Detail publikace

Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping

NYKRÝNOVÁ, M. BARTOŇ, V. SEDLÁŘ, K. BEZDÍČEK, M. LENGEROVÁ, M. ŠKUTKOVÁ, H.

Originální název

Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g. local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also noncoding regions are examined.

Klíčová slova

genotyping; entropy; genetic markers; closely related bacteria; MLST

Autoři

NYKRÝNOVÁ, M.; BARTOŇ, V.; SEDLÁŘ, K.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H.

Vydáno

3. 2. 2021

Nakladatel

Frontiers Media SA

ISSN

1664-302X

Periodikum

Frontiers in Microbiology

Ročník

12

Číslo

1

Stát

Švýcarská konfederace

Strany od

1

Strany do

8

Strany počet

8

URL

https://www.frontiersin.org/articles/10.3389/fmicb.2021.631605/full

Plný text v Digitální knihovně

http://hdl.handle.net/11012/196358

BibTex

@article{BUT167886,
  author="Markéta {Nykrýnová} and Vojtěch {Bartoň} and Karel {Sedlář} and Matěj {Bezdíček} and Martina {Lengerová} and Helena {Vítková}",
  title="Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping",
  journal="Frontiers in Microbiology",
  year="2021",
  volume="12",
  number="1",
  pages="1--8",
  doi="10.3389/fmicb.2021.631605",
  issn="1664-302X",
  url="https://www.frontiersin.org/articles/10.3389/fmicb.2021.631605/full"
}