Overview of conducted and planned Proficiency Tests on NGS by EURLs for Biorisks
Contributors
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1.
Istituto Superiore di Sanità
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2.
Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
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3.
National Institute for Public Health and the Environment
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4.
Swedish Veterinary Agency
- 5. Swedish Food Agency - Livsmedelsverket
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6.
Technical University of Denmark
Description
Next generation sequencing (NGS) is a new emerging technique in food microbiology, which currently is becoming increasingly mainstream since it provides fast results for an affordable price. Whole genome sequencing (WGS) of important microbes can easily be carried out and the results contain more background information compared to traditional phenotyping or other molecular techniques such as serotyping, pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST), where only a small part of the genome is analysed. Compared to traditional typing methods, WGS and genotyping offer significant advantages since it is possible to carry out analyses regarding antibiotic resistance, virulence, serotyping, MLST and phylogenetic relationship using one single technique. In addition, WGS data analysed for single nucleotide polymorphisms (SNPs) provide a much higher resolution compared to e.g. pulse-field gel electrophoresis. Therefore, NGS is an excellent tool for surveying antimicrobial resistance, virulence and outbreaks of various important food pathogens.
Files
Biorisks EURLs WG on NGS - Del1_overview-of-pts-20230904-v2.pdf
Files
(723.3 kB)
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