ArticleGigaScience2016
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing.
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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.
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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
47 citing papers in PubMed.
- Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting.Microbial genomics · 2026Article
- Immune Dysfunction and Infection Risk in Advanced Liver Disease.Gastroenterology · 2025Review
- Merging High-Throughput, Amplicon-Based Second and Third Generation Sequencing Data: An Integrative and Modular Data Analysis Framework for Haplotype Prediction and Output Evaluation.International journal of molecular sciences · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Article
- Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma.Cancers · 2024Article
- It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine.JMIR bioinformatics and biotechnology · 2024Article
- The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication.mBio · 2024Article
- Next-Generation Sequencing and Triple-Negative Breast Cancer: Insights and Applications.International journal of molecular sciences · 2023Review
- Isolation and Identification of Multidrug-ResistantPathogens (Basel, Switzerland) · 2023Article
- Analytical methods for assessing antimicrobial activity of nanomaterials in complex media: advances, challenges, and perspectives.Journal of nanobiotechnology · 2023Review
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.Life (Basel, Switzerland) · 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
- Whole-Genome Sequencing of Pathogenic Bacteria-New Insights into Antibiotic Resistance Spreading.Microorganisms · 2021Article
- Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing.Frontiers in genetics · 2021Article
- Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.PloS one · 2021Article
- Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing.International journal of molecular sciences · 2020Article
- Rapid isolation of rare targets from large fluid volumes.Scientific reports · 2020Article
- From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics.The Journal of infectious diseases · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance profile identification. Using four culture isolate samples, as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 min of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 h. While strain identification with multi-locus sequence typing required more than 15x coverage to generate confident assignments, our novel gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.
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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.