Photo: National Food Institute, Technical University of Denmark

The best way to determine salmonella type using whole genome sequencing

Wednesday 14 Jan 15


Pimlapas Leekitcharoenphon
National Food Institute
+45 35 88 71 83


Frank Møller Aarestrup
Professor, Head of Division
National Food Institute
+45 35 88 62 81
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 single time – maps the complete genetic pool of a bacteria’s DNA code.

Evaluation of 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 e.g. determining species, sub-species and serovar, or to relate sources to outbreaks.

Development of 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 is no simple, automated tools that can analyse data about individual nucleotide differences and use this data to construct a so-called phylogenetic tree. A phylogenetic tree is a diagram showing the relationship between various bacteria.

In response, Pimlapas Leekitcharoenphon – as part of her thesis – developed an online analytical tool. The tool uses data on bacteria’s whole genome sequencing to produce a quick, standardised 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 which gives users with limited bioinformatics experience access to bioinformatics tools that produce plain language reports.

Read more

Download a summary of Pimlapas Leekitcharoenphon’s PhD thesis: Whole Genome Epidemiological Typing of Salmonella (pdf).

A copy of the PhD thesis is available at the National Food Institute. Once the thesis articles have been published the entire thesis will become accessible on Please send an email to if you wish to be notified when this happens.

The free snpTree server is available from the Center for Genomic Epidemiology’s website. The center financed Pimlapas Leekitcharoenphon’s PhD project. On the website are other tools which the center has developed, including an updated version of the snpTree as well as a new but related tool called CSI Phylogeny.