Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
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Summary
It is explored whether MinION nanopore sequencing could accelerate diagnosis and resistance profiling, using complicated urinary tract infections as an exemplar, and whether bioinformatic pipeline optimization is needed to better detect resistances conferred by point mutations.
- Type
- article
- Published
- 2016-09-25
- Cited by
- 276
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W2521268641
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:36768843
Keywords
Metagenomics, Identification (biology), Microbiology, Antimicrobial, Computational biology
References
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- Poretools: a toolkit for analyzing nanopore sequence data
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- Incorporating sequence quality data into alignment improves DNA read mapping
Cited by
- Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO
- Diagnosing tuberculosis in the 21st century – Dawn of a genomics revolution?
- Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action.
- Clinical and biological insights from viral genome sequencing
- A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions
- Messages from the first International Conference on Clinical Metagenomics (ICCMg).
- Field-based species identification in eukaryotes using single molecule, real-time sequencing
- Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)
- Rapid Pathogen Identification in Bacterial Pneumonia Using Real-Time Metagenomics.
- Prediction of cephalosporin and carbapenem susceptibility in multi-drug resistant Gram-negative bacteria using liquid chromatography-tandem mass spectrometry
- The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance
- De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
- Nanopore sequencing data analysis: state of the art, applications and challenges
- Methods for the detection and identification of pathogenic bacteria: past, present, and future.
- Using metagenomics to investigate human and environmental resistomes
- Nanolock−Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue
- Rapid accurate point-of-care tests combining diagnostics and antimicrobial resistance prediction for Neisseria gonorrhoeae and Mycoplasma genitalium
- Toward Rapid Sequenced-Based Detection and Characterization of Causative Agents of Bacteremia
- A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
- A world of opportunities with nanopore sequencing.
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