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

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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Matej Bezdicek, Marketa Nykrynova, Karel Sedlar, Stanislava Kralova, Jana Hanslikova, Aja Komprdova, Helena Skutkova, Iva Kocmanova, Jiri Mayer, Martina Lengerova
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f40d483413004e129df96d4cdd5a08fe
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f40d483413004e129df96d4cdd5a08fe
record_format	dspace
spelling	oai:doaj.org-article:f40d483413004e129df96d4cdd5a08fe2021-12-02T16:45:54ZRapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms10.1038/s41598-021-96148-32045-2322https://doaj.org/article/f40d483413004e129df96d4cdd5a08fe2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96148-3https://doaj.org/toc/2045-2322Abstract 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’.Matej BezdicekMarketa NykrynovaKarel SedlarStanislava KralovaJana HanslikovaAja KomprdovaHelena SkutkovaIva KocmanovaJiri MayerMartina LengerovaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Matej Bezdicek Marketa Nykrynova Karel Sedlar Stanislava Kralova Jana Hanslikova Aja Komprdova Helena Skutkova Iva Kocmanova Jiri Mayer Martina Lengerova Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
description	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’.
format	article
author	Matej Bezdicek Marketa Nykrynova Karel Sedlar Stanislava Kralova Jana Hanslikova Aja Komprdova Helena Skutkova Iva Kocmanova Jiri Mayer Martina Lengerova
author_facet	Matej Bezdicek Marketa Nykrynova Karel Sedlar Stanislava Kralova Jana Hanslikova Aja Komprdova Helena Skutkova Iva Kocmanova Jiri Mayer Martina Lengerova
author_sort	Matej Bezdicek
title	Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
title_short	Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
title_full	Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
title_fullStr	Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
title_full_unstemmed	Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
title_sort	rapid high-resolution melting genotyping scheme for escherichia coli based on mlst derived single nucleotide polymorphisms
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/f40d483413004e129df96d4cdd5a08fe
work_keys_str_mv	AT matejbezdicek rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT marketanykrynova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT karelsedlar rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT stanislavakralova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT janahanslikova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT ajakomprdova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT helenaskutkova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT ivakocmanova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT jirimayer rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms AT martinalengerova rapidhighresolutionmeltinggenotypingschemeforescherichiacolibasedonmlstderivedsinglenucleotidepolymorphisms
_version_	1718383491025993728

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

Ejemplares similares