ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2022
Targeted Metagenomic Sequencing-based Approach Applied to 2146 Tissue and Body Fluid Samples in Routine Clinical Practice.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Methicillin-resistant Staphylococcus aureus.Nature reviews. Disease primers · 2026Review
- Performance and practicality of 16S nanopore sequencing for routine bacterial identification in clinical samples.Microbiology spectrum · 2026Article
- Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.Microbiology spectrum · 2026Article
- Microbial Detection in Community-Acquired Pleural Space Infections Using the BIOFIRE Joint Infection Panel and Individual Polymerase Chain Reaction Assays.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study.Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada · 2026Article
- Quantitative interpretation models for targeted next-generation sequencing in lower respiratory tract infections: a multicenter prospective study.Respiratory research · 2026Article
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- Detection of Pathogens by a Novel User-Developed Broad-Range BR 16S PCR rRNA Polymerase Chain Reaction/Gene Sequencing Assay: Multiyear Experience in a Large Canadian Healthcare Zone.Microorganisms · 2026Article
- 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
- Microbial next generation DNA sequencing of aspirated synovial fluid shows concordance with ICM criteria biomarkers for diagnosing periprosthetic joint infection in hip and knee arthroplasty.Frontiers in microbiology · 2026Article
- Integrating molecular and conventional diagnostics in native vertebral osteomyelitis: a narrative review.Journal of bone and joint infection · 2026Review
- Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.Frontiers in cellular and infection microbiology · 2026Article
- Clinical evaluation of probe capture-based targeted next-generation sequencing in suspected infected pancreatic necrosis: a prospective pilot diagnostic study.BMC infectious diseases · 2025Article
- [From rhinorrhea to 16S: meningitis caused byRevista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia · 2025Article
- Next Generation Sequencing Improves Diagnostic 16S rRNA Amplicon-Based Microbiota Analyses of Clinical Samples Compared to Sanger Sequencing.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2025Article
- BioFire in osteoarticular Infections: Rapid syndromic testing for early and accurate diagnosis - A narrative review.Journal of clinical orthopaedics and trauma · 2025Review
- An innovative fungal-specific targeted next-generation sequencing method: analytical performance and a single-center prospective clinical study.Journal of translational medicine · 2025Article
- [Diagnostic value of targeted next-generation sequencing for community-acquired respiratory virus infections in patients with hematological diseases].Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi · 2025Article
- UMPlex™: a targeted next-generation sequencing primer design workflow.Virology journal · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe yield of next-generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) assay was evaluated in clinical practice for diagnosis of bacterial infection.
methodsPCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq) or reported as negative, depending on the cycle threshold value. A total of 2146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 patients from whom clinical data were available.
resultsCompared with Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay that incorporated NGS was 53%, which was higher than culture (42%, P < .001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup that received antibiotics at sampling was 41% for culture and 63% for the sequencing assay (P < .001).
conclusionsAdding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, especially in patients who had received antibiotic therapy.
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