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

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dc.contributor.authorBezdíček, Matějcs
dc.contributor.authorJakubíčková, Markétacs
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorKrálová, Stanislavacs
dc.contributor.authorHanslikova, Janacs
dc.contributor.authorKomprdová, Ajacs
dc.contributor.authorVítková, Helenacs
dc.contributor.authorKocmanová, Ivacs
dc.contributor.authorMayer, Jiřícs
dc.contributor.authorLengerová, Martinacs
dc.coverage.issue1cs
dc.coverage.volume11cs
dc.date.issued2021-08-16cs
dc.description.abstractRoutinely 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'.en
dc.formattextcs
dc.format.extent1-11cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationScientific Reports. 2021, vol. 11, issue 1, p. 1-11.en
dc.identifier.doi10.1038/s41598-021-96148-3cs
dc.identifier.issn2045-2322cs
dc.identifier.orcid0000-0002-0205-6935cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.orcid0000-0003-4562-2746cs
dc.identifier.other172373cs
dc.identifier.researcheridR-3181-2018cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.researcheridD-5194-2014cs
dc.identifier.scopus57202469794cs
dc.identifier.scopus56309904900cs
dc.identifier.scopus36521691000cs
dc.identifier.urihttp://hdl.handle.net/11012/201340
dc.language.isoencs
dc.publisherSpringer Naturecs
dc.relation.ispartofScientific Reportscs
dc.relation.urihttps://www.nature.com/articles/s41598-021-96148-3cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2045-2322/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectrapiden
dc.titleRapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphismsen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-172373en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:39:48en
sync.item.modts2025.01.17 18:42:05en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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