ArticlemSystems2024
Nanopore adaptive sampling effectively enriches bacterial plasmids.
Article in mSystems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- Enhancing low-level genome-edited crop detection and identification in food mixtures using nanopore adaptive sampling: Rice-Soybean mixture as proof-of-concept.NPJ science of food · 2026Article
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Proof-of-principle: nanopore adaptive sampling enables full blood group genome analysis and resolution of hybrid alleles.Blood advances · 2026Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing.Genome biology · 2025Article
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.Molecular ecology resources · 2025Article
- Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens likeJournal of clinical microbiology · 2025Article
- Targeted sequencing ofmSystems · 2025Article
- Characteristics of phage-plasmids and their impact on microbial communities.Essays in biochemistry · 2024Review
- A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.Journal of clinical microbiology · 2024Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of IMPORTANCE: Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an
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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 Socratic graph.