There is no single analytical method for whole genome sequencing data, which can be used universally to determine salmonella bacteria’s type.
A PhD project at the National Food Institute, Technical University of Denmark has evaluated what methods are best suited for different purposes and developed an online analytical tool for use in determining various bacteria’s type.
Worldwide salmonella is one of the most common foodborne pathogens and in Denmark it is the second leading cause of foodborne disease.
The key to getting good results from ‘real-time’ monitoring and identification of outbreaks is rapid and reliable determination of bacterial type.
Technologies for the so-called typing of bacteria has been made faster and cheaper because of whole genome sequencing, a process that–at a time–maps the complete genetic pool of a bacteria’s DNA code.
Evaluating methods for the typing of salmonella
In a PhD project at the National Food Institute Pimlapas Leekitcharoenphon has evaluated the strengths and weaknesses of different whole genome sequencing methods for use in investigating salmonella outbreaks compared with the traditional method, which is based on typing of individual DNA fragments.
One of the project’s studies examined 18 different salmonella strains from six previous outbreaks to determine which approach is better suited for a particular purpose, such as determining species, sub-species and serovar, and to relate sources to outbreaks.
Online typing tool
The project has shown that the superior method for outbreak detection of salmonella is the analysis of single nucleotides, which are differences in the DNA’s building blocks.
The work has also shown that there are no simple, automated tools that can analyze data about individual nucleotide differences and use it to construct a so-called phylogenetic tree.
A phylogenetic tree is a diagram showing the relationship between various bacteria.
In response, Leekitcharoenphon developed an online analytical tool as part of her thesis, which uses data on bacteria’s whole genome sequencing to produce a quick, standardized and automated analysis that shows the single nucleotide differences.
The tool is one of many developed by the National Food Institute’s Center for Genomic Epidemiology that gives users with limited bioinformatics experience access to bioinformatics tools that produce plain language reports.
Story by Miriam Meister from Technical University of Denmark.