Publication result detail

Unveiling Diversity: Classification of Klebsiella Pneumoniae Plasmids from Long-read Assemblies

VÍTKOVÁ, H.; NYKRÝNOVÁ, M.; BEZDÍČEK, M.; LENGEROVÁ, M.

Original Title

Unveiling Diversity: Classification of Klebsiella Pneumoniae Plasmids from Long-read Assemblies

English Title

Unveiling Diversity: Classification of Klebsiella Pneumoniae Plasmids from Long-read Assemblies

Type

Paper in proceedings (conference paper)

Original Abstract

Plasmids, integral to bacterial evolution, pose challenges in their genome classification due to incomplete assembly data. While next-generation sequencing has improved plasmid classification, challenges persist in accurately assembling complete plasmid genomes. This study presents a novel plasmid classification methodology based on complete genome similarity, utilizing three metrics: nucleotide composition, gene occurrence, and structural dissimilarity. Tested on a local Klebsiella pneumoniae population, the method outperforms pMLST and PlasmidFinder, distinguishing plasmids even in fusion cases. Applied across diverse bacterial populations, this reference-free approach proves adaptable, offering a valuable tool for monitoring plasmid mobility and diversity. Third-generation sequencing advancements provide a comprehensive understanding of plasmid dynamics, which is essential for addressing antibiotic resistance and bacterial pathogenicity.

English abstract

Plasmids, integral to bacterial evolution, pose challenges in their genome classification due to incomplete assembly data. While next-generation sequencing has improved plasmid classification, challenges persist in accurately assembling complete plasmid genomes. This study presents a novel plasmid classification methodology based on complete genome similarity, utilizing three metrics: nucleotide composition, gene occurrence, and structural dissimilarity. Tested on a local Klebsiella pneumoniae population, the method outperforms pMLST and PlasmidFinder, distinguishing plasmids even in fusion cases. Applied across diverse bacterial populations, this reference-free approach proves adaptable, offering a valuable tool for monitoring plasmid mobility and diversity. Third-generation sequencing advancements provide a comprehensive understanding of plasmid dynamics, which is essential for addressing antibiotic resistance and bacterial pathogenicity.

Keywords

bacteria; diversity; genome alignment; pangenome; phylogenetics; plasmid type

Key words in English

bacteria; diversity; genome alignment; pangenome; phylogenetics; plasmid type

Authors

VÍTKOVÁ, H.; NYKRÝNOVÁ, M.; BEZDÍČEK, M.; LENGEROVÁ, M.

RIV year

2025

Released

28.08.2024

Publisher

Springer Nature

ISBN

978-3-031-64636-2

Book

Lecture Notes in Bioinformatics

Edition

14849

ISBN

1611-3349

Periodical

Lecture Notes in Computer Science

Volume

14849

Number

II.

State

Swiss Confederation

Pages from

314

Pages to

328

Pages count

15

URL

https://link.springer.com/chapter/10.1007/978-3-031-64636-2_24

BibTex

@inproceedings{BUT189778,
  author="Helena {Vítková} and Markéta {Jakubíčková} and Matěj {Bezdíček} and Martina {Lengerová}",
  title="Unveiling Diversity: Classification of Klebsiella Pneumoniae Plasmids from Long-read Assemblies",
  booktitle="Lecture Notes in Bioinformatics",
  year="2024",
  series="14849",
  journal="Lecture Notes in Computer Science",
  volume="14849",
  number="II.",
  pages="314--328",
  publisher="Springer Nature",
  doi="10.1007/978-3-031-64636-2\{_}24",
  isbn="978-3-031-64636-2",
  url="https://link.springer.com/chapter/10.1007/978-3-031-64636-2_24"
}