ArticlePloS one2013
Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07626073 (h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.), which is not on this map. Cited by 109 papers, 1 of them a synthesis that pooled it.
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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.
h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.
Who cites it
109 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Role of Gut Microbiota in Gastrointestinal Symptoms of Children with ASD.Medicina (Kaunas, Lithuania) · 2019Pooled it
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- Broad-range polymerase chain reaction and sequencing for the diagnosis of infectious diseases.Microbiology spectrum · 2025Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Integrated metagenomics and transcriptomics analysis reveals pathways associated with oral periapical lesions formation and progression.Current research in microbial sciences · 2025Article
- The Use of Next-Generation Sequencing in Personalized Medicine.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Pleural space infection microbiology as assessed using a clinical sequencing-based assay:Journal of clinical microbiology · 2024Article
- A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers.Journal of clinical microbiology · 2024Observational
- Use of Deep-Amplicon Sequencing (DAS), Real-Time PCR and In Situ Hybridization to DetectDiagnostics (Basel, Switzerland) · 2024Article
- Clinical applications of metagenomics next-generation sequencing in infectious diseases.Journal of Zhejiang University. Science. B · 2024Review
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- Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease: Research outline and call for collaboration.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Review
- Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria.Analytical chemistry · 2023Article
- Microbiome analysis of bile samples in patients with choledocholithiasis and hepatobiliary disorders.Germs · 2023Article
- Feasibility of 16S rRNA sequencing for cerebrospinal fluid microbiome analysis in cattle with neurological disorders: a pilot study.Veterinary research communications · 2023Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp) with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF) patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times) and inexpensive for routine clinical use.
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