ArticleGigaScience2020
Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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
24 citing papers in PubMed.
- Review
- Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.MicrobiologyOpen · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- New vectors and optimal conditions for allelic exchange in hypervirulent Klebsiella pneumoniae.Journal of microbiological methods · 2025Article
- Genomic insight on Klebsiella variicola isolated from wastewater treatment plant has uncovered a novel bacteriophage.BMC genomics · 2024Article
- Article
- Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA fromMicrobial genomics · 2024Article
- Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.Nucleic acids research · 2024Article
- HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.Briefings in bioinformatics · 2023Article
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
- Detection of Streptococcus pyogenes M1Nature communications · 2023Article
- Antimicrobial resistance-Do we share more than companionship with our dogs?Journal of applied microbiology · 2022Article
- Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii.mBio · 2022Article
- Nanopore sequencing of RNA and cDNA molecules inRNA (New York, N.Y.) · 2022Article
- Direct RNA Nanopore Sequencing of Pseudomonas aeruginosa Clone C Transcriptomes.Journal of bacteriology · 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
- Development of ONT-cappable-seq to unravel the transcriptional landscape ofComputational and structural biotechnology journal · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Quantitative Control for Stoichiometric Protein Synthesis.Annual review of microbiology · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundKlebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics to treat these bacterial infections. The MinION device can sequence native DNA and RNA in real time, providing an opportunity to compare the utility of DNA and RNA for prediction of antibiotic susceptibility. However, the effectiveness of bacterial direct RNA sequencing and base-calling has not previously been investigated. This study interrogated the genome and transcriptome of 4 extensively drug-resistant (XDR) K. pneumoniae clinical isolates; however, further antimicrobial susceptibility testing identified 3 isolates as pandrug-resistant (PDR).
resultsThe majority of acquired resistance (≥75%) resided on plasmids including several megaplasmids (≥100 kb). DNA sequencing detected most resistance genes (≥70%) within 2 hours of sequencing. Neural network-based base-calling of direct RNA achieved up to 86% identity rate, although ≤23% of reads could be aligned. Direct RNA sequencing (with ∼6 times slower pore translocation) was able to identify (within 10 hours) ≥35% of resistance genes, including those associated with resistance to aminoglycosides, β-lactams, trimethoprim, and sulphonamide and also quinolones, rifampicin, fosfomycin, and phenicol in some isolates. Direct RNA sequencing also identified the presence of operons containing up to 3 resistance genes. Polymyxin-resistant isolates showed a heightened transcription of phoPQ (≥2-fold) and the pmrHFIJKLM operon (≥8-fold). Expression levels estimated from direct RNA sequencing displayed strong correlation (Pearson: 0.86) compared to quantitative real-time PCR across 11 resistance genes.
conclusionOverall, MinION sequencing rapidly detected the XDR/PDR K. pneumoniae resistome, and direct RNA sequencing provided accurate estimation of expression levels of these genes.
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