ArticleAnnals of clinical microbiology and antimicrobials2022
Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting.
Article in Annals of clinical microbiology and antimicrobials, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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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
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.
- Review of the aetiologies of central nervous system infections in Vietnam.Frontiers in public health · 2024Pooled it
- Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.Frontiers in microbiology · 2026Review
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Evaluating the Diagnostic Utility of 16S Oxford Nanopore Technology Sequencing in Patients With Central Nervous System Infections and Its Usefulness in Antimicrobial Stewardship.The Journal of infectious diseases · 2025Article
- Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.Genome medicine · 2025Article
- Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance.ACS synthetic biology · 2025Article
- Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.Scientific reports · 2025Article
- Rapid detection ofFrontiers in cellular and infection microbiology · 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
- Optimization of the Diagnosis of Central Nervous System Infections in Vietnamese Hospitals: Results From a Retrospective Multicenter Study.Open forum infectious diseases · 2024Article
- Review
- Molecular epidemiology of SARS-CoV-2 in Mongolia, first experience with nanopore sequencing in lower- and middle-income countries setting.Immunity, inflammation and disease · 2023Article
- Applying Metagenomic Analysis Using Nanopore Sequencer (MinION) for Precision Medicine in Bacterial Keratoconjunctivitis: Comprehensive Validation of Molecular Biological and Conventional Examinations.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
16 authors at 5 institutions in 3 countries.
Funding
Abstract
aimThe aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise.
methodsDNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics.
resultsNanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30).
conclusionNext-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise.
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Registered trials
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