Whole genome sequencing (WGS) is being used in the food safety laboratories of more than half of countries surveyed in Europe. By the end of 2016, the technique was present in labs in 17 of 30 countries, according to results of a survey by the European Commission and European Food Safety Authority (EFSA).
The main reason for not having WGS was a lack of expertise and financial resources.
Implementation was also not considered a priority as there are no official requirements to use WGS for official
investigations (i.e. it is not included in European legislation).
Other labs considered that WGS techniques were not harmonized or mature enough to be adopted yet. WGS was mainly used to support outbreak investigations followed by surveillance, and mostly for Listeria monocytogenes, E. coli, and Salmonella analysis.
Countries that did not perform WGS at the time of the survey included Bulgaria, Croatia, Cyprus, Estonia, Greece, Hungary, Latvia, Malta, Portugal, Romania, Slovakia, Spain, and Switzerland.
Answers to the survey of 15 questions were received by December 2016.
Other molecular typing techniques are Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Variable-Number Tandem Repeat Analysis (MLVA). Some labs indicated they do not expect to keep all methods active in routine work when WGS is fully implemented.
WGS was used in all consulted EU Reference laboratories (EURLs), almost half of the National Reference Laboratories (44 percent of 71 respondents) and only a few Official Laboratories (seven percent of 76).
Around half of the NRLs that had not implemented, it was planning to within two to three years.
EURLs support the EU Commission on risk management and assessment in laboratory analysis and receive annual EU funding.
NRLs are nominated by authorities of the EU Member States to ensure compliance with food law.
OLs carry out the analysis of samples taken during official controls and other activities.
Only 12 percent of the EURLs, NRLs, and OLs which performed WGS at the end of 2016 were doing it routinely for all isolates.
Many respondents reported participation in research projects in which WGS was used.
Most of these (ENGAGE, INNUENDO, COMPARE, EFFORT, Liseq, ELITE) get funds from the EC and agencies such as EFSA or ECDC underlining their role to support capacity building at European level.
The sequencing platform mostly used by labs was the MiSeq (Illumina) sequencer (33 respondents), mostly alone, although a few labs use it in combination with other sequencing platforms with higher capacity or using long read technologies.
Storage of the WGS generated data (e.g. raw reads) was done mainly ‘in-house’ (39/43, using private servers) and only a few (seven labs) reported using public repositories.
MLST was commonly used as a type of WGS analysis for all pathogens and purposes. SNP analysis was one of the main methods in surveillance and outbreak investigation in most of the pathogens.
The survey provided an inventory on WGS capacity for analysis of foodborne pathogens (Salmonella spp., E. coli including VTEC, Campylobacter spp., L. monocytogenes, Coagulase Positive Staphylococci including Staphylococcus aureus) and antimicrobial resistant isolates from animals, food, and feed as well as their environmental samples.
The EC created a working group on Next Generation Sequencing (NGS) which has performed a similar questionnaire on WGS capacity to cover recent developments and better address the needs of NRLs networks with results to be made public at a later date.
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