The discovery of unexpected, emerging contaminants and their by-products and metabolites or newly produced pesticides through suspected and non-targeted approaches is gaining more and more attention and open new horizons in many fields such as food safety, ecotoxicology, environment, health… Nevertheless, the process of moving from annotation to identification can be time-consuming, complex and fraught. The prediction of liquid chromatographic retention times (RT) by different approaches can be an useful and operational way to efficiently discriminate and select between several molecular formulas and between several molecular structures. The development of quantitative structure-retention relationship (QSRR) models, which are types of models allowing to establish a link between a chemical structure and a property, here the chromatographic retention time, requires an adequate selection of molecular descriptors necessarily obtained based on a chemical structure known. This requires also a selection of the best machine learning/IA algorithm and its optimization. Here we will present different strategies for the selection of descriptors, different types of machine learning/IA algorithms according to the different situations we are confronted with. These strategies may vary depending on the level of information/annotation we have. We will conclude by proposing a methodology based in part on QSRR to improve and secure the annotation process as it has been published by Schymanski and colleagues in 2014. We published this article in relation with this presentation: https://doi.org/10.1016/j.talanta.2023.125214

EURL-CPS announces that the Proficiency Trial - 2023 dedicated to the enumeration of CPS is completely cancelled.

Last week, EFSA & inter-Biorisks EURLs working group on NGS organised the 2nd “Science Meets Policy” conference on “Using Next Generation Sequencing to tackle foodborne threats” in EFSA (Parma, Italy) & online. We had the chance to chair the session dedicated to "Effort on interoperability and the development of new standards". The outcome shows that: Protocols to get NGS typing data have been dispatched by EURLs, EFSA and ECDC have settled for the European Union the One Health WGS system to collect and compare it for E.coli, Listeria monocytogenes and Salmonella, Other initiatives like GenomeTrkr in also in place in the USA, Efficient Implementations are possible in EU: Denmark, Germany and the Netherlands and also in Norway. The final moderated discussion focused on the "Opportunities and obstacles in sharing genomic data for tackling foodborne threats". You can now access to the presentations: https://www.efsa.europa.eu/en/events/science-meets-policy-conference-using-next-generation-sequencing-tackle-foodborne-threats - the replay of the event will be soon available.  

The video on the assessment of the state of consciousness after waterbath stunning in turkeys can be found on the website page "Stunning" or directly here.

The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) published a work illustrating the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection. The article is available here 

From 26 to 29 June 2023, the eleven European Symposium on Poultry Welfare took place in Prague (Czech Republic). Seven members of the EURCAW-Poultry-SFA participated and two members had an oral communication based on results arising from the Centre’s work. EURCAW-Poultry-SFA members (from the left to the right: A.Contreras, F.Mocz, A.B.Riber, V.Michel, K.E.Wurtz., A.Velarde)   Session 4 – Bone quality, 27.06.23, proceeding p46 Effect of environmental enrichments on leg health and behaviour of fast-growing broiler chick-ens reared at two different stocking densities. Frédérique Mocz, Virginie Michel, Mathilde Janvrot, Jean-Philippe Moysan, Alassane Keita, Anja B. Riber, Maryse Guinebretière Keywords: broiler, enrichment, footpad dermatitis, hock burn, stocking density   F. Mocz Session 8 – Open session, 28.06.23, proceeding p81 Alternative gas mixtures to carbon dioxide in two phases in broiler chickens. Alexandra Contreras-Jodar, Daniel Santiago Rucinque, Troy John Gibson, Virginie Michel, Antonio Velarde Keywords: broiler chickens, gas stunning, slaughter, aversion, welfare   A. Contreras   More information is available on the event website: https://www.espw2023.org/      

On 20 June, the 3 EURCAWs hosted the Common EURCAW meeting for the National Reference Centres (NRCs) & Supporting Bodies (SBs). At the start of the meeting, the EURCAWs presented highlights of their current activities. The next session introduced two relatively new NRCs for Animal Welfare – Spain (established in March 2023) and Slovenia (established in January 2022).  The National Centre Group for Animal Welfare (NCGAW) then led an interactive session. The NCGAW currently comprises six NRCs for Animal Welfare: France (coordinator), Finland, Greece, Italy, Sweden, and Spain. The final session of the meeting considered, ‘Ways to Collaborate’ where the EURCAWs presented priority topics that they would welcome collaboration from the NRCs and SBs. In total 42 participants from 15 Member States participated, including 14 members from the three EURCAWs.   The report is available here.  The slides from this meeting are available here. 

The Slovenian capital Ljubljana was the venue for the annual rabies meeting organised by EURL on June 21-22, 2023. This year’s edition was marked by great joy for the reunion and very constructive exchanges on various rabies topics as well as on future joint work. In addition to the representative of the European Commission, Thierry Chalus, and representatives of the World Organisation for Animal Health (WOAH) (formerly known as “OIE”), the Food and Agriculture Organisation (FAO) and the European Food Safety Authority (EFSA), the EURL team was pleased to welcome Florence Cliquet, WOAH/WHO Rabies expert and  Guillaume Crozet from the Ecole Nationale Vétérinaire d'Alfort. Presentations given during the workshop will be uploaded to the EURL website soon (accessible only to members of the network). Finally, the EURL team would like to sincerely thank all the participants as well as all the people who contributed in one way or another to the organisation of this wonderful event.

The 2023 session of the inter-laboratory test (ILT) for rabies diagnosis has ended. Samples have been dispatched to more than thirty laboratories who registered to take part to this ILT. The objective of this interlaboratory test was to evaluate the rabies diagnosis conclusion of participating laboratories. Techniques used were reference technique used under routine condition. Deadline for submission of the results was June 19, 2023. The EURL Team wishes the best to all participants and remains available in the eventuality of any questions or demands regarding this test.

The EURL for Listeria monocytogenes  (Lm) together with the Italian, the Hungarian NRLs and the Dutch associated NRL have developed a PCR test for the rapid and inexpensive (10€ reagent cost) identification of 30 Lm strains Multi locus sequence typing clonal complexes (CC). It has already been used in Greece, Italy, the Netherlands and Hungary to investigate the origin of human cases of listeriosis.  The project was conducted by a working group of 11 NRLs (BE, CH, CY, DE, IT, NL (RIVM and WFSR), PT, SK, SE, SI) that shaped the method to fit with their needs.  This is a significant step forward compared with the method normally used, multilocus sequencing typing (MLST), which requires three to five days of analysis and costs €150 per strain tested.    Already four training sessions were organised on the method for the NRLs CY, GR, HU, MK, PT, XK. The EURL Lm re-conducts every year the budget to finance their organisation.    Identify the 30 most common strain groups "The test we have developed can identify the 30 Listeria monocytogenes CC, known as clonal complexes, most commonly found in food in Europe" explains Benjamin Félix, project leader of the EURL for Lm. "Our method is very useful for countries that don't have the financial resources to carry out routine sequencing of whole genomes, or when a large number of samples need to be analysed, as it can be used to quickly make an initial selection."  This new method was published in the journal Microbiology Spectrum in May - link. An example of its use: fish-based products responsible for listeriosis in the Netherlands Reference laboratories in several European countries have already been trained in this new method, showing its value in real-life situations. For example, the Dutch food safety authority used the test to determine the source of listeriosis cases that have been reported in the last few years. Two manufacturers of fish-based products were suspected of being behind the contamination. Samples were taken from areas of the plants most at risk of contamination, such as cutting machines, trays and conveyor belts. Thanks to the speed and low cost of the PCR test, it was possible to run 200 analyses in order to select six strains for priority sequencing. This then identified the plant responsible for the contamination.