ArticleFrontiers in microbiology2022
Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections.
Article in Frontiers in microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis.Journal of clinical microbiology · 2023Pooled it
- High throughput sequencing in the diagnosis and surveillance of tick-borne diseases: A narrative review.One health (Amsterdam, Netherlands) · 2026Review
- Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.Critical care (London, England) · 2026Article
- Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems.Frontiers in microbiology · 2026Review
- Analyzing human gut microbiome data from global populations: challenges and resources.Trends in microbiology · 2025Review
- Rapid DNA/eDNA-Based ID Tools for Improved Chondrichthyan Monitoring and Management.Molecular ecology resources · 2025Review
- Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.Journal of clinical microbiology · 2025Article
- Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine.Scientific reports · 2025Article
- Advances in Donkey Disease Surveillance and Microbiome Characterization in China.Microorganisms · 2025Review
- Leveraging innovative diagnostics as a tool to contain superbugs.Antonie van Leeuwenhoek · 2025Review
- Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.Microbiome · 2025Article
- Performance of 16S rRNA Gene Next-Generation Sequencing and the Culture Method in the Detection of Bacteria in Clinical Specimens.Diagnostics (Basel, Switzerland) · 2024Article
- Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis.Veterinary medicine and science · 2024Article
- Novel Diagnostic Methods for Infective Endocarditis.International journal of molecular sciences · 2024Review
- Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis.Open forum infectious diseases · 2023Article
- Alterations of lower respiratory tract microbiome and short-chain fatty acids in different segments in lung cancer: a multiomics analysis.Frontiers in cellular and infection microbiology · 2023Article
- Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review.Antibiotics (Basel, Switzerland) · 2022Review
- Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing.Cancers · 2022Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
18 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients' samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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