In this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the consensus sequence. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer pairs on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer pairs on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer pairs. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer pairs required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.
EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing / M. Perini, A. Piazza, S. Panelli, D. Di Carlo, M. Corbella, F. Gona, F. Vailati, P. Marone, D.M. Cirillo, C. Farina, G. Zuccotti, F. Comandatore. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - 10:1(2020 Jan 28).
Titolo: | EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing |
Autori: | PERINI, MATTEO (Primo) PIAZZA, AURORA (Secondo) COMANDATORE, FRANCESCO (Ultimo) (Corresponding) |
Settore Scientifico Disciplinare: | Settore MED/07 - Microbiologia e Microbiologia Clinica Settore BIO/11 - Biologia Molecolare |
Data di pubblicazione: | 28-gen-2020 |
Rivista: | |
Tipologia: | Article (author) |
Data ahead of print / Data di stampa: | 28-lug-2019 |
Digital Object Identifier (DOI): | http://dx.doi.org/10.1038/s41598-020-57742-z |
Appare nelle tipologie: | 01 - Articolo su periodico |
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