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NYKRÝNOVÁ, M. BARTOŇ, V. SEDLÁŘ, K. BEZDÍČEK, M. LENGEROVÁ, M. ŠKUTKOVÁ, H.
Original Title
Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping
Type
journal article in Web of Science
Language
English
Original Abstract
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.
Keywords
genotyping; entropy; genetic markers; closely related bacteria; MLST
Authors
NYKRÝNOVÁ, M.; BARTOŇ, V.; SEDLÁŘ, K.; BEZDÍČEK, M.; LENGEROVÁ, M.; ŠKUTKOVÁ, H.
Released
3. 2. 2021
Publisher
Frontiers Media SA
ISBN
1664-302X
Periodical
Frontiers in Microbiology
Year of study
12
Number
1
State
Swiss Confederation
Pages from
Pages to
8
Pages count
URL
https://www.frontiersin.org/articles/10.3389/fmicb.2021.631605/full
Full text in the Digital Library
http://hdl.handle.net/11012/196358
BibTex
@article{BUT167886, author="Markéta {Jakubíčková} 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" }