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.

Základní údaje

Originální název

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

Autoři

BEZDÍČEK, Matěj (203 Česká republika, domácí), Marketa NYKRYNOVA (203 Česká republika), Karel SEDLAR (203 Česká republika), Stanislava KRÁLOVÁ (703 Slovensko, domácí), Jana HANSLIKOVA (203 Česká republika), Aja KOMPRDOVA (203 Česká republika), Helena SKUTKOVA (203 Česká republika), Iva KOCMANOVA (203 Česká republika), Jiří MAYER (203 Česká republika) a Martina LENGEROVÁ (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.996

Kód RIV

RIV/00216224:14110/21:00122323

Organizační jednotka

Lékařská fakulta

DOI

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

UT WoS

000686663200027

Klíčová slova anglicky

Bacteriology; Clinical microbiology; Infectious-disease epidemiology

Štítky

14110212, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 24. 7. 2023 12:55, Mgr. Tereza Miškechová

Anotace

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'.

Návaznosti

MUNI/A/1595/2020, interní kód MU

Název: Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VIII (Akronym: VýDiTeHeMa VIII)

Investor: Masarykova univerzita, Nové přístupy ve výzkumu, diagnostice a terapii hematologických malignit VIII

Citovat

BEZDÍČEK, Matěj, Marketa NYKRYNOVA, Karel SEDLAR, Stanislava KRÁLOVÁ, Jana HANSLIKOVA, Aja KOMPRDOVA, Helena SKUTKOVA, Iva KOCMANOVA, Jiří MAYER a Martina LENGEROVÁ. Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms. Scientific Reports. London: Nature Research, 2021, roč. 11, č. 1, s. "16572", 11 s. ISSN 2045-2322. Dostupné z: 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 a 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, roč.~11, č.~1, s.~''16572'', 11 s. ISSN~2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-021-96148-3.

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