Abstract
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. © 2020, The Author(s).
Original language | English |
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Article number | 1307 |
Journal | Sci. Rep. |
Volume | 10 |
Issue number | 1 |
DOIs | |
Publication status | Published - 2020 |
Keywords
- article
- consensus sequence
- high resolution melting analysis
- Klebsiella pneumoniae
- nonhuman
- polymerase chain reaction
- bacterial genome
- classification
- genetics
- genomics
- Klebsiella infection
- microbiology
- phylogeny
- procedures
- software
- outer membrane protein
- primer DNA
- Bacterial Outer Membrane Proteins
- DNA Primers
- Genome, Bacterial
- Genomics
- Klebsiella Infections
- Phylogeny
- Polymerase Chain Reaction
- Software