ArticleScientific reports2020
EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Cultivation and sequencing-free protocol foriScience · 2024Article
- Rapid Identification of Pseudomonas aeruginosa International High-Risk Clones Based on High-Resolution Melting Analysis.Microbiology spectrum · 2023Article
- A Novel High Discriminatory Protocol for the Detection ofPathogens (Basel, Switzerland) · 2022Article
- Hypervariable-Locus Melting Typing: a Novel Approach for More Effective High-Resolution Melting-Based Typing, Suitable for Large Microbiological Surveillance Programs.Microbiology spectrum · 2022Article
- Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.Genes & genomics · 2022Article
- Whole-Genome Sequencing Investigation of a Large Nosocomial Outbreak Caused by ST131 H30Rx KPC-ProducingAntibiotics (Basel, Switzerland) · 2021Article
- MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data.BMC bioinformatics · 2021Article
- Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing.AMB Express · 2020Article
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Authors and funding
12 authors.
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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.
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