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

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

Rok publikování 2021
Druh Článek v odborném periodiku
Časopis / Zdroj Scientific Reports
Citace
www https://doi.org/10.1038/s41598-021-96148-3
Doi http://dx.doi.org/10.1038/s41598-021-96148-3
Klíčová slova Bacteriology; Clinical microbiology; Infectious-disease epidemiology
Popis 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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