Next Generation Sequencing (NGS of Next Generation Sequencing or WGS of Whole Genome Sequencing) means the determination of the complete genome of an organism. This means that the complete structure of DNA is known - with a precision that cannot be achieved by other methods.
In this way, for example, not only the differences between bacterial species can be precisely determined, but also differences within a bacterial species. These subtle differences in the genetic makeup of a bacterium are particularly important when the bacterium is a pathogen that is spread through food: Ideally, these differences can be used to precisely identify relationships between diseases and food.
Faster, more and more accurate
When food-borne outbreaks are diagnosed, bacterial strains from diseased persons, food or the environment are ideally compared. This comparison is currently carried out using pulse field gel electrophoresis (PFGE): This compares certain parts of the genome (a band pattern similar to a bar code is formed). However, this method is time-consuming. Moreover, not all bacterial strains can be distinguished accurately enough and comparability between different laboratories is difficult.
In comparison, modern NGS instruments can analyse 30 to 90 samples within 48 hours, depending on the size of the genome of the respective bacterial species. Per run, 15 billion bases (the individual DNA building blocks) are determined. The analysis data obtained can be stored centrally so that laboratories from different countries can access it and compare results. In this way, outbreaks can be detected more quickly.
Of course, the prerequisite for this is that the data are comparable. For example, AGES has developed a sequencing scheme for listeria (Listeria monocytogenes). The genomes of Listeria monocytogenes were compared gene by gene. 1,701 genes were identified that are present in all isolates. This "heart" of the Listeria genome forms the basis for exact comparisons between pathogen isolates: isolates that differ in less than 10 genes belong to the same outbreak strain. In this way, it can be determined which food samples correspond to patient samples.
The scientific paper "Defining and Evaluating a Core Genome MLST Scheme for Whole Genome Sequence-Based Typing of Listeria monocytogenes" was published in the Journal of Clinical Microbiology.
Article in the scientific magazine APA Science "CSI Quargel": On the trail of Listeria with genome sequencing.
As a binational consulting laboratory for listeria, AGES was also involved in the clarification of a listeria outbreak in Germany. Using Next Generation Sequencing, it was shown that no cases of disease in other countries were associated with the outbreak in Germany.
Eurosurveillance, Volume 20, Issue 50, 17 December 2015: Ongoing outbreak of invasive listeriosis, Germany, 2012 to 2015