A report from the European Centre for Disease Prevention and Control (ECDC) presents the results of a proficiency test to evaluate the inter-laboratory reproducibility and portability of Listeria monocytogenes genome assemblies in the EU and EEA.
The aim of the proficiency test was to support national public health reference laboratories performing whole genome sequencing (WGS)-based typing in generating good quality and comparable genome assemblies for L. monocytogenes. All national public health reference laboratories with WGS typing capabilities in the EU/EEA were invited to take part in the exercise.
There were 14 participants, who submitted assembled genomes for 15 sets of raw sequence reads. Assemblies can be used for many analyses and good quality assemblies are necessary to produce data that are comparable between laboratories.
ECDC supports the integration of WGS data into surveillance and multi-country outbreak investigations of foodborne diseases including listeriosis as one of the priority diseases.
Countries can perform the typing at national level or submit assemblies to the European Surveillance System (TESSy). For European surveillance of listeriosis, ECDC will only accept data from laboratories assemblies that have been generated by a concordant pipeline as verified according to the methodology described in this report.
Source: ECDC, 16 May 2019