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- Source attribution of human Campylobacter infection: a multi-country model in the European UnionPublication . Thystrup, Cecilie; Brinch, Maja Lykke; Henri, Clementine; Mughini-Gras, Lapo; Franz, Eelco; Wieczorek, Kinga; Gutierrez, Montserrat; Prendergast, Deirdre M.; Duffy, Geraldine; Burgess, Catherine M.; Bolton, Declan; Alvarez, Julio; Lopez-Chavarrias, Vicent; Rosendal, Thomas; Clemente, Lurdes; Amaro, Ana; Aldert L. Zomer; Joensen, Katrine Grimstrup; Nielsen, Eva Møller; Scavia, Gaia; Skarżyńska, Magdalena; Pinto, Miguel; Oleastro, Mónica; Cha, Wonhee; Thépault, Amandine; Rivoal, Katell; Denis, Martine; Chemaly, Marianne; Hald, TineIntroduction: Infections caused by Campylobacter spp. represent a severe threat to public health worldwide. National action plans have included source attribution studies as a way to quantify the contribution of specific sources and understand the dynamic of transmission of foodborne pathogens like Salmonella and Campylobacter. Such information is crucial for implementing targeted intervention. The aim of this study was to predict the sources of human campylobacteriosis cases across multiple countries using available whole-genome sequencing (WGS) data and explore the impact of data availability and sample size distribution in a multi-country source attribution model. Methods: We constructed a machine-learning model using k-mer frequency patterns as input data to predict human campylobacteriosis cases per source. We then constructed a multi-country model based on data from all countries. Results using different sampling strategies were compared to assess the impact of unbalanced datasets on the prediction of the cases. Results: The results showed that the variety of sources sampled and the quantity of samples from each source impacted the performance of the model. Most cases were attributed to broilers or cattle for the individual and multi-country models. The proportion of cases that could be attributed with 70% probability to a source decreased when using the down-sampled data set (535 vs. 273 of 2627 cases). The baseline model showed a higher sensitivity compared to the down-sampled model, where samples per source were more evenly distributed. The proportion of cases attributed to non-domestic source was higher but varied depending on the sampling strategy. Both models showed that most cases could be attributed to domestic sources in each country (baseline: 248/273 cases, 91%; down-sampled: 361/535 cases, 67%;). Discussion: The sample sizes per source and the variety of sources included in the model influence the accuracy of the model and consequently the uncertainty of the predicted estimates. The attribution estimates for sources with a high number of samples available tend to be overestimated, whereas the estimates for source with only a few samples tend to be underestimated. Reccomendations for future sampling strategies include to aim for a more balanced sample distribution to improve the overall accuracy and utility of source attribution efforts.
- SOLARIS project: a portable 3D-printed bioaerosol sampler for environmental bacterial collectionPublication . Dobroes Fonseca, Pedro Henrique; Duarte, Filipe Miguel Borgas Henriques; Alves, Frederico Silva de Sousa; Borges, Jose Alberto de Jesus; Cardoso, Susana Isabel Pinheiro; Silverio, Vania Cristina Henriques; Antunes, Wilson David TalhaoBioaerosols, a subset of aerosols released from the biosphere, can carry pathogens, and include particles with diameters from nanometres to a few micrometres. They can remain suspended indoors and travel significant distances. Bioaerosol studies play a vital role in public health, as bioaerosols are an effective route for human and animal pathogen transmission, especially in animal production and handling facilities, which are considered hotspots for the emergence of zoonotic pathogens. The 'One Health' approach, which interconnects human, animal and environmental health, underscores the need for robust biomonitoring and biosurveillance systems. We introduce the SOLARIS project, a novel bioaerosol sampler manufactured through three-dimensional printing with a biocompatible material. Our sampler is compact, portable and uses a liquid collection medium, increasing bioefficiency. Our sampler's laboratory testing demonstrated the successful separation of viable bacteria from artificially generated bioaerosols. Collected samples were found suitable for downstream analysis methods such as culturing, mass spectrometry, molecular detection and electron microscopy. A field trial at a swine facility was performed, in which spores were successfully collected from bioaerosols and identified using microbiological and molecular methods, reinforcing our sampler's utility and emphasizing the significance of incorporating aerosol samples in research studies within the One Health approach.
- From health impact to green choices: The dual impact of fermented foodsPublication . Assunção, Ricardo; Laranjo, MartaFermented foods (FF) have been an essential part of human diets across cultures, cherished for their distinctive flavors and preservation capabilities. Beyond their culinary value, FF have shown significant potential health benefits (1). Studies link fermented foods to antioxidation, lower blood lipid levels, enhanced immunity, tumor inhibition, delayed aging, and prevention of gastrointestinal disorders (2). However, their consumption needs caution regarding potential risks, such as pathogenic contamination or the formation of harmful by-products during fermentation. The safety of fermented foods is currently being systematically revised within the PIMENTO CA20128 under WG3-Health benefits and risks of fermented foods. To navigate these complexities, risk-benefit assessment methodologies provide a robust scientific framework to evaluate the trade-offs, enabling evidence-based dietary recommendations (3). Sustainability is another pivotal aspect of fermented foods. In the face of global challenges like food waste and climate change, fermentation emerges as a key strategy (4). For instance, kimchi and sauerkraut help preserve surplus vegetables, while yogurt and kefir optimize dairy utilization. Nonetheless, the production of certain products, such as fermented meats, underscores the need for strategies to mitigate their environmental impacts while maintaining their benefits. This communication highlights the dual role of fermented foods in promoting health and enhancing sustainability. By bridging tradition and innovation, fermented foods hold the potential to support the transition towards sustainable food systems, paving the way for future diets that address pressing public health and environmental priorities.