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 gene. 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 sets 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 sets 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 sets. 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 sets required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.
Fast Klebsiella pneumoniae typing for outbreak reconstruction: an highly discriminatory HRM protocol on wzi capsular gene developed using EasyPrimer tool / M. Perini, A. Piazza, S. Panelli, D.D. Carlo, M. Corbella, F. Gona, F. Vailati, P. Marone, D.M. Cirillo, C. Farina, G.V. Zuccotti, F. Comandatore. - (2019 Jun 28).
Titolo: | Fast Klebsiella pneumoniae typing for outbreak reconstruction: an highly discriminatory HRM protocol on wzi capsular gene developed using EasyPrimer tool |
Autori: | PERINI, MATTEO (Primo) PIAZZA, AURORA (Secondo) |
Settore Scientifico Disciplinare: | Settore MED/07 - Microbiologia e Microbiologia Clinica |
Data di pubblicazione: | 2019-06-28 |
URL: | https://www.biorxiv.org/content/biorxiv/early/2019/06/28/679001.full.pdf |
Digital Object Identifier (DOI): | 10.1101/679001 |
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Perini_Manuscript_BioaRxiv.pdf | Pre-print (manoscritto inviato all'editore) | Open Access Visualizza/Apri |