2021
DOI: 10.1038/s41598-021-96148-3
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Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

Abstract: 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 = 0.94… Show more

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Cited by 7 publications
(6 citation statements)
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“…An in-house MELT2MELT algorithm based on MATLAB software was used to generate a MelT key as described by Bezdicek et al ( 24 ). The final MelT key is available at www.cmbgt.cz/mini-mlst/t6353 and is regularly updated as new STs are consistently released.…”
Section: Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…An in-house MELT2MELT algorithm based on MATLAB software was used to generate a MelT key as described by Bezdicek et al ( 24 ). The final MelT key is available at www.cmbgt.cz/mini-mlst/t6353 and is regularly updated as new STs are consistently released.…”
Section: Methodsmentioning
confidence: 99%
“…The mini-MLST laboratory protocol was designed to be applicable for K. pneumoniae ( 31 ), E. coli ( 24 ), and P. aeruginosa typing simultaneously in the same PCR run. Real-time PCRs contained 10 μL 2× SensiFAST HRM mix (Bioline, UK), 0.4 μM each primer, 1 μL of DNA (30 ng/μL), and deionized water to a final volume of 20 μL.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Analyzing these positions can accurately predict the MLST genotype, eliminating the need to sequence all seven loci. Genotyping isolates using the mini-MLST scheme significantly reduces the time and labor required for a single study and is suitable for rapid and mass screening [ 25 ].…”
Section: Introductionmentioning
confidence: 99%
“…A combination of individual loci’s alleles enables the isolate to be assigned as a melting type (MelT). So far, mini-MLST schemes have been published not only for S. aureus ( 5 ) but also for Klebsiella pneumoniae ( 6 ), Streptococcus pyogenes ( 7 ), Enterococcus faecium ( 8 ), Campylobacter jejuni ( 9 ), and Escherichia coli ( 10 ). In S. aureus typing, HRM was similarly used to modify spa-typing (spa-HRM) ( 11 18 ).…”
Section: Introductionmentioning
confidence: 99%