ArticleJournal of clinical microbiology2016
Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens.
Article in Journal of clinical microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.Drugs · 2021Pooled it
- Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.Microbial genomics · 2026Article
- Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.Diagnostics (Basel, Switzerland) · 2026Review
- Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.Gut pathogens · 2026Article
- Diagnostic efficacy of targeted next-generation sequencing in suspected lower respiratory tract infections of patients with cancer: a retrospective study.Scientific reports · 2025Article
- Metagenomic identification of disease-causingMicrobial genomics · 2025Article
- China Expert consensus on the application of metagenomic next-generation sequencing for the etiological diagnosis of infections in hematological disorders (2024).Blood science (Baltimore, Md.) · 2025Article
- Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study.BMC infectious diseases · 2025Article
- HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.Frontiers in cellular and infection microbiology · 2025Article
- Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.Infection and drug resistance · 2025Article
- Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis.PloS one · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Identification of Pathogens in HIV-Infected Patients Using Metagenomic Next-Generation Sequencing (mNGS) as Compared to Conventional Microbiological Tests (CMTs).Infection and drug resistance · 2025Article
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 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
- Nanopore R10.4 metagenomic detection of blaNature communications · 2024Article
- Article
- Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance.BMC infectious diseases · 2024Article
- Advances in diagnostic assays forFrontiers in cellular and infection microbiology · 2024Review
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing (r(2) = -0.60) and MSS (r(2) = -0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge.
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