ArticleScientific reports2018
Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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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.
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Who cites it
37 citing papers in PubMed, 74 citations in OpenAlex.
- Diagnostic Performance of Nanopore-targeted Sequencing for Sputum Smear-negative Pulmonary Tuberculosis: A Retrospective Study.Open forum infectious diseases · 2026Article
- Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.Frontiers in microbiology · 2026Review
- Comparison of Illumina and Oxford Nanopore sequencing data quality for Clostridioides difficile genome analysis and their application for epidemiological surveillance.BMC genomics · 2025Article
- Global trends in the application of nanopore sequencing technology in the detection of infectious disease pathogens: a bibliometric analysis from 2014 to 2024.Frontiers in medicine · 2025Article
- Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia.BMC genomics · 2024Article
- Time Required for Nanopore Whole-Genome Sequencing of Neisseria gonorrhoeae for Identification of Phylogenetic Relationships.The Journal of infectious diseases · 2023Article
- Predictive Power of Long-Read Whole-Genome Sequencing for Rapid Diagnostics of Multidrug-Resistant Brachyspira hyodysenteriae Strains.Microbiology spectrum · 2023Article
- Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA.Antibiotics (Basel, Switzerland) · 2022Article
- Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective.Clinical microbiology reviews · 2022Review
- Rapid Detection of Antimicrobial Resistance in Mycoplasma genitalium by High-Resolution Melting Analysis with Unlabeled Probes.Microbiology spectrum · 2022Article
- 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study.BMJ open ophthalmology · 2022Article
- Prediction of antimicrobial minimal inhibitory concentrations forSaudi journal of biological sciences · 2022Article
- Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection.Journal of clinical microbiology · 2022Article
- Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing.Molecular biology and evolution · 2022Article
- Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections.Lab on a chip · 2022Review
- Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies.International journal of molecular sciences · 2022Review
- Prediction of Antibiotic Susceptibility Profiles ofFrontiers in microbiology · 2022Article
- Comparative Whole-Genome Analysis ofFrontiers in cellular and infection microbiology · 2022Article
- Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2022Article
- Antimicrobial Resistance Mechanisms, Multilocus Sequence Typing, and NG-STAR Sequence Types of Diverse Neisseria gonorrhoeae Isolates in KwaZulu-Natal, South Africa.Antimicrobial agents and chemotherapy · 2021Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
Abstract
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.
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Registered trials
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