RT Journal Article
SR Electronic
T1 Fast <em>Klebsiella pneumoniae</em> typing for outbreak reconstruction: an highly discriminatory HRM protocol on <em>wzi</em> capsular gene developed using EasyPrimer tool
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 679001
DO 10.1101/679001
A1 Matteo Perini
A1 Aurora Piazza
A1 Simona Panelli
A1 Domenico Di Carlo
A1 Marta Corbella
A1 Floriana Gona
A1 Francesca Vailati
A1 Piero Marone
A1 Daniela Maria Cirillo
A1 Claudio Farina
A1 Gian Vincenzo Zuccotti
A1 Francesco Comandatore
YR 2019
UL http://biorxiv.org/content/early/2019/06/28/679001.abstract
AB 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.