Software application profile: MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data

Abstract

MeltingPlot is an open source web tool for pathogen typing and epidemiological investigations using High Resolution Melting (HRM) data. The tool implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. MeltingPlot also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological studies. HRM technique allows pathogen typing in less than 5 hours with ~5 euros per sample. MeltingPlot is the first tool specifically designed for HRM-based epidemiological studies and it can analyse hundreds of isolates in a few seconds. Thus, the use of MeltingPlot makes HRM-based typing suitable for large surveillance programs as well as for rapid outbreak reconstructions.

Repeatability and reproducibility of thewziHigh Resolution Melting-based clustering analysis forKlebsiella pneumoniaetyping

“…This result shows that strain clustering analysis can only be performed using melting temperatures obtained from the same instrument. Nevertheless, the strains clusters obtained using the MeltingPlot tool (Perini, Batisti Biffignandi, et al, 2020) were perfectly conserved among the three instruments ( Figure 2 and Table 1). These results show that the melting temperature measurement process is not reproducible on different instruments.…”

“…HRM data obtained for each instrument (CFX96, Eco_RT and QS_Flex6) were independently subjected to HRM clustering analysis using the MeltingPlot tool (Perini, Batisti Biffignandi, et al, 2020) (available at https://skynet.unimi.it/index.php/tools/meltingplot/). More in detail, for each strain the tool computes the replicates average melting temperatures (aTms) for each primer set.…”

“…More in detail, for each strain the tool computes the replicates average melting temperatures (aTms) for each primer set. Using the igraph R library (http://igraph.org / ), the tool builds a graph connecting the strains with aTm distance <= 0.5 °C for every primer set, and it clusters the strains on the basis of their betweenness (Perini, Batisti Biffignandi, et al, 2020).…”

“…For each of the three instruments (CFX96, Eco_RT and QS_6Flex), the 14 strains were clustered on the basis of wzi-3 and wzi-4 aTms using the MeltingPlot tool (Perini, Batisti Biffignandi, et al, 2020). The results are reported in Figure 2 and Table 1.…”

“…The strains clusters resulted totally conserved among the instruments. (Perini, Batisti Biffignandi, et al, 2020)…”