ArticleGenomics, proteomics & bioinformatics2022
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 27 citations in OpenAlex.
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- Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation.FEMS microbiology reviews · 2026Review
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- The global genomic landscape of hypervirulentmLife · 2025Article
- Insights into incompatible plasmids in multidrug-resistant Raoultella superbugs.BMC microbiology · 2025Article
- KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration.Bioinformatics advances · 2025Article
- Genetic Characteristics of Novel IncInfection and drug resistance · 2024Article
- Replicon-Based Typing About IncG Plasmids and Molecular Characterization of Five IncG Plasmids Carrying Carbapenem Resistance GeneInfection and drug resistance · 2024Article
- Genomic epidemiology and heterogeneity ofEmerging microbes & infections · 2023Article
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- Abundant diversity of accessory genetic elements and associated antimicrobial resistance genes in pseudomonas aeruginosa isolates from a single Chinese hospital.Annals of clinical microbiology and antimicrobials · 2023Article
- Characterization of Three Novel IMP Metallo-β-Lactamases, IMP-89, IMP-91, and IMP-96, and DiverseMicrobiology spectrum · 2023Article
- Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis.Scientific reports · 2023Article
- AFrontiers in microbiology · 2023Article
- Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China.Genomics, proteomics & bioinformatics · 2022Article
- VIM-encoding IncAnnals of clinical microbiology and antimicrobials · 2022Article
- A Genomic and Bioinformatics View of the Classification and Evolution ofMicrobiology spectrum · 2022Article
- Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes inInfection and drug resistance · 2022Article
- IncFIB-4.1 and IncFIB-4.2 Single-Replicon Plasmids: Small Backbones with Large Accessory Regions.Infection and drug resistance · 2022Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an important pathogen that can cause severe hospital- and community-acquired infections. To systematically investigate its methylation features, we determined the whole-genome sequences of 14 K. pneumoniae strains covering varying serotypes, multilocus sequence types, clonal groups, viscosity/virulence, and drug resistance. Their methylomes were further characterized using Pacific Biosciences single-molecule real-time and bisulfite technologies. We identified 15 methylation motifs [13 N6-methyladenine (6mA) and two 5-methylcytosine (5mC) motifs], among which eight were novel. Their corresponding DNA methyltransferases were also validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distribution patterns of some hemi-/un-methylated GATC motifs, which tend to be located within intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slow methylation of the GATC motifs in the replication origin (oriC) regions and IGRs implicates the epigenetic regulation of replication initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumoniae at single-base resolution, and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.
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