Publication detail

Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

BEZDÍČEK, M. NYKRÝNOVÁ, M. SEDLÁŘ, K. KRÁLOVÁ, S. HANSLIKOVA, J. KOMPRDOVÁ, A. ŠKUTKOVÁ, H. KOCMANOVÁ, I. MAYER, J. LENGEROVÁ, M.

Original Title

Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

Type

journal article in Web of Science

Language

English

Original Abstract

Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.

Keywords

rapid

Authors

BEZDÍČEK, M.; NYKRÝNOVÁ, M.; SEDLÁŘ, K.; KRÁLOVÁ, S.; HANSLIKOVA, J.; KOMPRDOVÁ, A.; ŠKUTKOVÁ, H.; KOCMANOVÁ, I.; MAYER, J.; LENGEROVÁ, M.

Released

16. 8. 2021

Publisher

Springer Nature

Location

BERLIN

ISBN

2045-2322

Periodical

Scientific Reports

Year of study

11

Number

1

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1

Pages to

11

Pages count

11

URL

https://www.nature.com/articles/s41598-021-96148-3

Full text in the Digital Library

http://hdl.handle.net/11012/201340

BibTex

@article{BUT172373,
  author="Matěj {Bezdíček} and Markéta {Jakubíčková} and Karel {Sedlář} and Stanislava {Králová} and Jana {Hanslikova} and Aja {Komprdová} and Helena {Vítková} and Iva {Kocmanová} and Jiří {Mayer} and Martina {Lengerová}",
  title="Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms",
  journal="Scientific Reports",
  year="2021",
  volume="11",
  number="1",
  pages="1--11",
  doi="10.1038/s41598-021-96148-3",
  issn="2045-2322",
  url="https://www.nature.com/articles/s41598-021-96148-3"
}