• Genomic characterization of Mycobacterium tuberculosis lineage 7 and a proposed name: 'Aethiops vetus'.

      Nebenzahl-Guimaraes, Hanna; Yimer, Solomon A; Holm-Hansen, Carol; de Beer, Jessica; Brosch, Roland; van Soolingen, Dick (2016-06)
      Lineage 7 of the Mycobacterium tuberculosis complex has recently been identified among strains originating from Ethiopia. Using different DNA typing techniques, this study provides additional information on the genetic heterogeneity of five lineage 7 strains collected in the Amhara Region of Ethiopia. It also confirms the phylogenetic positioning of these strains between the ancient lineage 1 and TbD1-deleted, modern lineages 2, 3 and 4 of Mycobacterium tuberculosis. Four newly identified large sequence polymorphisms characteristic of the Amhara Region lineage 7 strains are described. While lineage 7 strains have been previously identified in the Woldiya area, we show that lineage 7 strains circulate in other parts of the Amhara Region and also among foreign-born individuals from Eritrea and Somalia in The Netherlands. For ease of documenting future identification of these strains in other geographical locations and recognizing the place of origin, we propose to assign lineage 7 strains the lineage name 'Aethiops vetus'.
    • Genomic epidemiology of emerging ESBL-producing Kentucky in Europe.

      Coipan, Claudia E; Westrell, Therese; Hoek, Angela H A M van; Alm, Erik; Kotila, Saara; Berbers, Bas; Keersmaecker, Sigrid C J De; Ceyssens, Pieter-Jan; Borg, Maria Louise; Chattaway, Marie; et al. (2020-09-08)
      Global dissemination of ciprofloxacin-resistant Salmonella Kentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum β-lactamase (ESBL) producing S. Kentucky. Routine surveillance at the European Centre for Disease Prevention and Control (ECDC) detected cases with a ciprofloxacin-resistant S. Kentucky with the ESBL-gene blaCTX-M-14b. Ensuing research identified 78 cases in 2013-2018 in eight European countries. Compared to other S. Kentucky and non-typhoidal Salmonella infections, reported to the European Surveillance System, these cases were more likely to be elderly and to present urinary-tract infections. Bayesian time-scaled phylogeny on whole genome sequences of isolates from these cases and supplementary isolates from public sequence databases was used to infer the origin and spread of this clone. We dated the origin of the blaCTX-M-14b clone to approximately 2005 in Northern Africa, most likely in Egypt. The geographic origin predicted by the phylogenetic analysis is consistent with the patients' travel history. Next to multiple introductions of the clone to Europe from Egypt, our analysis suggests that in some parts of Europe the clone might have formed a stable population, from which further spread has occurred. Comparative genomics indicated that the blaCTX-M-14b gene is present on the bacterial chromosome, within the type VI secretion system region. The blaCTX-M-14b gene is integrated downstream of the hcp1 gene, on a 2854 bp plasmid fragment containing also ISEcp1. This is the first report of a chromosomally integrated CTX-M gene in Salmonella spp. in Europe, previous studies having identified similar genes only on plasmids.
    • Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018.

      Oude Munnink, B Bas; Münger, E; Nieuwenhuijse, D F; Kohl, R; van der Linden, A; Schapendonk, C M E; van der Jeugd, H; Kik, M; Rijks, J M; Reusken, C B E M; et al. (2020-02-18)
    • Genospecies of Borrelia burgdorferi sensu lato detected in 16 mammal species and questing ticks from northern Europe.

      Mysterud, Atle; Stigum, Vetle M; Jaarsma, Ryanne I; Sprong, Hein (2019-03-25)
      Lyme borreliosis is the most common vector-borne zoonosis in the northern hemisphere, and the pathogens causing Lyme borreliosis have distinct, incompletely described transmission cycles involving multiple host groups. The mammal community in Fennoscandia differs from continental Europe, and we have limited data on potential competent and incompetent hosts of the different genospecies of Borrelia burgdorferi sensu lato (sl) at the northern distribution ranges where Lyme borreliosis is emerging. We used qPCR to determine presence of B. burgdorferi sl in tissue samples (ear) from 16 mammalian species and questing ticks from Norway, and we sequenced the 5S-23 S rDNA intergenic spacer region to determine genospecies from 1449 qPCR-positive isolates obtaining 423 sequences. All infections coming from small rodents and shrews were linked to the genospecies B. afzelii, while B. burgdorferi sensu stricto (ss) was only found in red squirrels (Sciurus vulgaris). Red squirrels were also infected with B. afzelii and B. garinii. There was no evidence of B. burgdorferi sl infection in moose (Alces alces), red deer (Cervus elaphus) or roe deer (Capreolus capreolus), confirming the role of cervids as incompetent hosts. In infected questing ticks in the two western counties, B. afzelii (67% and 75%) dominated over B. garinii (27% and 21%) and with only a few recorded B. burgdorferi ss and B. valaisiana. B. burgdorferi ss were more common in adult ticks than in nymphs, consistent with a reservoir in squirrels. Our study identifies potential competent hosts for the different genospecies, which is key to understand transmission cycles at high latitudes of Europe.
    • Genotyping of Giardia in Dutch patients and animals: a phylogenetic analysis of human and animal isolates.

      Giessen, J W B van der; Vries, A de; Roos, M; Wielinga, Peter; Kortbeek, L M; Mank, T G (2006-06-01)
      Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis) is a protozoan organism that can infect the intestinal tract of many animal species including mammals. Genetic heterogeneity of G. duodenalis is well described but the zoonotic potential is still not clear. In this study, we analysed 100 Giardia DNA samples directly isolated from human stool specimens, to get more insight in the different G. duodenalis assemblages present in the Dutch human population. Results showed that these human isolates could be divided into two main Assemblages A and B within the G. duodenalis group on the basis of PCR assays specific for the Assemblages A and B and the DNA sequences of 18S ribosomal RNA and the glutamate dehydrogenase (gdh) genes. Genotyping results showed that G. duodenalis isolates originating from Dutch human patients belonged in 35% of the cases to Assemblage A (34/98) and in 65% of the cases to Assemblage B (64/98) whereas two human cases remained negative in all assays tested. In addition, we compared these human samples with animal samples from the Netherlands and human and animal samples from other countries. A phylogenetic analysis was carried out on the DNA sequences obtained from these Giardia and those available in GenBank. Using gdh DNA sequence analysis, human and animal Assemblage A and B Giardia isolates could be identified. However, phylogenetic analysis revealed different sub-clustering for human and animal isolates where host-species-specific assemblages (C, D, E, F and G) could be identified. The geographic origin of the human and animal samples was not a discriminating factor.
    • Geographical Distribution of Ljungan Virus in Small Mammals in Europe.

      Fevola, Cristina; Rossi, Chiara; Rosso, Fausta; Girardi, Matteo; Rosà, Roberto; Manica, Mattia; Delucchi, Luca; Rocchini, Duccio; Garzon-Lopez, Carol X; Arnoldi, Daniele; et al. (2020-06-02)
      Ljungan virus (LV), which belongs to the Parechovirus genus in the Picornaviridae family, was first isolated from bank voles (Myodes glareolus) in Sweden in 1998 and proposed as a zoonotic agent. To improve knowledge of the host association and geographical distribution of LV, tissues from 1685 animals belonging to multiple rodent and insectivore species from 12 European countries were screened for LV-RNA using reverse transcriptase (RT)-PCR. In addition, we investigated how the prevalence of LV-RNA in bank voles is associated with various intrinsic and extrinsic factors. We show that LV is widespread geographically, having been detected in at least one host species in nine European countries. Twelve out of 21 species screened were LV-RNA PCR positive, including, for the first time, the red vole (Myodes rutilus) and the root or tundra vole (Alexandromys formerly Microtus oeconomus), as well as in insectivores, including the bicolored white-toothed shrew (Crocidura leucodon) and the Valais shrew (Sorex antinorii). Results indicated that bank voles are the main rodent host for this virus (overall RT-PCR prevalence: 15.2%). Linear modeling of intrinsic and extrinsic factors that could impact LV prevalence showed a concave-down relationship between body mass and LV occurrence, so that subadults had the highest LV positivity, but LV in older animals was less prevalent. Also, LV prevalence was higher in autumn and lower in spring, and the amount of precipitation recorded during the 6 months preceding the trapping date was negatively correlated with the presence of the virus. Phylogenetic analysis on the 185 base pair species-specific sequence of the 5' untranslated region identified high genetic diversity (46.5%) between 80 haplotypes, although no geographical or host-specific patterns of diversity were detected.
    • Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays.

      Gruber, Cesare E M; Bartolini, Barbara; Castilletti, Concetta; Mirazimi, Ali; Hewson, Roger; Christova, Iva; Avšič, Tatjana; Grunow, Roland; Papa, Anna; Sánchez-Seco, María P; et al. (2019-10-16)
    • Het gesprek met de patiënt is essentieel voor goede farmacotherapeutische zorg.

      Lemmens LC; Delwel GO; Hoefman RJ; de Jong JD; Weda M (2018-02)
    • Getting under the birds' skin: tissue tropism of Borrelia burgdorferi s.l. in naturally and experimentally infected avian hosts.

      Norte, Ana Cláudia; Lopes de Carvalho, Isabel; Núncio, Maria Sofia; Araújo, Pedro Miguel; Matthysen, Erik; Albino Ramos, Jaime; Sprong, Hein; Heylen, Dieter (2019-10-15)
    • Gewijzigde Nederlandse rabiësrichtlijnen.

      de Pijper, CA; Schreuder, I; Vollaard, AM; Visser, LG; van Kessel, R; van den Kerkhof, JHTC; Stijnis, C (2019-05-27)
    • Gezondheid werkt

      Polder J (2017-01-26)
    • Gezondheidsindicator van het schone lucht akkoord.

      Gerlofs-Nijland, M; Ruyssenaars, P; Ameling, C; Houthuijs, D; Maas, R; Marra, M; de Ruiter, H; Swart, W; Visser, S; de Vries, W; et al. (2019-04-14)
    • Gezondheidsraad had voor een polyvalent HPV-vaccin moeten kiezen.

      van der Vleuten, C; Oldhoff, M; Pajkrt, D; Rinkel, R; van Bergen, J (2020-05-04)
    • Gezondheidsrisico's, leefstijl en interventies.

      Proper, K I; Loef, B; van der Beek, A J (2020-01-22)
    • Giardia duodenalis multi-locus genotypes in dogs with different levels of synanthropism and clinical signs.

      Uiterwijk, Mathilde; Mughini-Gras, Lapo; Nijsse, Rolf; Wagenaar, Jaap A; Ploeger, Harm W; Kooyman, Frans N J (2020-12-02)
    • The global cropland footprint of Denmark's food supply 2000-2013

      Osei-Owusa, AK; Kastner, T; de Ruiter, H; Thomsen, M; Caro, D (2019-09-16)
    • Global estimates of mortality associated with long-term exposure to outdoor fine particulate matter.

      Burnett, Richard; Chen, Hong; Szyszkowicz, Mieczysław; Fann, Neal; Hubbell, Bryan; Pope, C Arden; Apte, Joshua S; Brauer, Michael; Cohen, Aaron; Weichenthal, Scott; et al. (2018)
      Exposure to ambient fine particulate matter (PM2.5) is a major global health concern. Quantitative estimates of attributable mortality are based on disease-specific hazard ratio models that incorporate risk information from multiple PM2.5 sources (outdoor and indoor air pollution from use of solid fuels and secondhand and active smoking), requiring assumptions about equivalent exposure and toxicity. We relax these contentious assumptions by constructing a PM2.5-mortality hazard ratio function based only on cohort studies of outdoor air pollution that covers the global exposure range. We modeled the shape of the association between PM2.5 and nonaccidental mortality using data from 41 cohorts from 16 countries-the Global Exposure Mortality Model (GEMM). We then constructed GEMMs for five specific causes of death examined by the global burden of disease (GBD). The GEMM predicts 8.9 million [95% confidence interval (CI): 7.5-10.3] deaths in 2015, a figure 30% larger than that predicted by the sum of deaths among the five specific causes (6.9; 95% CI: 4.9-8.5) and 120% larger than the risk function used in the GBD (4.0; 95% CI: 3.3-4.8). Differences between the GEMM and GBD risk functions are larger for a 20% reduction in concentrations, with the GEMM predicting 220% higher excess deaths. These results suggest that PM2.5 exposure may be related to additional causes of death than the five considered by the GBD and that incorporation of risk information from other, nonoutdoor, particle sources leads to underestimation of disease burden, especially at higher concentrations.