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Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.
No full textWhole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing and by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.</p
Future of opioid markets in Europe: Foresight approaches
No full textSources such as UNODC report about the ban on opium production in Afghanistan in 2023. This ban might have an impact on the heroin market in Europe. It is difficult to foresee what the consequences will be for people who use heroin, drug treatment, drug prevention and harm reduction organizations, police or customs.
Within the framework of the European DRUG-PREP-project, a workshop was organized during Lisbon Addictions following the foresight methodology. The objective of the workshop was to discuss the impact of the ban on opium in Afghanistan, building on a scenario building exercise carried out on this topic in Belgium. Workshop participants discussed and validated the developed scenarios, and used the wind-tunnelling technique to test the resilience of the European Drugs Strategy across the scenarios.
The workshop allowed participants to support national and European policy makers in how to deal with the consequences of the situation and how to prepare for different scenarios. The methodology used was developed within the aforementioned DRUG-PREP project and tested by the Belgian National Focal Point among Belgian experts.</p
Applying foresight methods at the national level in the field of substance use: Experience from the DRUGPREP project
No full textThis presentation will focus on the experience from the DRUGPREP project. While foresight has been used in other sectors, its implementation in the drugs field has previously remained relatively limited. The application of foresight to the drugs sphere is important in recognition of the fast-changing and intersectional nature of drugs and addiction. At the European level, a futures exercise was organized by the EMCDDA (as of July 2024 the European Union Drugs Agency, EUDA) to explore the future of drugs at the European level until 2030. In this landscape, the DRUG-PREP project implemented foresight approaches at the national level, to support preparedness of national drug monitoring and response systems. The DRUG-PREP partners carried out individual national exercises in six countries: Belgium, Czechia, Finland, Ireland, the Netherlands, and Portugal. The link to policy was a key aspect of the project, with each country organising a national dialogue to directly engage policymakers. The presentation will focus on the Belgian research. Horizon Scanning was performed to identify trends and megatrends with potential implications on the national drugs ecosystem, through a literature review. An expert workshop was organized to validate the trends and explore their implications. Subsequently, a small scenario building exercise was organised to explore the consequences of a clearly defined ‘disruptor’: the ban on opium production in Afghanistan. Finally, a national dialogue allowed discussion with stakeholders on how foresight can be integrated more structurally in the drugs field in Belgium. A summary of the results will be presented. Policymakers across all levels (local, regional, federal) have been active participants in the foresight activities and workshops. The link to policymaking has been crystallized in the integration of foresight into the new Belgian National Drugs Strategy 2024-2025.</p
Exploring the multiple dimensions of perceived food access in the local food environment in Flanders: Perceptions of adults in socioeconomically disadvantaged situations
No full textPersons in socioeconomically disadvantaged situations are more susceptible and disproportionally exposed to unhealthy food environments, which results in limited access to healthy foods and poorer dietary outcomes. This qualitative paper examines the various dimensions of perceived food access to healthy and unhealthy foods (i.e., availability, affordability, accessibility, accommodation, desirability, convenience and acceptability) within the local food environment among persons in socioeconomically disadvantaged situations.
A total of 23 participants in socioeconomically disadvantaged situations expressed their perceptions of food access within their local food environment and its role in their eating behaviour through participant-driven photo-elicitation in a focus group context (n = 7) and researcher-driven photo-elicitation interviews (n = 16). Reflexive thematic analysis has been used to analyse our data through an access framework.
Four overarching themes were constructed. The first two themes concern barriers to perceived food access in respectively the home and community food environment – including the importance of kitchen infrastructure, household composition and transport options. The third theme encompasses the interaction of perceived food access with the sociocultural environment, highlighting its dual role as facilitator (e.g., through food sharing practices) and barrier (e.g., through social stigma and shame). The fourth theme concerns awareness and the ability to navigate within the information food environment, which has also been proposed as a novel dimension of food access.
This study emphasizes the complexity of food access and the need for a multifaceted approach that integrates perceptions to ensure equitable access to healthy foods.</p
Advancing automated identification of airborne fungal spores: Guidelines for cultivation and reference dataset creation
No full textAirborne bioparticles, notably fungal spores, pose health risks, necessitating precise monitoring. While manual methods exist, interest is shifting towards automated systems employing machine learning. However, challenges persist due to diverse particle properties and limited training data. This study, part of SYLVA and COST Action ADOPT, addresses these gaps by establishing best practices for cultivating reference material and creating tailored datasets. Seventeen fungal species were tested on Plair RapidE+ and SwisensPoleno Jupiter. Proof-of-principle models using holography and fluorescence data were developed, achieving variable genus classification accuracy (0.43-0.95). The protocol enhances automatic identification of airborne fungal spores, promising more efficient monitoring systems.</p
Surveillance des bactéries résistantes aux antibiotiques dans les hôpitaux belges - protocole décembre 2024
No full textA systematic review and meta-analysis of human population studies on the association between exposure to toxic environmental chemicals and left ventricular dysfunction (LVD).
No full textBACKGROUND: Exposure to environmental chemicals has been associated with an elevated risk of heart failure (HF). However, the impact on early markers of HF, such as left ventricular dysfunction (LVD), remains limited.
OBJECTIVE: To establish a foundation of evidence regarding early HF markers and their association with environmental pollutants, a systematic review and meta-analysis was conducted.
METHODS: The search, conducted on October 13th, 2023, encompassed PubMed, Embase, and Web of Science without filters, focusing on observational studies reporting myocardial geometrical, structural, or functional alterations in individuals without a history of heart disease. This included the general adult population, workers, young people, and the elderly. The risk of bias was assessed using the ROBINS-I tool at both study and item levels.
RESULTS: The systematic review included 17 studies involving 43.358 individuals exposed to air pollution and 2038 exposed to heavy metals. Approximately 41% of the effect measures of associations reported significant abnormalities in myocardial structure or function. The metanalyses by pollutants categories indicated positive associations between LV systolic and diastolic abnormalities and exposure to PM2.5 [-0.069 (-0.104, -0.033); -0.044 (-0.062, -0.025)] and PM10 [-0.055 (-0.087, -0.022); -0.030 (-0.050, -0.010)] and NO2 [-0.042 (-0.071, -0.013); -0.021 (-0.037, -0.004)], as well as positive associations between lead exposure and LV systolic abnormalities [-0.033 (-0.051, -0.016)].
CONCLUSIONS: Existing evidence shows that specific early markers of HF may be associated with exposure to chemical pollutants. It is recommended to include such endpoints in new longitudinal and case-control studies to confirm further risk associations. These studies should consider co-exposures, account for vulnerable groups, and identify cardiotoxic compounds that may require regulation. When examining the link between myocardial abnormalities and environmental exposure, it is also advisable to explore the supportive use of Adverse Outcome Pathway (AOP) approaches to confirm a causal relationship.</p