D3.7 First periodic report on ongoing JRPs WP3 Joint Research Projects Responsible Partner: Sciensano Contributing partners: / 1 GENERAL INFORMATION European Joint Programme Promoting One Health in Europe through joint actions on foodborne full title zoonoses, antimicrobial resistance and emerging microbiological hazards European Joint Programme One Health EJP acronym Funding This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No 773830. Grant Agreement Grant agreement n° 773830 Starting Date 01/01/2018 Duration 60 Months DOCUMENT MANAGEMENT Deliverable D3.7 First periodic report on ongoing JRPs WP and Task WP3; Task 3.2 Leader Sciensano Other contributors ANSES, SVA, WBVR, INSA Due month of the deliverable M13 Actual submission month M14 Type R R: Document, report DEC: Websites, patent fillings, videos, etc. OTHER Dissemination level PU PU: Public CO: confidential, only for members of the consortium (including the Commission Services) First periodic report on ongoing JRP Introduction Joint Research Projects serve as an instrument that help OneHealth EJP partners to work together in developing new detection methods, improved diagnostic tests, fast and accurate typing methods, in gaining new insight in the spread of pathogens and their resistance traits etc. At the same time, through setting up these scientific collaborations, researchers spread over Europe identify new possible partners and strengthen links between known colleagues. As such, the JRP help in creating and consolidating a firm network of organizations that have reference tasks in their scope and that deal with foodborne zoonoses, antimicrobial resistance and emerging threats. Summary of the performance of the Joint Research Projects Project deliverables and milestones The 11 joint research projects planned to submit a total of 77 deliverables. While most deliverables have been finalized at the end of 2018 (50 deliverables or 65%, see Table), only 32% of the deliverables have been uploaded to the private area of the OHEJP website. Probably, the project leaders are not yet familiar with using the private space. The WP3 team will further support them to ensure that the deliverables will be uploaded in due time. About one-fifth of the expected deliverables have been postponed to the second year. The delays were mainly due to recruitment and leave of staff, delays in the availability of samples or equipment or to minor reorganization of the activities in agreement with the project consortium partners. These delays are unlikely to have a major impact on most projects. MoMIR-PPC however, faced the loss of expertise (Norwegian public health institute FHI), difficulties with co-funding (Bulgarian SAIM) and the reorganization in DTU (that saw DTU-Vet move to the Copenhagen university who is not a partner of the OneHealth EJP). These setbacks induced considerable delays in performing several tasks, resulting in modification of the work plan. Similarly, changes in the management of Tox-Detect, both at the level of the project leader and of a key task leader, made that strategic and operational responsibilities had to be re-allocated. Consequent loss of commitment of one partner needs to be corrected and appropriate actions have been proposed in January 2019. About thirteen percent of the project deliverables will not result in a written document and should therefore be considered as milestones (NR category in table). To avoid this for the second call, the difference between milestones and deliverables will be better documented. Finalized and Finalized but not Delayed to NR Deliverables Total submitted on yet submitted on 2019 (no report) OHEJP website OHEJP website Number of 77 25 25 17 10 Deliverables Percentage 100 32 32 22 13 Of the 50 project deliverables reported as finalized (submitted or not) at the end of 2018, 6 were submitted late (estimated delay of 1 to 6 months) and having no major impact on the final outcome of the projects. 3 Finalized and Finalized but not Delayed to NR Deliverables Total submitted on yet submitted on 2019 (no report) OHEJP website OHEJP website IMPART 9 3 0 2 4 ARDIG* 4 4 0 0 0 RaDAR 4 1 3 1 0 MAD-Vir 5 3 0 1 1 Tox-Detect* 3 0 2 1 0 NOVA* 10 10 0 0 0 LISTADAPT 10 0 7 3 0 METASTAVA 8 2 1 3 2 AIR Sample 2 2 0 0 0 MoMIR-PPC 11 0 5 4 2 MedVetKlebs 11 0 8 3 0 Total 77 20 31 18 9 Finally, the 11 joint research projects planned to achieve a total of 77 milestones. Seventy-three percent of the milestones were finalized while 27% have been delayed, again due to recruitment and departure of staff, delays in the delivery of samples / equipment or as agreed by project consortium partners. 4 Publications Published Project DOI ISSN ISBN Title Garrido-Estepa, M., Latasa, P., Ordóñez-León, G.Y. et al. Non-Typhi, non-Paratyphi Salmonella-related 10.1007/s10096-018- NOVA 1435-4373 hospitalisations in Spain: trends, clinical aspects, risk factors for worse prognosis and hospital costs. Eur J 3433-1 Clin Microbiol Infect Dis (2018). 10.2807/1560- Møller Frederik T, Mølbak Kåre, Ethelberg Steen. Analysis of consumer food purchase data used for outbreak NOVA 7917.ES.2018.23.24.17 investigations, a review. Euro Surveill. 2018;23(24):pii=1700503 00503 Félix B, Feurer C, Maillet A, Guillier L, Boscher E, Kerouanton A, Denis M, Roussel S. Population Genetic 10.3389/fmicb.2018.0 LISTADAPT Structure of Listeria monocytogenes Strains Isolated From the Pig and Pork Production Chain in France. 0684 Front. Microbiol., 06 April 2018 Moreno MA., Florez-Cuadrado D., Ugarte-Ruiz M. and Dominguez L Veterinarios y antibióticos: destinados a MoMIR-PPC 2253-7244. 2018. entenderse. Profesión Veterinaria. Asis, 2018 10.1016/bs.afnr.2018. 9780128139776. Florez-Cuadrado D., Moreno MA., Ugarte-Ruiz M. and Dominguez L Antimicrobial Resistance in the Food MoMIR-PPC 04.004 2018 Chain in the European Union. Advances in Food and Nutrition Research. Elsevier, 2018. Menanteau P, Kempf F, Trotereau J, Virlogeux-Payant I, Guitton E, Dalifard J, Gabriel I, Rychlik I, and Velge P. 10.1111/1462- MoMIR-PPC (2018) Role of systemic infection, cross contaminations and super-shedders in Salmonella carrier state in 2920.14294 chicken. Environmental Microbiology. Rodrigues C, Passet V, Rakotondrasoa A, Brisse S (2018). Identification of Klebsiella pneumoniae, Klebsiella 10.3389/fmicb.2018.0 MedVetKlebs quasipneumoniae, Klebsiella variicola and related phylogroups by MALDI-TOF Mass Spectrometry. Front. 3000 Microbiol. 9:3000 In preparation or submitted Project DOI ISSN ISBN Title Petersen A, Rosenstierne MW, Rasmussen M, Fuursted K, Nielsen HV, Andersen LOB, Bødker R, Fomsgaard A. Field samplings of (Ixodus ricinus ticks from a tick-borne encephalitis virus (TBEV) MAD-Vir micro-focus in Northern Zealand, Denmark demonstrate an apparent disappearance of TBEV but a plenitude of other virus and bacteria. Submitted to Tick and Tick borne diseases 2018 (not yet published) Giuliano Garofolo, Gro S. Johannessen, Ivana, Renata, Kinga, Jasek, Julia, Mona Torp, Jeffrey AIR-Sample Hoorfar. Campylobacter in chicken houses – critical parameters for international, multicentre evaluation of sampling and detection methods. For submission to Food Control. (in preparation) 5 Integrative activities and impact of the research projects Even if the principal objective of a research project is the delivery of high quality scientific outcome, most if not all JRP also comprise integrative activities, i.e. capacity building (including building expertise with ring trials and developing tools that are useful for risk analysis), experimental facilities, detection and typing methods, strains and biobanks collections, reference materials, digital infrastructures and databases, surveillance strategies and legal or policy aspects. An overview of such integrative activities per JRP is shown below. Capacity building, Detection, Strain Digital Legal, training + Experimental typing collection, Surveillance infrastructure, Policy ring trial facilities methods, ref strategies DB aspects + tools PRO material for RA IMPART X X X X X ARDIG X X X X RaDAR X X TOX-Detect X X MAD-VIR X X X NOVA X X X ListAdapt X X X Metastava X X AIR Sample X X X X MoMIR-PPC X X MedVetKlebs X X X In all 11 JRP, training activities or the organization of ring trials are done. On the contrary, no specific experimental facilities (biosafety 2, 3 or 4 capacities for instance) were identified. Detection and typing methods and the drafting of protocols are also well appreciated activities that can be shared and thus make partners collaborating. These are developed in the domains of antimicrobial resistance, for the detection and typing of various foodborne zoonoses, as well as for the detection of a broad range of viruses and of toxins produced by foodborne bacteria. Often, the creation of new or improved harmonized protocols, ring trials, etc. are based on a collection of well-defined strains or biobank samples and reference materials; these are often set up in the various JRP. Also activities that may lead to improved surveillance strategies or better protocols for policy (risk assessment and risk management tools) are being developed. Examples are the specific surveillance of colistine resistance in Enterobacteriaceae and of resistance in Clostridium difficile (IMPART), the improved detection of Campylobacter in poultry houses (AIR-Sample) and the efficient detection of K. pneumonia in samples from various origins (MedVetKlebs). Finally, two JRP set up databases for modelling of AMR transmission on farm and through the food chain (RaDAR) and for the exploitation of existing food purchase data in outbreak investigation and for syndromic surveillance (NOVA). Interactions with other JRP/JIPs, European and national projects Most of the Joint Research Projects (JRPs) collaborate with other European projects and some also have collaborations at national level (see figure blow). In order to identify possible synergies and avoid overlap with major European projects, OHEJP WP4 Team (Joint Integrative Projects) organized two cogwheel workshops in 2018: one with COMPARE and one with EFFORT.