The advantages and disadvantages of the various NGS methods are analysed in the context of the microbiological methods cited in current European Union legislation.
The German Federal Institute for Risk Assessment (BfR), in coordination with the Friedrich Loeffler Institute (FLI), has evaluated the application of the NGS methods concerning food safety and animal health based on the EFSA opinion. This evaluation investigates topics such as the challenges for data exchange and for the harmonisation of new methods among various laboratories. Therefore, staff working in institutions, laboratories and regulatory authorities, who are involved in the typing and characterisation of pathogens in food and animals, are the target audience.
NGS stands for the second and third generation of genetic sequencing, and offers the highest resolution yet available for determining the nucleotide sequence of a DNA molecule or genome.
For pathogens readily available as pure cultures, whole-genome sequencing (WGS) has established itself worldwide as an NGS method. In this process, the genetic material of the causative agent is isolated from the sick individual and compared with isolates of the same pathogen from food or animals. This enables the detection of relationships in the genetic material, allowing cases to be traced back to specific disease outbreaks at various locations. Another NGS method, known as whole-metagenome or shotgun metagenomic sequencing, involves harvesting the genetic material directly from a food or animal sample (for example), which may often contain an array of microbes. This enables the detection of non-culturable or difficult-to-culture microorganisms such as parasites or viruses. Metagenomic sequencing is suitable for use as an initial diagnostic method in cases where a specific pathogen is not yet suspected. Metagenomic sequencing also enables the discovery of new, previously unknown pathogens--such as Schmallenberg virus in 2011.
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