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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F21%3APU141499" target="_blank" >RIV/00216305:26220/21:PU141499 - isvavai.cz</a>
Alternative codes found
RIV/65269705:_____/21:00074830 RIV/00216224:14110/21:00122323
Result on the web
<a href="https://www.nature.com/articles/s41598-021-96148-3" target="_blank" >https://www.nature.com/articles/s41598-021-96148-3</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41598-021-96148-3" target="_blank" >10.1038/s41598-021-96148-3</a>

Result language
angličtina
Original language name
Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms
Original language description
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'.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10700 - Other natural sciences

Project
<a href="/en/project/NV19-09-00430" target="_blank" >NV19-09-00430: Whole-Genome Sequencing for Hospital Epidemiology and Multi-drug Resistant Bacteria Outbreaks Detection</a><br>
Continuities
S - Specificky vyzkum na vysokych skolach

Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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