ArticleProceedings of the National Academy of Sciences of the United States of America2002
Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches.Journal of the American Chemical Society · 2023Article
- Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach.Frontiers in microbiology · 2023Review
- "Omic" Approaches to Bacteria and Antibiotic Resistance Identification.International journal of molecular sciences · 2022Review
- Ultrafast enzymatic digestion of deoxyribonucleic acid in aqueous microdroplets for sequence discrimination and identification.QRB discovery · 2021Article
- Article
- Rapid pathogen identification using a novel microarray-based assay with purulent meningitis in cerebrospinal fluid.Scientific reports · 2018Article
- Application of mass spectrometry to molecular diagnostics of viral infections.Expert review of molecular diagnostics · 2013Review
- Rapid detection of Salmonella sp. by means of a combination of selective enrichment broth and MALDI-TOF MS.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2012Article
- Molecular microbiological methods in the diagnosis of neonatal sepsis.Expert review of anti-infective therapy · 2010Review
- Identification of pathogens by mass spectrometry.Clinical chemistry · 2010Review
- The era of molecular and other non-culture-based methods in diagnosis of sepsis.Clinical microbiology reviews · 2010Review
- Mass spectrometry tools for the classification and identification of bacteria.Nature reviews. Microbiology · 2010Review
- Current applications and future trends of molecular diagnostics in clinical bacteriology.Analytical and bioanalytical chemistry · 2009Review
- Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping.Nucleic acids research · 2009Article
- [Microbiological diagnosis: Etiologic driven and syndrome driven].Antibiotiques (Paris, France : 1999) · 2009Article
- Toward universal flavivirus identification by mass cataloging.The Journal of molecular diagnostics : JMD · 2008Article
- Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.PLoS genetics · 2006Review
- Bacterial genotyping by 16S rRNA mass cataloging.BMC bioinformatics · 2006Article
- Microbial identification by mass cataloging.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines uracil-DNA-glycosylase (UDG)-mediated base-specific fragmentation of PCR products with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). 16S rDNA signature sequences were PCR-amplified from both cultured and as-yet-uncultured bacteria in the presence of dUTP instead of dTTP. These PCR products then were immobilized onto a streptavidin-coated solid support to selectively generate either sense or antisense templates. Single-stranded amplicons were subsequently treated with uracil-DNA-glycosylase to generate T-specific abasic sites and fragmented by alkaline treatment. The resulting fragment patterns were analyzed by MALDI-TOF MS. Mass signals of 16S rDNA fragments were compared with patterns calculated from published 16S rDNA sequences. MS of base-specific fragments of amplified 16S rDNA allows reliable discrimination of sequences differing by only one nucleotide. This approach is fast and has the potential for high-throughput identification as required in clinical, pharmaceutical, or environmental microbiology. In contrast to identification by MS of intact whole bacterial cells, this technique allows for the characterization of both cultured and as-yet-uncultured bacteria.
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