ReviewThe Journal of infectious diseases2020
From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics.
Review in The Journal of infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 3 of them syntheses that pooled it.
What it found
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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
76 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Comparative diagnostic accuracy of next-generation sequencing in different specimen types for periprosthetic joint infection: A systematic review and meta-analysis.Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA · 2026Pooled it
- Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis.BMC infectious diseases · 2024Pooled it
- A systematic review and critical appraisal of metagenomic and culture studies in hidradenitis suppurativa.Experimental dermatology · 2021Pooled it
- Integrating mathematical modelling and artificial intelligence to combat emerging viral syndemics: A systematic review.New microbes and new infections · 2026Review
- Rickettsia massiliae and its public health significance across Palearctic and Oriental regions: a scoping review.Infectious diseases of poverty · 2026Article
- Clinical Significance of Intestinal Fungal Overgrowth: Integrating the Gut Mycobiome into Modern Gastroenterology.Microorganisms · 2026Review
- Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.One health (Amsterdam, Netherlands) · 2026Article
- Rapid Microbiological Diagnostics for Sepsis: Narrative Review of Current and Prospective Approaches.Critical care explorations · 2026Review
- A Global Delphi Consensus on Acne and the Microbiome: Integrating International Expertise for Innovative Prevention and Therapeutic Strategies.Pharmaceuticals (Basel, Switzerland) · 2026Review
- From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.Orthopaedic surgery · 2026Review
- Early detection of nosocomial pathogens in air and surfaces using an innovative genetic approach for surveillance in healthcare settings.Antimicrobial resistance and infection control · 2026Article
- Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Navigating the gut-metabolite-immune axis: enhancing efficacy and mitigating toxicity of immune checkpoint inhibitors.Frontiers in immunology · 2026Review
- Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.Frontiers in veterinary science · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients.Cell reports. Medicine · 2025Article
- Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.BMC microbiology · 2025Article
- Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis.BMC microbiology · 2025Article
- Cross-sectional Study: Diagnostic Accuracy of Next-generation Sequencing in a Tertiary Care Intensive Care Unit.Indian journal of critical care medicine : peer-reviewed, official publication of Indian Society of Critical Care Medicine · 2025Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.