Publication details

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

Authors

BEZDÍČEK Matěj NYKRYNOVA Marketa SEDLAR Karel KRÁLOVÁ Stanislava HANSLIKOVA Jana KOMPRDOVA Aja SKUTKOVA Helena KOCMANOVA Iva MAYER Jiri LENGEROVÁ Martina

Year of publication 2021
Type Article in Periodical
Magazine / Source Scientific Reports
Citation
Web https://doi.org/10.1038/s41598-021-96148-3
Doi http://dx.doi.org/10.1038/s41598-021-96148-3
Keywords Bacteriology; Clinical microbiology; Infectious-disease epidemiology
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'.
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