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

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 exis...

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Bibliographic Details
Published in:Scientific reports 2021-08, Vol.11 (1), p.16572-16572, Article 16572
Main Authors: Bezdicek, Matej, Nykrynova, Marketa, Sedlar, Karel, Kralova, Stanislava, Hanslikova, Jana, Komprdova, Aja, Skutkova, Helena, Kocmanova, Iva, Mayer, Jiri, Lengerova, Martina
Format: Article
Language:English
Subjects:
631/326/107
631/326/1320
631/326/41/1470
Antibiotics
Clinical isolates
E coli
Escherichia coli
Genomes
Genotyping
Hematology
Humanities and Social Sciences
Infections
Internal medicine
Melting
Methods
multidisciplinary
Oncology
Power
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
Surveillance
Whole genome sequencing
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Summary: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’.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-96148-3