Mughini-Gras, Lapo; Franz, Eelco; van Pelt, Wilfrid (2018-05)
Microbial subtyping is the most common approach for Salmonella source attribution. Typically, attributions are computed using frequency-matching models like the Dutch and Danish models based on phenotyping data (serotyping, phage-typing, and antimicrobial resistance profiling). Herewith, we critically review three major paradigms facing Salmonella source attribution today: (i) the use of genotyping data, particularly Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA), which is replacing traditional Salmonella phenotyping beyond serotyping; (ii) the integration of case-control data into source attribution to improve risk factor identification/characterization; (iii) the investigation of non-food sources, as attributions tend to focus on foods of animal origin only. Population genetics models or simplified MLVA schemes may provide feasible options for source attribution, although there is a strong need to explore novel modelling options as we move towards whole-genome sequencing as the standard. Classical case-control studies are enhanced by incorporating source attribution results, as individuals acquiring salmonellosis from different sources have different associated risk factors. Thus, the more such analyses are performed the better Salmonella epidemiology will be understood. Reparametrizing current models allows for inclusion of sources like reptiles, the study of which improves our understanding of Salmonella epidemiology beyond food to tackle the pathogen in a more holistic way.
O'Connor, Daniel; Png, Eileen; Khor, Chiea Chuen; Snape, Matthew D; Hill, Adrian V S; van der Klis, Fiona; Hoggart, Clive; Levin, Michael; Hibberd, Martin L; Pollard, Andrew J (2019-06-11)
Vaccines have revolutionized public health, preventing millions of deaths each year, particularly in childhood. Yet, there is considerable variability in the magnitude and persistence of vaccine-induced immunity. Maintenance of specific antibody is essential for continuity of vaccine-induced serological protection. We conducted a genome-wide association study into the persistence of immunity to three childhood vaccines: capsular group C meningococcal (MenC), Haemophilus influenzae type b, and tetanus toxoid (TT) vaccines. We detail associations between variants in a locus containing a family of signal-regulatory proteins and the persistence MenC immunity. We postulate a regulatory role for the lead SNP, with supporting epigenetic and expression quantitative trait loci data. Furthermore, we define associations between SNPs in the human leukocyte antigen (HLA) locus and the persistence of TT-specific immunity. Moreover, we describe four classical HLA alleles, HLA DRB1∗0301, HLA DQB1∗0201, HLA DQB1∗0602, and HLA DRB1∗1501, associated with TT-specific immunity, independent of the lead SNP association.
Identifying and characterising nanomaterials require additional information on physico-chemical properties and test methods, compared to chemicals in general. Furthermore, regulatory decisions for chemicals are usually based upon certain toxicological properties, and these effects may not be equivalent to those for nanomaterials. However, regulatory agencies lack an authoritative decision framework for nanomaterials that links the relevance of certain physico-chemical endpoints to toxicological effects. This paper investigates various physico-chemical endpoints and available test methods that could be used to produce such a decision framework for nanomaterials. It presents an overview of regulatory relevance and methods used for testing fifteen proposed physico-chemical properties of eleven nanomaterials in the OECD Working Party on Manufactured Nanomaterials' Testing Programme, complemented with methods from literature, and assesses the methods' adequacy and applications limits. Most endpoints are of regulatory relevance, though the specific parameters depend on the nanomaterial and type of assessment. Size (distribution) is the common characteristic of all nanomaterials and is decisive information for classifying a material as a nanomaterial. Shape is an important particle descriptor. The octanol-water partitioning coefficient is undefined for particulate nanomaterials. Methods, including sample preparation, need to be further standardised, and some new methods are needed. The current work of OECD's Test Guidelines Programme regarding physico-chemical properties is highlighted.
Rico, Andreu; Jacobs, Rianne; Van den Brink, Paul J; Tello, Alfredo (2017-12)
Estimating antibiotic pollution and antibiotic resistance development risks in environmental compartments is important to design management strategies that advance our stewardship of antibiotics. In this study we propose a modelling approach to estimate the risk of antibiotic resistance development in environmental compartments and demonstrate its application in aquaculture production systems. We modelled exposure concentrations for 12 antibiotics used in Vietnamese Pangasius catfish production using the ERA-AQUA model. Minimum selective concentration (MSC) distributions that characterize the selective pressure of antibiotics on bacterial communities were derived from the European Committee on Antimicrobial Susceptibility Testing (EUCAST) Minimum Inhibitory Concentration dataset. The antibiotic resistance development risk (RDR) for each antibiotic was calculated as the probability that the antibiotic exposure distribution exceeds the MSC distribution representing the bacterial community. RDRs in pond sediments were nearly 100% for all antibiotics. Median RDR values in pond water were high for the majority of the antibiotics, with rifampicin, levofloxacin and ampicillin having highest values. In the effluent mixing area, RDRs were low for most antibiotics, with the exception of amoxicillin, ampicillin and trimethoprim, which presented moderate risks, and rifampicin and levofloxacin, which presented high risks. The RDR provides an efficient means to benchmark multiple antibiotics and treatment regimes in the initial phase of a risk assessment with regards to their potential to develop resistance in different environmental compartments, and can be used to derive resistance threshold concentrations.
Kieft, R A M M; Vreeke, E M; de Groot, E M; de Graaf-Waar, H I; van Gool, C H; Koster, N; Ten Napel, H; Francke, A L; Delnoij, D M J (2018-03)
Nurses register data in electronic health records, which can use various terminology and coding systems. The net result is that information cannot be exchanged and reused properly, for example when a patient is transferred from one care setting to another. A nursing subset of patient problems was therefore developed in the Netherlands, based on comparable and exchangeable terms that are used throughout the healthcare sector and elsewhere (semantic interoperability). The purpose of the current research is to develop a mapping between the subset of patient problems and three classifications in order to improve the exchangeability of data. Those classifications are the Omaha System, NANDA International, and ICF (the International Classification of Functioning, Disability and Health).
Hoornenborg, Elske; Prins, Maria; Achterbergh, Roel C A; Woittiez, Lycke R; Cornelissen, Marion; Jurriaans, Suzanne; Kootstra, Neeltje A; Anderson, Peter L; Reiss, Peter; de Vries, Henry J C; et al. (2017-11)
Pre-exposure prophylaxis (PrEP) with emtricitabine and tenofovir disoproxil fumarate is highly effective against acquisition of HIV infection, and only two cases of infection with a multidrug-resistant virus have been reported under adequate long-term adherence, as evidenced by tenofovir diphosphate concentrations in dried blood spots. We report a case of wild-type HIV-1 infection despite consistent use of emtricitabine and tenofovir disoproxil fumarate.
The South Durban (SD) area of Durban, South Africa, has a history of air pollution issues due to the juxtaposition of low-income communities with industrial areas. This study used measurements of oxides of nitrogen (NOx) to develop a land use regression (LUR) model to explain the spatial variation of air pollution concentrations in this area.
Li, Xingxing; Ke, Mingjing; Zhang, Meng; Peijnenburg, W J G M; Fan, Xiaoji; Xu, Jiahui; Zhang, Zhenyan; Lu, Tao; Fu, Zhengwei; Qian, Haifeng (2018-01)
Diclofop-methyl (DM), a common post-emergence herbicide, is frequently used in agricultural production. Silver nanoparticles (AgNPs) are one of the most widely used nanoparticles, and as such, have been detected and monitored in several environmental systems. Here we investigated the interactive effects of DM and AgNPs on the physiological morphology, photosynthesis and antioxidant system of Arabidopsis thaliana. Our results demonstrated that a 1.0 mg/L DM treatment had no significant effect on the fresh weight of plant shoots and the content of total chlorophyll and anthocyanin. However, a 0.5 mg/L AgNPs treatment was found to significantly inhibit plant growth and chlorophyll synthesis, and was found to cause more severe oxidative damage in plants compared to the effects observed in a hydroponic suspension in which DM and AgNPs were jointly present. Meanwhile, the relative transcript levels of photosynthesis related genes (psbA, rbcL, pgrl1A and pgrl1B) in the combined group were found to be slightly increased compared to transcript levels in the AgNPs group, in order to maintain ATP generation at relatively normal levels in order to repair light damage. One explanation for these observed antagonistic effects was that the existence of DM affects the stability of AgNPs and reduced Ag+ release from AgNPs in the mixed solution. Thereupon, the Ag+-content was found to decrease in shoots and roots in the combined group by 15.2% and 9.4% respectively, compared to the AgNPs group. The coexistence of herbicides and nanomaterials in aquatic environments or soil systems will continue to exist due to their wide usages. Our current study highlights that the antagonistic effects between DM and AgNPs exerted a positive impact on A. thaliana growth.
Ohajinwa, Chimere May; van Bodegom, Peter M; Vijver, Martina G; Peijnenburg, Willie J G M (2018-03-20)
Electronic and electrical equipment contains over 1000 different substances, including metals. During informal e-waste recycling some of these substances such as metals, are released into the environment causing environmental pollution. This study assessed the impact of different informal e-waste recycling activities (burning, dismantling, and repairing) on metal concentrations in top soils and various dust. A comparative cross-sectional study design was adopted to assess metal concentrations in top soils and in various dust samples from multiple e-waste recycling sites. Metal concentrations at e-waste recycling sites were compared to the concentrations at control sites in three study locations in Nigeria (Lagos, Ibadan, and Aba). In the three study locations, mean metal concentrations at the e-waste recycling sites exceeded the concentrations at the control sites and the Nigerian standard guideline values by 100 s to 1000 s times. Burning sites showed the highest pollution level, followed by dismantling sites, then repair sites. Our findings show serious environmental and public health concerns. The metal concentrations were also higher than levels reported in other studies at the same locations in Nigeria, indicating that the situation is worsening. This study provides scientific evidence for an urgent need to develop effective strategies to strengthen enforcement of existing e-waste regulations in Nigeria.
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