RIVM Publications Repository

Recent Submissions

  • Publication
    Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies
    (2025-03-29) van Kessel, SAM; Wielders, CCH; Schoffelen, AF; Verbon, A
    Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.
  • Publication
    Phylodynamic assessment of SNP distances from whole genome sequencing for determining Mycobacterium tuberculosis transmission
    (2025-03-28) van der Roest, Bastiaan R; Bootsma, Martin CJ; Fischer, Egil AJ; Gröschel, Matthias I; Anthony, Richard M; de Zwaan, Rina; Kretzschmar, Mirjam EE; Klinkenberg, Don
    The global tuberculosis (TB) epidemic is driven by primary transmission. Pathogen genome sequencing is increasingly used in molecular epidemiology and outbreak investigations. Based on contact tracing and epidemiological links, Single Nucleotide Polymorphism (SNP) cut-offs, ranging from 3 to 12 SNPs, identify probable transmission clusters or exclude direct transmission. However, contact tracing can be limited by recall bias and inconsistent methodologies across TB settings. We propose phylodynamic models, i.e. methods to infer transmission processes from pathogen genomes and associated epidemiological data, as an alternative reference to infer transmission events. We analyzed 2,008 whole-genome sequences from Dutch TB patients collected from 2015 to 2019. Genetic clusters were defined within a 20-SNP range, and the phylodynamic model phybreak was employed to infer transmission. Probable transmission SNP cut-offs were assessed by the proportion of inferred transmission events with a SNP distance below these cut-offs. A total of 79 clusters were identified, with a median size of 4 isolates (IQR = 3-8). A SNP cut-off of 4 captured 98% of inferred transmission events while reducing pairs without transmission links. A cut-off beyond 12 SNPs effectively excluded transmission. Phylodynamic approaches provide a valuable alternative to contact tracing for defining SNP cut-offs, allowing for a more precise assessment of transmission events.
  • Publication
    Diversity of dietary protein patterns across Europe - Impact on nutritional quality and environmental sustainability
    (2025-03-04) Daas, Merel C; van 't Veer, Pieter; Temme, Elisabeth HM; Kuijsten, Anneleen; Gurinović, Mirjana; Biesbroek, Sander
    Transitioning from animal-based to plant-rich diets could potentially improve both human and planetary health, but a thorough understanding of the protein component in the diet is essential. This research aimed to identify dietary protein patterns in the European adult population and evaluate differences in nutritional quality and environmental sustainability. Individual-level food consumption data were obtained from 25 European countries (40,101 participants, 18-64 years), available from the EFSA Comprehensive European Food Consumption Database. We applied statistical clustering to classify individuals according to their consumption of 24 protein source food groups. The patterns were evaluated for nutrient requirements, the Nutrient Rich Diet (NRD) 15.3 score, greenhouse gas emissions (GHGE) and land use (LU). Six patterns emerged: (42.2%), (19.5%), (14.8%), (12.0%), (9.8%) and (1.6%), with country-specific variations. Most patterns obtained 64-69% of their protein intake from animal products, except for the pattern (52%). The pattern achieved the highest NRD15.3 (+11%), and lowest GHGE (-20%) and LU (-25%) compared to the population average and was most commonly consumed in Austria, Finland, Spain, Portugal and Belgium (4.1-4.5%). The pattern also scored high in nutritional quality (NRD15.3: +9%), whereas the pattern showed higher environmental impacts (GHGE: +5%, LU: +7%). These findings highlight the diversity of dietary protein patterns across Europe, each with unique nutritional profiles and varying environmental impacts. The pattern provides a promising example for healthier, more sustainable diets, but tailored approaches that consider the cultural and demographic contexts of individual countries are needed to optimize health and environmental outcomes for all patterns.
  • Publication
    Role of tick infestation in the progression of Anaplasma phagocytophilum infection in lambs
    (2025-03-25) Groenevelt, M; Wijburg, SR; Sprong, H; Kerkhof, K; Stuen, S
    Tick Borne Fever (TBF) is a serious health condition in sheep, caused by infection with Anaplasma phagocytophilum. When secondary bacterial infections occur in TBF, it can progress to tick pyemia, a condition causing severe morbidity and mortality in flocks. The mechanisms that underly the severe effects of tick pyemia are not fully understood. Here, we hypothesized that tick bites during an established A. phagocytophilum bacteremia could aggravate immunosuppression, increasing the risk of secondary infections. In this study, four groups of four lambs were compared based on their clinical and hematological outcomes. Group A received an intravenous injection of A. phagocytophilum on day 0. Group AT received the same injection on day 0, followed by tick placement on their backs on day 4. Group T was exposed only to tick placement on day 4, while Group C received no treatment. The animals were clinically and hematologically assessed over 28 days, and ticks collected off their backs after feeding were analyzed. Both clinically and hematologically, no additional detrimental effects were seen in Group AT compared to Group A. All lambs in Group T also developed TBF, but their clinical and hematological outcomes were less severe than those in Groups A and AT. Serologically, all animals responded similarly, corresponding to the day of exposure to A. phagocytophilum. PCR results showed no significant differences among groups, although duration of follow-up may have influenced the results, as only Group AT lambs remained PCR positive on the final testing day. When ticks that fed on Group AT lambs were compared to either ticks fed on Group T lambs or unengorged ticks harvested from the same fields, it became clear that sheep act as amplifier hosts for A. phagocytophilum in ticks shortly after exposure to infected ticks. Among the unengorged ticks, 10.2 % were infected with A. phagocytophilum, compared to 67 % and 99.2 % of the engorged ticks from Groups T and AT, respectively. In contrast to A. phagocytophilum, sheep were refractory hosts for Borrelia burgdorferi s.l., as the percentage of infected ticks was 10.2 % in the unengorged ticks and only 1 and 1.7 % in engorged ticks from groups T and AT, respectively. In this study, additional tick bites did not contribute to immunosuppression in lambs during an established A. phagocytophilum bacteremia.
  • Publication
    Microbial Keratitis Before, During and After the COVID-19 Pandemic, and the Role of Contact Lens Wear and Hand Hygiene
    (2025-03-21) Randag, Anna C; Wellens, Liesbeth; Kazemian, Nelly; Schimmer, Barbara; van Rooij, Jeroen
    During the COVID-19 pandemic, there was a significant decline in the number of patients with both non-urgent and urgent ophthalmologic conditions presenting to emergency departments, leading to concerns about the whereabouts of patients in need of care. We hypothesized that there was an actual decrease in microbial keratitis (MK) cases, due to reduced contact lens (CL) wear and improved hand hygiene, including alcohol-based hand disinfection. Besides, we questioned if non-pharmaceutical interventions would have a sustained effect after the COVID-19 pandemic.

Communities in RIVM Publications Repository

Select a community to browse its collections.

Now showing 1 - 2 of 2