Abstract Infections at the animal-human or wildlife-livestock interfaces have severe health and socio-economic consequences. Combined with empirical data, mathematical models can contribute to a better understanding of the reservoirs of these infections, which is a priority for mitigating their impact by using appropriate management interventions. Taking brucellosis in the Bargy massif (French Alps) as an example of a zoonosis at the wildlife-livestock interface, we developed and calibrated a multi-host model integrating data on direct and environment-mediated cross-species contacts from field observations. Estimates of the basic reproduction number ( R 0 ) allowed to identify the population of Alpine ibex ( Capra ibex ) and its environment as an essential host in the reservoir, driving both pathogen maintenance (within-species R 0 ≥1: 1.66, 95% credible interval: 1.42-2.03) and its transmission to livestock (between-species R 0 >0: 0.035, 0.01-0.05). Our approach can be adapted to other multi-host pathogens, which will contribute to improve the understanding and management of these complex systems.

Abstract The Pathogens‐in‐Foods (PIF) database is a database of systematically formatted occurrence data of the most important pathogenic bacteria, parasites and viruses present in foods produced, commercialised or consumed in Europe. Under standardised and harmonised structures, PIF brings together data from published peer‐reviewed articles according to protocolled systematic reviews that are conducted by trained reviewers twice a year. PIF has adhered to the four dimensions (Findability, Accessibility, Interoperability and Reusability) of the FAIR guiding principles for scientific data management; and has currently a series of mechanisms implemented to assure data quality and integrity. Currently, PIF comprises circa 20,000 records, duly organised in four catalogues. As a freely available tool, the PIF team aims to evaluate strategies and opportunities to further promote the use of the database. Thus, a feasibility study has been conducted to evaluate the viability of PIF in terms of adoptability, as well as technical and ethical/legal aspects, through the identification of areas for enhancement and the recommendation of improvements to ensure its sustainability and use. The multidimensional assessment was carried out by the PIF team by a critical appraisal of the current weaknesses and challenges, and by the analysis of evaluation surveys from target users. As a result of the feasibility study, the strategic roadmap for the PIF database is centred beyond the update of the current five catalogues, and extends over the AI‐based data analytics and interpretation, the creation of an antimicrobial resistance (AMR) catalogue, and the assessment of Large Language Model (LLM) algorithms to support systematic review automation and/or data verification.

Wildlife and domestic populations frequently share diseases with a potential for cross-species transmission, posing significant threats to animal and human health, economy and biodiversity conservation. While quantifying disease transmission in natural populations is critical to understand the dynamics of infectious diseases, transmission processes remain difficult to assess as they are difficult to observe directly. Brucellosis, caused by Brucella melitensis and Brucella abortus, is one of the most important worldwide zoonotic diseases and affects both domestic and wild ruminants. Here, we investigated the transmission of B. melitensis in an Alpine ibex (Capra ibex) population, the first known wild-living reservoir for this pathogen. We aimed to quantify disease transmission within the population by disentangling the contributions of four alternative transmission routes: abortion products, infectious parturition products, venereal transmission and vertical transmission. We modelled host-disease dynamics developing a spatially explicit, sex- and age-structured individual-based model that reproduces host demography and pathogen transmission by contacts among susceptible and infectious individuals. By fitting our model on 13 years of host-population and disease monitoring, we estimated the relative importance of the four transmission routes. We quantified the proportion of transmissions attributed to each route and estimated the effective reproduction number (Reff), distinguishing age- and sex-specific contribution. We identified abortion products as the primary driver of Brucella transmission, accounting for 57%-85% of all transmissions. All other routes were of secondary importance, although the contribution of venereal transmission remained uncertain (from 4% to 25%). Females played a central role in disease maintenance, with an effective reproduction number well above one (2.1), while males' contribution was quantitatively negligible with a value below one (0.4). Our results provide key insights to implement targeted management operations. Since most transmissions occur through abortion products, targeting recently infected females could reduce the effective reproduction number below one, promoting pathogen extinction. Furthermore, because abortions are expected to peak in late spring, control measures aiming to limit transmission from ibex to other species, including livestock, should be prioritized during this high-risk period.Read the free for this article on the Journal blog.

Phytoplankton serve as a source of nutrients for bacteria in the marine environment. The interactions between algae and bacteria are known to include mutualism, commensalism, competition, or antagonism. This occurs in the microenvironment surrounding phytoplankton cells, the phycosphere, an interface rich in nutrients and organic molecules exuded by the cells. Here, based on in situ observations and on an in vitro interaction study, we report on a novel form of starvation-induced hunting that the cells of selected Vibrio species exert on dinoflagellates. The results showed that Vibrio atlanticus was capable of attacking and killing the dinoflagellate Alexandrium pacificum ACT03. Briefly, the observed mechanism of algal-killing consists of first, the ‘immobilization stage’ involving the secretion of algicidal metabolites that disrupt the flagella of the algae. In the ‘attack stage’, Vibrios simultaneously surround algal cells at high density for a brief period without invading them. Finally, the ‘killing stage’ in which the lysis and consumption of the dinoflagellates occur. By using a combination of biochemical, proteomic, molecular, and fluorescence microscopy approaches, we showed that this relationship is not related to the decomposition of algal organic matter, Vibrio quorum-sensing pathways, toxicity of the algae, or pathogenicity of the bacterium but is conditioned by nutrient stress, iron availability, and linked to the iron-vibrioferrin transport system of V. atlanticus. This is the first evidence of a new mechanism that could be involved in regulating Alexandrium spp. blooms and giving Vibrio a competitive advantage in obtaining nutrients from the environment. The interaction model we propose here suggests that Vibrio could play a role in regulating the proliferation of Alexandrium spp., giving it a competitive advantage in obtaining nutrients from the environment.

Abstract The Pathogens‐in‐Foods (PIF) database is an open‐access European repository that centralises and harmonises data on the occurrence of biological hazards in foods produced, commercialised, or consumed in Europe. The core features of PIF are: (1) the prevalence and enumeration data are extracted from peer‐reviewed scientific literature; (2) trained screeners update the database twice a year through trackable systematic literature reviews; (3) the sampling scope covers primary production, processing plants, retail, restauration and catering services; and (4) the database is built strictly on FAIR (Findable, Accessible, Interoperable, and Reusable) to support global scientific collaboration. Given that the PIF database is at a development stage that has allowed it to reach the key attributes of comprehensiveness, reliability, stability and security; the team has identified different mechanisms to boost use engagement and maximise the platform's impact in the risk assessment community. One of the mechanisms for the uptake of PIF in the risk assessment work is the inclusion of the database in training material sets. Such training materials can be used by EFSA focal points, EFSA courses such as EU‐FORA, national food safety agencies and other stakeholders to support relevant dissemination and/or training activities. Thus, the objective of this publication is to showcase, in a detailed manner, the training materials developed during the implementation of the project GP/EFSA/BIOHAW/202/01, which span from the presentation of the concept and nature of PIF, to practical exercises requiring the access to PIF data to solve microbiology safety questions.

The collection of occurrence data of foodborne pathogens in foods faces the hindrances of dispersion of information, lack of standardisation and harmonisation, and ultimately, high expenditure in time and resources. The Pathogens-in-Foods (PIF) database was conceived as a solution to centralise published data on prevalence and concentration of pathogenic bacteria, viruses and parasites occurring in foods, obtained through systematic review (SR), and categorised in harmonised data structures under controlled terminologies. The present article outlines how PIF was constructed to adhere to the FAIR (findability, accessibility, interoperability and reusability) principles for scientific data management; and proceeds with a description of the PIF concept, which entails two phases: the SR process and the population of PIF. The protocolled SR process is supported by a welldefined search strategy, inclusion criteria, and rules for internal validation assessment; whereas the population of PIF with new data relies in data extraction, validation and release. The article then introduces a novel data quality approach, named as the CCC approach (data consistency, conformity and completeness), which ensures proper interpretation of data, richness of data, and flawless transcription of data. After a brief explanation of the three PIF components - database, back-end and front-end - the article proceeds with the exposition of the data model, as well as the capabilities of the front-end, including data search, insertion and curation. The future of PIF lies in expanding its capabilities, addressing emerging challenges, and leveraging technological advancements to maintain its relevance and utility in the evolving landscape of food safety.

Identification of Endocrine-Disrupting Chemicals (EDCs) in a regulatory context requires a high level of evidence. However, lines of evidence (e.g. human, in vivo, in vitro or in silico) are heterogeneous and incomplete for quantifying evidence of the adverse effects and mechanisms involved. To date, for the regulatory appraisal of metabolism-disrupting chemicals (MDCs), no harmonised guidance to assess the weight of evidence has been developed at the EU or international level. To explore how to develop this, we applied a formal Expert Knowledge Elicitation (EKE) approach within the European GOLIATH project. EKE captures expert judgment in a quantitative manner and provides an estimate of uncertainty of the final opinion. As a proof of principle, we selected one suspected MDC -triphenyl phosphate (TPP) - based on its related adverse endpoints (obesity/adipogenicity) relevant to metabolic disruption and a putative Molecular Initiating Event (MIE): activation of peroxisome proliferator activated receptor gamma (PPARγ). We conducted a systematic literature review and assessed the quality of the lines of evidence with two independent groups of experts within GOLIATH, with the objective of categorising the metabolic disruption properties of TPP, by applying an EKE approach. Having followed the entire process separately, both groups arrived at the same conclusion, designating TPP as a “suspected MDC” with an overall quantitative agreement exceeding 85%, indicating robust reproducibility. The EKE method provides to be an important way to bring together scientists with diverse expertise and is recommended for future work in this area.

Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.

Brucellosis due to Brucella melitensis affects domestic and wild ruminants, as well as other mammals, including humans. Despite France being officially free of bovine brucellosis since 2005, two human cases of Brucella melitensis infection in the French Alps in 2012 led to the discovery of one infected cattle herd and of one infected population of wild Alpine ibex (Capra ibex). In this review, we present the results of 10 years of research on the epidemiology of brucellosis in this population of Alpine ibex. We also discuss the insights brought by research and expert assessments on the efficacy of disease management strategies used to mitigate brucellosis in the French Alps.

Shellfish are a source of nutrients but are also a matter of concern in terms of food safety due to natural contaminants such as phycotoxins or anthropogenic contaminants including microbial agents and heavy metals. However, data related to consumption for each mollusk species are scarce and missing for appropriate exposure calculation. The objective of the study was to generate shellfish consumption data in the adult coastal population in France to assess exposure to health risks, the effects of determinants on the frequency of consumption and usual intake, and shellfish food risk perception. Our study, named the CONSOMER study, was carried out using an online survey in 2016 and 2017 and included a food frequency questionnaire. After validation, 2,479 individual questionnaires were available for statistical analysis. Our findings provide estimates of shellfish consumption frequency, portion sizes, weekly intake in g/week, and g/week/body weight that can be used for acute and chronic exposure calculations. For the acute risk, the 97.5th percentile of the portion size was found to be around 290 g for the adult coastal population. For chronic exposure, recreational shellfish harvesting activities were associated with higher weekly intakes. A non-negligible part of this subpopulation is not aware of food safety recommendations concerning harvesting areas. Results for shellfish harvester consumption in particular are consistent with other available data. Exposure calculations and safety recommendations should target shellfish harvesters.

Consumption of seafood contaminated by phycotoxins produced by harmful algae is a major issue in human public health. Harmful algal blooms are driven by a multitude of environmental variables; therefore predicting human dietary exposure to phycotoxins based on these variables is a promising approach in health risk management. In this study, we attempted to predict the human health risks associated with Vulcanodinium rugosum and its neurotoxins, pinnatoxins (PnTXs), which have been regularly found in Mediterranean lagoons since their identification in 2011. Based on environmental variables collected over 1 year in four Mediterranean lagoons, we developed linear mixed models to predict the presence of V. rugosum and PnTX G contamination of mussels. We found that the occurrence of V. rugosum was significantly associated with seawater temperature. PnTX G contamination of mussels was highest in summer but persisted throughout the year. This contamination was significantly associated with seawater temperature and the presence of V. rugosum with a time lag, but not with dissolved PnTX G in seawater. By using the contamination model predictions and their potential variability/uncertainty, we calculated the human acute dietary exposures throughout the year and predicted that 25% of people who consume mussels could exceed the provisional acute benchmark value during the warmest periods. We suggest specific recommendations to monitor V. rugosum and PnTX G.

Risk Assessment Strategies for Contaminants in Seafood (RASCS) is an EFSA Partnering Grant focusing on KEamong seven European Institutions. The project lasted from June 2021 to June 2023. The proposal was built to establish links among seven major research and regulatory institutions in the EU dealing with seafood safety: IPMA (Portugal), Istituto Superiore di Sanità (Italy), Ghent University (Belgium), BfR (Germany), ANSES (France), CREDA and IRTA (Spain). The purpose was to increase KEto foster harmonization and improve strategies for RA of contaminants in seafood products and the related risk communication to the population. RASCS included 6 work-packages (WPs) focused on Hazard Identification, Dietary Exposure Assessment, RA: present and future strategies in a changing world and balance with nutritional benefits, Risk/Benefit Perception and Communication, Dissemination and outreach, and Management of the project. The project started during the COVID pandemic, and interaction during the first year was exclusively online. Although this circumstance partially limited interactions, the execution of the project was not significantly impacted. Exchange among partners was ensured through monthly meetings and additional exchanges by mail or web meetings, while during the second year also physical meetings were organised: the first meeting in Paris in June 2022, was followed by an additional interim meeting focused on specific webinars in Barcelona in November 2022. Four sessions of ToS were held in 2023 in Rome, Lisbon, Barcelona and Paris, and a final meeting in Parma at EFSA's premises in June 2023. The RASCS Partnering Grant has allowed to reach three main goals: i) Significantly improve the participant's knowledge within the subject of RA of contaminants in seafood, ii) Increase awareness on EFSA's goals and tools regarding RA, and iii) Strengthen links and network among multidisciplinary institutions and experts also for future consortia.

La brucellose à Brucella melitensis touche les ruminants domestiques et sauvages, ainsi que d’autres mammifères, dont les humains. Bien que la France soit officiellement indemne depuis 2005, deux cas humains reportés en Haute-Savoie en 2012 ont conduit à la découverte de l’infection dans un élevage bovin et chez les bouquetins des Alpes (Capra ibex) du massif du Bargy. Nous présentons dans cette synthèse les principales découvertes de ces dix dernières années sur le système brucellose-bouquetins. Nous discuterons également de l’apport de la recherche et de l’expertise sur l’évaluation de l’efficacité des mesures de gestion sanitaire mises en place dans le massif du Bargy pour lutter contre la brucellose.

Pathogens-in-Foods (PIF) is a dynamic database constructed using systematic literature searches of occurrence data (prevalence and enumeration) of important pathogenic agents (Bacillus cereus, Campylobacter spp., Clostridium perfringens, Listeria monocytogenes, Salmonella spp., Shiga toxin-producing Escherichia coli, Staphylococcus aureus, Yersinia enterocolitica, Cryptosporidium spp., Giardia spp., Toxoplasma gondii, Hepatitis A virus, Hepatitis E virus and Norovirus) in foods randomly surveyed across Europe. After filtering the primary studies, these were screened for relevance and methodological quality, and the data were extracted into the PIF database following a systematic categorisation of microbiological methods, food types and outcomes. The database is freely accessible through a web application that facilitates data retrieval according to several relevant variables. The PIF spans data published from 2000 onwards and is intended for use by researchers and food authorities after meta-analysis, in microbiological risk assessment.