ArticleNature microbiology2020
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens.
Article in Nature microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers, 2 of them syntheses that pooled it.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
105 citing papers in PubMed, 2 syntheses or guidelines pooled it, 186 citations in OpenAlex.
- A Research Agenda for Precision Medicine in Sepsis and Acute Respiratory Distress Syndrome: An Official American Thoracic Society Research Statement.American journal of respiratory and critical care medicine · 2021Guideline
- Pooled it
- Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.Gut microbes · 2026Trial
- Age- and diet-driven assembly of the gut antibiotic resistome in humans and food-producing animals.Gut microbes · 2026Review
- Comparative analysis of MinION and MiSeq using 16S rRNA gene amplicon sequencing in human gut microbiome.BMC biotechnology · 2026Article
- L-EasyARG: A long-read metagenomics tool for rapid antibiotic-resistance-gene profiling.iMetaOmics · 2026Article
- Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.Scientific reports · 2026Article
- MinION Sequencer Demonstrates Strong DNA Sequencing Accuracy and Identity.microPublication biology · 2026Article
- Article
- Targeting Horizontal Gene Transfer to Combat Antimicrobial Resistance: A Review of Mechanisms, Drivers, and Multi-Omics Strategies.Infection and drug resistance · 2026Review
- Significant impact of threshold adjustments on microbiome characterization following Nanopore sequencing.ISME communications · 2026Article
- Rapid culture-free diagnosis of clinical pathogens via integrated microfluidic-Raman micro-spectroscopy.Nature communications · 2025Article
- Real-time analysis and visualization of nanopore metagenomic samples with MARTi.Genome research · 2025Article
- Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland.Journal of fish diseases · 2025Article
- Engineering Linker-Enhanced OmpG Nanopores for Rapid Single-Molecule Protease Detection.Sensors (Basel, Switzerland) · 2025Article
- Consequences of host-microbiome interactions in preterm infants.Infection and immunity · 2025Review
- Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling.Briefings in bioinformatics · 2025Article
- Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs.JAC-antimicrobial resistance · 2025Article
- Nanopore full length 16S rRNA gene sequencing increases species resolution in bacterial biomarker discovery.Scientific reports · 2025Article
- Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.Microorganisms · 2025Review
45 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 5 institutions in 1 country.
Funding
Abstract
The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.
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What OpenQuestion holds
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.