology · 2018Review
- A novel approach to eliminate detection of contaminating Staphylococcal species introduced during clinical testing.PloS one · 2017Article
- Enrichment of bacterial DNA for the diagnosis of blood stream infections.BMC infectious diseases · 2016Article
- The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data.American journal of translational research · 2016Article
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.BMC biology · 2014Article
- Article
- Article
- Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens.Annals of laboratory medicine · 2012Article
- Comparative analysis of two broad-range PCR assays for pathogen detection in positive-blood-culture bottles: PCR-high-resolution melting analysis versus PCR-mass spectrometry.Journal of clinical microbiology · 2012Article
- BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay.BMC microbiology · 2012Article
- Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.PloS one · 2012Article
- A novel eukaryote-made thermostable DNA polymerase which is free from bacterial DNA contamination.Journal of clinical microbiology · 2011Article
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Contamination of polymerase chain reaction (PCR) reagents continues to be a major problem when consensus primers are used for detection of low concentrations of bacterial DNA. We designed a real-time polymerase chain reaction (PCR) for quantification of bacterial DNA by using consensus primers that bind specifically to the 16S region of bacterial DNA. We have tested four different methods of decontamination of PCR reagents in a project aimed at detecting bacterial DNA at low concentrations: deoxyribonuclease (DNAse) treatment, restriction endonuclease digestion, UV irradiation, and 8-methoxypsoralen in combination with long-wave UV light to intercalate contaminating DNA into double-stranded DNA. All four methods result in inhibition of the PCR reaction, and most of the decontamination procedures failed to eliminate the contaminating bacterial DNA. Only the DNAse decontamination proved to be efficient in eliminating contaminating DNA while conserving PCR efficiency. All four decontamination methods are time consuming and have the possibility of carrying new contamination into the reaction mixture. However, decontamination with DNAse may help, together with the use of highly purified PCR reagents, in detecting small amounts of bacterial DNA in clinical specimens.
Indexed as
Identifiers
What OpenQuestion holds
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.