ArticleJournal of medical microbiology2011
Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis.
Article in Journal of medical microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
- Molecular quantification and differentiation of Candida species in biological specimens of patients with liver cirrhosis.PloS one · 2018Trial
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- From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.Orthopaedic surgery · 2026Review
- Odontogenic Brain Abscess in a Hereditary Haemorrhagic Telangiectasia (HHT) Patient: Case Report with a Comprehensive Literature Review.Tropical medicine and infectious disease · 2026Article
- A Host-Directed Approach to the Detection of Infection in Hard-to-Heal Wounds.Diagnostics (Basel, Switzerland) · 2022Review
- Comparison of an automated DNA extraction and 16S rDNA real time PCR/sequencing diagnostic method using optimized reagents with culture during a 15-month study using specimens from sterile body sites.BMC microbiology · 2022Article
- Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification.Microbiology spectrum · 2022Article
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.Clinical microbiology reviews · 2020Review
- Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures.iScience · 2020Article
- Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study.SpringerPlus · 2016Article
- Identification of occult Fusobacterium nucleatum central nervous system infection by use of PCR-electrospray ionization mass spectrometry.Journal of clinical microbiology · 2014Article
- Massive parallel sequencing provides new perspectives on bacterial brain abscesses.Journal of clinical microbiology · 2014Article
- Purification of DNA eluates from the ProbeTec GC Q(x) assay on BD Viper™ XTR allows for further analysis and confirmation of gonorrhea.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2014Article
- Non-culture-based methods to diagnose bloodstream infection: Does it work?European journal of microbiology & immunology · 2013Article
- Direct sequencing and RipSeq interpretation as a tool for identification of polymicrobial infections.Journal of clinical microbiology · 2013Article
- Sequencing-based genotyping of mixed human papillomavirus infections by use of RipSeq software.Journal of clinical microbiology · 2013Article
- Hyperbaric oxygen treatment in three cases of necrotizing infection of the neck.Infectious disease reports · 2012Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The standard use of a single universal broad-range PCR in direct 16S rDNA sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial DNA will be competing for the same reagents. In this article we introduce a set of three broad-range group-specific 16S rDNA PCRs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. Mixed DNA chromatograms from samples containing more than one species per primer group were analysed using RipSeq Mixed (iSentio, Norway), a web-based application for the interpretation of chromatograms containing up to three different species. The group-specific PCRs reduced complexity in the resulting DNA chromatograms and made the assay more sensitive in situations with unequal species concentrations. Together this allowed for identification of a significantly higher number of bacterial species than did standard direct sequencing with a single universal primer pair and RipSeq analysis (95 vs 51). The method could improve microbiological diagnostics for important groups of patients and can be established in any laboratory with experience in direct 16S rDNA sequencing.
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