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

J 2021

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

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Karel SEDLAR, Stanislava KRÁLOVÁ, Jana HANSLIKOVA et. al.

Basic information

Original name

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

Authors

BEZDÍČEK, Matěj (203 Czech Republic, belonging to the institution), Marketa NYKRYNOVA (203 Czech Republic), Karel SEDLAR (203 Czech Republic), Stanislava KRÁLOVÁ (703 Slovakia, belonging to the institution), Jana HANSLIKOVA (203 Czech Republic), Aja KOMPRDOVA (203 Czech Republic), Helena SKUTKOVA (203 Czech Republic), Iva KOCMANOVA (203 Czech Republic), Jiří MAYER (203 Czech Republic) and Martina LENGEROVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Scientific Reports, London, Nature Research, 2021, 2045-2322

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.996

RIV identification code

RIV/00216224:14110/21:00122323

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1038/s41598-021-96148-3

UT WoS

000686663200027

Keywords in English

Bacteriology; Clinical microbiology; Infectious-disease epidemiology

Abstract

V originále

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'.

Links

MUNI/A/1595/2020, interní kód MU

Name: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VIII (Acronym: VýDiTeHeMa VIII)

Investor: Masaryk University

Citovat

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Karel SEDLAR, Stanislava KRÁLOVÁ, Jana HANSLIKOVA, Aja KOMPRDOVA, Helena SKUTKOVA, Iva KOCMANOVA, Jiří MAYER and Martina LENGEROVÁ. Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms. Scientific Reports. London: Nature Research, 2021, vol. 11, No 1, p. "16572", 11 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-96148-3.

@article{1791665,
   author = {Bezdíček, Matěj and Nykrynova, Marketa and Sedlar, Karel and Králová, Stanislava and Hanslikova, Jana and Komprdova, Aja and Skutkova, Helena and Kocmanova, Iva and Mayer, Jiří and Lengerová, Martina},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41598-021-96148-3},
   keywords = {Bacteriology; Clinical microbiology; Infectious-disease epidemiology},
   language = {eng},
   issn = {2045-2322},
   journal = {Scientific Reports},
   title = {Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms},
   url = {https://doi.org/10.1038/s41598-021-96148-3},
   volume = {11},
   year = {2021}
}

TY  - JOUR
ID  - 1791665
AU  - Bezdíček, Matěj - Nykrynova, Marketa - Sedlar, Karel - Králová, Stanislava - Hanslikova, Jana - Komprdova, Aja - Skutkova, Helena - Kocmanova, Iva - Mayer, Jiří - Lengerová, Martina
PY  - 2021
TI  - Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
JF  - Scientific Reports
VL  - 11
IS  - 1
SP  - "16572"
EP  - "16572"
PB  - Nature Research
SN  - 20452322
KW  - Bacteriology
KW  - Clinical microbiology
KW  - Infectious-disease epidemiology
UR  - https://doi.org/10.1038/s41598-021-96148-3
N2  - 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'.
ER  -

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Karel SEDLAR, Stanislava KRÁLOVÁ, Jana HANSLIKOVA, Aja KOMPRDOVA, Helena SKUTKOVA, Iva KOCMANOVA, Jiří MAYER and Martina LENGEROVÁ. Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms. \textit{Scientific Reports}. London: Nature Research, 2021, vol.~11, No~1, p.~''16572'', 11 pp. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-96148-3.

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