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: 4.997

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

EID Scopus

2-s2.0-85112687944

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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