ArticlePeerJ2021
Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis.
Article in PeerJ, 2021. 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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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
17 citing papers in PubMed, 33 citations in OpenAlex.
- 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
- From air to insight: the evolution of airborne DNA sequencing technologies.Microbiology (Reading, England) · 2025Review
- A Tear-Based Approach for Rapid Identification of Bacterial Pathogens in Corneal Ulcers Using Nanopore Sequencing.Translational vision science & technology · 2025Observational
- Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.Scientific reports · 2025Article
- Clinical features, risk factors and outcomes of contact lens-related bacterial keratitis in Nottingham, UK: a 7-year study.Eye (London, England) · 2024Article
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- Oxford Nanopore Technology-Based Identification of anMicroorganisms · 2024Article
- EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale.Microbiology spectrum · 2024Article
- A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.Archives of microbiology · 2024Article
- Microbiological culture versus 16S/18S rRNA gene PCR-sanger sequencing for infectious keratitis: a three-arm, diagnostic cross-sectional study.Frontiers in medicine · 2024Article
- Diagnosis ofDiagnostics (Basel, Switzerland) · 2023Review
- FluoroPi Device With SmartProbes: A Frugal Point-of-Care System for Fluorescent Detection of Bacteria From a Pre-Clinical Model of Microbial Keratitis.Translational vision science & technology · 2023Article
- Article
- Metagenomic next-generation sequencing to investigate infectious keratitis byFrontiers in medicine · 2023Article
- Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.American journal of ophthalmology · 2022Article
- Application Progress of High-Throughput Sequencing in Ocular Diseases.Journal of clinical medicine · 2022Review
- 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study.BMJ open ophthalmology · 2022Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundMicrobial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis.
methodsUsing full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix
resultsWe found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (
conclusionWe have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.
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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.