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Comparison of food extraction techniques and impact of nitrogen fertilization on the potential allergenicity of soybean related to birch pollen-food allergy syndrome.
No full textBACKGROUND: Birch pollen-food allergy syndrome is triggered by cross-reactive allergens in plant-based foods. Environmental factors such as nitrogen fertilization may influence food allergenicity, but this has not been studied before.
METHODS: We compared and optimized protein extraction protocols for birch-homologue foods, including apple, carrot, and soybean. Various extraction buffers and mixing methods were tested for consistency and protein yield. We applied this to a pilot study assessing potential changes in the allergenic potential of plant-based foods due to altered nitrogen availability. A greenhouse experiment was conducted in which soybean plants were subjected to different nitrogen fertilization treatments. Allergenicity was evaluated using basophil activation testing in five individuals with birch pollen-food allergy syndrome.
RESULTS: No major differences were observed between the tested extraction protocols, and key allergens were detectable in all food sources. In the pilot experiment, fertilized soybeans showed visible changes in size, a smaller shape, a different protein profile, and lower basophil reactivity compared to unfertilized soybeans.
CONCLUSION: Our findings support the feasibility of standardized extraction methods. Varying nitrogen fertilization in soybeans resulted in altered physical, proteomic, and allergenic characteristics in this pilot study. Our results highlight the need for further research on environmental influences on food allergy.</p
Historische gegevens voor surveillance van de mortaliteit door alle oorzaken in België, Vlaanderen, Wallonië en Brussel
No full textEnquête nationale de consommation alimentaire 2022-2023 - Rapport sur la sécurité alimentaire
No full textL’Enquête de consommation alimentaire (ECA) 2022-2023 a examiné non seulement ce que mangent les personnes vivant en Belgique, mais aussi quelles sont leurs pratiques vis-à-vis de différents aspects de sécurité alimentaire. Le présent module, dédié à la sécurité alimentaire, a recueilli des informations sur certaines pratiques quotidiennes, notamment l’hygiène des mains, la cuisson de certains aliments, le stockage des aliments et la connaissance de la signification des dates d’expiration. Les adultes âgés de 18 ans et plus, de même que les parents (ou tuteurs) des enfants âgés de 3 à 9 ans participant à l’enquête, ont répondu à ces questions. Ce module permet de cartographier les habitudes actuelles et de comparer certaines d’entre elles avec celles observées lors de l’enquête précédente menée en 2014-2015.
Davantage de résultats sont disponibles sur notre site web.</p
Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.
No full textINTRODUCTION: Antimicrobial resistance is an alarming public health problem, and comprehensive surveillance across environments is required to reduce its impact. Phenotypic testing and whole-genome sequencing of isolates are efficient, but culture-free approaches like metagenomic sequencing potentially allow for broader investigation of resistance gene occurrence, evolution and spread. However, technical challenges such as difficulties in associating antimicrobial resistance genes with their bacterial hosts and the collapse of strain-level variation during metagenome assembly, hinder its implementation.
METHODS: To illustrate how these challenges can be overcome, we applied Oxford Nanopore Technologies long-read metagenomic sequencing and novel bioinformatic methods to a case study focused on fluoroquinolone resistance in chicken fecal samples.
RESULTS: We demonstrate plasmid-host linking based on detecting common DNA methylation signatures. Additionally, we use new bioinformatic approaches for strain haplotyping, enabling phylogenomic comparison and uncovering fluoroquinolone resistance determining point mutations in metagenomic datasets.
DISCUSSION: We leverage long-read sequencing, including DNA methylation profiling and strain-level haplotyping, to identify antimicrobial resistance gene hosts, link plasmids to their bacterial carriers, and detect resistance-associated point mutations. Although some limitations remain, our work demonstrates how these improvements in metagenomic sequencing can enhance antimicrobial resistance surveillance.</p
BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows.
No full textBACKGROUND: The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) networks ‘Seq4AMR’ and ‘B2B2B AMR Dx’ were established to promote collaboration between microbial whole genome sequencing (WGS) and antimicrobial resistance (AMR) stakeholders. A key topic discussed was the frequent variability in results obtained between different microbial WGS-related AMR gene prediction workflows. Further, comparative benchmarking studies are difficult to perform due to differences in AMR gene prediction accuracy and a lack of agreement in the naming of AMR genes (semantic conformity) for the results obtained. To illustrate this problem, and as a capacity-building exercise to encourage stakeholder involvement, a comparative Galaxy-based BenchAMRking platform was developed and validated using datasets from bacterial species with PCR-verified AMR gene presence or absence information from abritAMR.
RESULTS: The Galaxy-based BenchAMRking platform ( https://erasmusmc-bioinformatics.github.io/benchAMRking/ ) specifically focusses on the steps involved in identifying AMR genes from raw reads and sequence assemblies. The platform currently comprises four well-characterised and published workflows that have previously been used to identify AMR genes using WGS data from several different bacterial species. These four workflows, which include the ISO certified abritAMR workflow, make use of different computational tools (or tool versions), and interrogate different AMR gene sequence databases. By utilising their own data, users can investigate potential AMR gene-calling problems associated with their own in silico workflows/protocols, with a potential use case outlined in this publication.
CONCLUSIONS: BenchAMRking is a Galaxy-based comparison platform where users can access, visualise, and explore some of the major discrepancies associated with AMR gene prediction from microbial WGS data.</p
EU-HIP – Country visit report – Iceland
No full textThis report has been developed within the remit of the project EU interoperability with HERA’s IT Platform (EU-HIP). EU-HIP is a consortium of 15 European countries, coordinated by Statens Serum Institute (SSI), Denmark. The scope of the project is to support countries to enhance and improve national IT systems in an efficient and coordinated manner, to obtain interoperability with the centralised IT platform of the EU Health Emergency Preparedness and Response Authority (HERA).
HERA’s IT platform (ATHINA) is currently under development and seeks to gather intelligence on public health surveillance and medical countermeasures (MCM) to support threat assessment and crisis management across Europe. The priority areas are pathogens with high pandemic potential (PHPP), antimicrobial resistance (AMR), and chemical, biological, radiological and nuclear (CBRN) threats, as well as appropriate MCM, such as medicinal products, medical devices and personal protective equipment (PPE).
A baseline activity of the EU-HIP project was to perform a landscape assessment of countries’ IT systems, in relation to the above-mentioned priorities, across all countries involved in the consortium. In addition, in-depth country visits were performed in a selected number of countries to gain detailed insights into the countries’ IT systems for health threat detection and assessment.
This report presents the findings from the landscape assessment and in-depth country visit in Iceland.</p
Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches
No full textDiscovery and Development of an Advanced Lead for the Treatment of African Trypanosomiasis.
No full textAfrican trypanosomiasis is a widespread disease of human and veterinary importance caused by various with a globally devastating impact and a need for novel treatment options. We here provide a comprehensive preclinical evaluation of nucleoside analogues, 6-thioether-modified tubercidins, with curative activity against African trypanosomiasis. Promising hits were identified following screening against the most relevant trypanosome species. Selected hit compounds were extensively tested for metabolic stability, potency in mouse models for the various species, genotoxicity in an testing battery, and mode of action studies (i.e., genome-wide RNA interference library screening and metabolomics). Among the nucleoside analogues, analogue was curative in mouse models with no indication of genotoxicity and a low ecotoxicological footprint. Mode-of-action studies revealed that P1-type nucleoside transporters and adenosine kinase are involved in the uptake and activation, respectively. Analogue represents a potent, advanced lead fitting the preferred target product profile for a broad-spectrum trypanocide regardless of the causative species.</p