ArticleBMC infectious diseases2017
Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study.
Article in BMC infectious diseases, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 120 citations in OpenAlex.
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- Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.Clinical microbiology reviews · 2026Review
- Emerging point-of-care technologies for bacterial pathogen detection.Journal of Zhejiang University. Science. B · 2026Review
- Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.Acute and critical care · 2026Article
- Improved Microbiological Diagnosis of Bone and Joint Infections Using Mechanical Bead-Milling Extraction of Bone Specimens with the Ultra-TurraxDiagnostics (Basel, Switzerland) · 2026Article
- Surface-Imprinted Polymer Coupled with Diffraction Gratings for Low-Cost, Label-Free and DifferentialBiosensors · 2026Article
- Comparative diagnostic evaluation of real-time PCR and culture for detecting pathogens in podiatric wound infections.Microbiology spectrum · 2026Article
- Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.Frontiers in cellular and infection microbiology · 2026Article
- 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
- The wound microbiome associated with deep sternal wound infection: a scoping review.Journal of thoracic disease · 2025Review
- Beyond Infection: How Antimicrobial Therapies Influence the Urinary Microbiome and Stone Disease.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Real-TimeACS biomaterials science & engineering · 2025Article
- Biosensor Technology: Advances and Applications in Livestock Infectious Disease Diagnosis.Veterinary sciences · 2025Review
- Characterizing the seminal microbiota in mature rams managed on divergent planes of nutrition, and their male offspring.Journal of animal science · 2025Article
- Universal, untargeted detection of bacteria in tissues using metabolomics workflows.Nature communications · 2025Article
- Prevalence ofFrontiers in cellular and infection microbiology · 2025Article
- Characterizing the resistome ofFrontiers in microbiology · 2025Article
- The skin microbiome on healthy and inflammatory altered canine skin determined by next generation sequencing.Frontiers in microbiology · 2025Article
- Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections.Pathogens (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInfectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings.
methodsCredence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab.
resultsMetagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively.
conclusion16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis.
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