ArticleClinical & translational immunology2019
Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia.
Article in Clinical & translational immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Enhanced blood parasite species identification using V4-V9 18S rDNA barcoding by universal primers on a nanopore platform.Scientific reports · 2025Article
- Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.Scientific reports · 2025Article
- Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution.Scientific reports · 2023Article
- A Refined, Controlled 16S rRNA Gene Sequencing Approach Reveals Limited Detection of Cerebrospinal Fluid Microbiota in Children with Bacterial Meningitis.Microbiology spectrum · 2023Article
- Predicting β-lactam susceptibility from the genome ofFrontiers in microbiology · 2023Article
- Full-Length 16S rRNA Gene Analysis Using Long-Read Nanopore Sequencing for Rapid Identification of Bacteria from Clinical Specimens.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting.Annals of clinical microbiology and antimicrobials · 2022Article
- MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting.BMC medical genomics · 2022Article
- Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.Frontiers in microbiology · 2022Article
- Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review.EBioMedicine · 2021Review
- Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer.Scientific reports · 2021Article
- Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution.BMC microbiology · 2021Article
- Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections.Frontiers in microbiology · 2021Review
- Nanopore sequencing and its application to the study of microbial communities.Computational and structural biotechnology journal · 2021Review
- Immunosuppression and cardiovascular dysfunction in patients with severe versus mild coronavirus disease 2019: a case series.Clinical & translational immunology · 2020Article
- A lab in the field: applications of real-time,Biology methods & protocols · 2020Article
- Frontiers in antiviral therapy and immunotherapy.Clinical & translational immunology · 2020Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesWe have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology-based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof-of-concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.
methodsWe extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.
resultsThe sequencing results of four of the six culture-positive samples were consistent with those of conventional culture-based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3 min. Although the major bacterial species were also detected from the other two culture-positive samples and five culture-negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis.
conclusionOur results suggest that time-effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.
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