ReviewMolecular diagnosis & therapy2023
Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.
Review in Molecular diagnosis & therapy, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
30 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Pooled it
- Diagnostic accuracy of nanopore sequencing for detecting Mycobacterium tuberculosis and drug-resistant strains: a systematic review and meta-analysis.Scientific reports · 2025Pooled it
- Modular integration of nanopore sequencing, alphafold modeling, and statistical design boosts 1-hydroxyphenazine yield in Pseudomonas aeruginosa strain KAEH25.BMC microbiology · 2026Article
- Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.Microbiology spectrum · 2026Article
- Accuracy of nanopore-based targeted next-generation sequencing assay for detection ofJournal of clinical microbiology · 2026Article
- Article
- Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.Frontiers in microbiology · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Construction of an auxiliary diagnostic model for secondary pulmonary bacterial infection in influenza based on routine detection indicators.American journal of translational research · 2026Article
- Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.Molecular & cellular proteomics : MCP · 2025Review
- Precision medicine in liver transplantation for hepatocellular carcinoma: applications and prospects of third-generation sequencing technology.Journal of cancer research and clinical oncology · 2025Review
- Epitranscriptomic alterations induced by environmental toxins: implications for RNA modifications and disease.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2025Review
- Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- An exploratory study on the application of nanopore sequencing for detecting Mycobacterium tuberculosis drug resistance in respiratory specimens.BMC pulmonary medicine · 2025Article
- Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.Journal of clinical microbiology · 2025Article
- Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers.BMC infectious diseases · 2025Article
- Analytical techniques for nucleic acid and protein detection with single-molecule sensitivity.Experimental & molecular medicine · 2025Review
- Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance.Frontiers in cellular and infection microbiology · 2025Article
- Recent advances in biomarker detection of oral squamous cell carcinoma.Frontiers in oncology · 2025Review
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This review provides an in-depth discussion of the development, principles and utility of nanopore sequencing technology and its diverse applications in the identification of various pulmonary pathogens. We examined the emergence and advancements of nanopore sequencing as a significant player in this field. We illustrate the challenges faced in diagnosing mixed infections and further scrutinize the use of nanopore sequencing in the identification of single pathogens, including viruses (with a focus on its use in epidemiology, outbreak investigation, and viral resistance), bacteria (emphasizing 16S targeted sequencing, rare bacterial lung infections, and antimicrobial resistance studies), fungi (employing internal transcribed spacer sequencing), tuberculosis, and atypical pathogens. Furthermore, we discuss the role of nanopore sequencing in metagenomics and its potential for unbiased detection of all pathogens in a clinical setting, emphasizing its advantages in sequencing genome repeat areas and structural variant regions. We discuss the limitations in dealing with host DNA removal, the inherent high error rate of nanopore sequencing technology, along with the complexity of operation and processing, while acknowledging the possibilities provided by recent technological improvements. We compared nanopore sequencing with the BioFire system, a rapid molecular diagnostic system based on polymerase chain reaction. Although the BioFire system serves well for the rapid screening of known and common pathogens, it falls short in the identification of unknown or rare pathogens and in providing comprehensive genome analysis. As technological advancements continue, it is anticipated that the role of nanopore sequencing technology in diagnosing and treating lung infections will become increasingly significant.
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