Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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On the role of vaccine dose and antigenic distance in the transmission dynamics of Highly Pathogenic Avian Influenza (HPAI) H5N1 virus and its selected mutants in vaccinated animals
Sitaras, Ioannis - \ 2017
Wageningen University. Promotor(en): M.C.M. Jong, co-promotor(en): B. Peeters. - Wageningen : Wageningen University - ISBN 9789463438063 - 209
avian influenza viruses - avian influenza - disease transmission - vaccines - vaccination - dosage - antigenic variation - mutants - mutations - immunity - vaccine development - virology - epidemiology - aviaire influenzavirussen - aviaire influenza - ziekteoverdracht - vaccins - vaccinatie - dosering - antigene variatie - mutanten - mutaties - immuniteit - vaccinontwikkeling - virologie - epidemiologie

Influenza virus infections can cause high morbidity and mortality rates among animals and humans, and result in staggering direct and indirect financial losses amounting to billions of US dollars. Ever since it emerged in 1996 in Guangdong province, People’s Republic of China, one particular highly pathogenic avian influenza (HPAI) H5N1 virus has spread globally, and is responsible for massive losses of poultry, as well as human infections. For these reasons, HPAI H5N1 is considered as one of the viruses possible to cause a future influenza pandemic.

One of the main reasons why influenza is a recurring problem is its ability to constantly evolve through the selection of mutants that are able to avoid immunity (be it natural or acquired). Due to the accumulation of mutations during genome replication, diverse/variant influenza genome sequences co-exist in a virus pool (quasispecies). These sequences can contain mutations that are able to confer selective advantages to the influenza virus given the opportunity. As a consequence, whenever a situation arises that places the virus under any type of pressure that the dominant virus sequence cannot cope with (i.e. immune pressure, selective receptor binding, etc.), the virus with the genome sequence that allows it to better adapt to that particular pressure becomes selected and takes over.

Because of the influenza virus’s high rate of mutations, a global surveillance network is in place to monitor changes in circulating strains among humans that would warrant an update of the vaccines used. For human influenza strains, vaccines are updated frequently (every one or two years) and a similar situation holds true for racehorse vaccination. For avian influenza vaccination, however, the situation is different. In most countries, vaccination against avian influenza is not used, and in the countries where vaccines are used (either as routine or emergency measures), they are not updated as frequently as human vaccines are. In addition, in many instances vaccination against avian influenza viruses has met with some spectacular failures, since it failed to produce a level of immunity that would protect against circulating field strains. These vaccination failures have often been attributed to the fact that without constant vaccine updating (as is done for human influenza), the vaccines used are not able to keep up with continuously evolving antigenic variants selected in the field, and thus to protect poultry against them. In addition, since it is known that immune pressure resulting from vaccination can be a driving force in the evolution of influenza viruses and the selection of immune-escape mutants, there is a school of thought that posits that vaccination against avian influenza is not only a very expensive affair (especially if vaccines need to be frequently updated), but can also lead to selection of mutants that are able to avoid vaccination-induced immunity.

The research reported in this thesis started with addressing the gaps in the knowledge regarding the role of vaccination-induced immunity in the selection of immune-escape mutants of HPAI H5N1, and if there is a way for vaccines to still be able to protect against antigenically-distant variants of the vaccine seed strain, without the need for frequent vaccine updates.

Our first step in studying influenza virus evolution and selection of immune-escape mutants was to investigate how antigenic pressure may drive the selection of such mutants, and what the effect of the selected mutations on the pathogenicity and transmissibility of the mutants may be. Although there exist a variety of methods to select for influenza virus mutations (i.e. monoclonal antibodies, site-directed mutagenesis, reverse genetics, etc.), none of them is representative of selection as it happens in a vaccinated animal. In Chapter 2, we discuss in detail a laboratory-based system we have developed, in which immune-escape mutants are selected using homologous polyclonal chicken sera, similar to how they are selected in the field due to vaccination- induced immune pressure. We find that selection takes place early on, and additional mutations are selected when immune pressure is increased. Antigenic distances between the selected mutants and their parent strains are also increased throughout the selection process, but not in a linear fashion. Our selection system proved to be robust and replicable, and to be representative of selection in the field, since the mutations we selected for are also found in naturally-selected field isolates, and the antigenic distances between our selected mutants and their parent strains are similar to antigenic distances between vaccine strains and field isolates.

We continued our research by addressing the roles played by vaccine dose (and resulting immunity) and antigenic distance between vaccine and challenge strains, in the transmission of HPAI H5N1 viruses, by employing transmission experiments using vaccinated chickens (Chapter 3). To our surprise, we found that the effect of antigenic distances between vaccine and challenge strains on transmission is very small compared to the effect of vaccine dose. We then quantified, for the first time, the minimum level of immunity and minimum percentage of the vaccinated population exhibiting said immunity, in order for vaccines to be able to protect against transmission even of strains that are antigenically distant to the vaccine seed strain. Transmission of such strains in well-vaccinated populations would allow for a scenario where vaccination- induced immunity may drive the selection of immune-escape mutants. Our results show that in order for vaccines to prevent transmission of antigenically distant strains (such as the ones resulting from selection due to immune pressure), the threshold level of immunity against these strains should be ≥23 haemagglutination inhibition units (HIU), in at least 86.5% of the vaccinated population. This level of immunity can be estimated by knowing the antigenic distance between the vaccine and challenge (field) strain, and the HI titre against the vaccine strain, which would then allow the approximate level of immunity against the field strain to be deduced. For example, assuming the HI titre against a vaccine strain is 210 HIU, and the distance with the challenge (field) strain is 24 HIU, according to our results the vaccine should be able to protect against the challenge strain, because the difference in HI titres should be around 26 HIU (i.e. above 23 HIU). These results, taken together with our previous work on selection of mutants, where we showed that the antigenic distances between our mutants and their parent strains are representative of distances found in the field, point to the fact that it is unlikely that vaccination-induced immunity can lead to selection of mutants able to escape it, given that a threshold level of immunity in a minimum percentage of the vaccinated population is achieved. As a consequence, we believe that constant vaccine updating may not be necessary for avian influenza viruses, as long as a threshold level of immunity is maintained. This makes vaccination a more attractive control measure, both from a health perspective and a financial one, than just applying biosecurity measures.

To examine the effect the mutations in the haemagglutinin protein of our selected mutants may have in their transmission among chickens vaccinated with the parent strain, we used reverse genetics techniques to insert the HA gene of our most antigenically distant mutant into the parent strain backbone (Chapter 4). We vaccinated animals with a sub-optimal dose of vaccine, and we concluded that the mutations we selected for did not allow the mutant to avoid even low levels of immunity, such as the ones resulting from a sub-optimal vaccine dose (which resembles a poor field vaccination scenario). At the same time, the HA mutations we selected for did not appear to have a negative effect either on the pathogenicity of the mutant, or its ability to transmit to unvaccinated animals, since both parameters were comparable to the parent strain.

Finally, we studied the role inter-animal variation in immunity – as measured by HI titres – has in the accuracy of antigenic cartography calculations (Chapter 5). We found that using sera from more than one animal significantly increased the accuracy of antigenic distance calculations, since it takes into account individual differences in immune responses to vaccination, an inevitable phenomenon documented in both humans and animals. In addition, we increased the accuracy of antigenic maps by avoiding the use of dimension-reducing algorithms as is currently done. By not reducing the dimensionality of virus positioning in space, our maps retain the original geometry between strains or sera, leading to more accurate positioning (Chapters 2 and 5). We hope that improving the accuracy of antigenic cartography can lead to a more precise surveillance of influenza evolution and better informed decisions regarding the need to update vaccines.

Taken collectively, our results can improve field vaccination outcomes, since they provide guidelines on how to increase vaccination efficiency in stopping transmission of even antigenically-distant strains. In addition, our method for selecting for immune- escape mutants can be a valuable addition to research on influenza virus evolution. Moreover, policy making decisions regarding vaccination against any type of influenza can also benefit from our improvement on antigenic cartography accuracy, saving unnecessary costs in vaccine updating, and reducing morbidity and mortality of both animals and humans.

ESBL Evaluation framework
Bondt, N. ; Asseldonk, M.A.P.M. van; Bergevoet, R.H.M. - \ 2016
The Hague : LEI Wageningen UR (Report / LEI Wageningen UR 2016-020) - ISBN 9789462578517 - 45 p.
extended spectrum beta-lactamases - livestock - epidemiology - animal welfare - animal health - public health - food safety - risk management - verbreed spectrum bèta-lactamases - vee - epidemiologie - dierenwelzijn - diergezondheid - volksgezondheid - voedselveiligheid - risicobeheersing
Extended-spectrum bèta-lactamases (ESBL)-producing bacteria have become increasingly common in animals and humans. The goal of the presented ESBL evaluation framework is to help policy makers to evaluate the effectiveness of possible interventions aimed to reduce ESBL levels in livestock. An objective-driven ESBL policy approach (i.e., setting more clear and stringent objectives, for example maximum ESBL prevalence on national level) is preferable since much is unknown about other potential relevant measures and moreover the accountability of individual agents is hampered, which are both requisites for a measure-driven policy approach. In addition, for the nearby future, an additional measure is to extend the ban on some other antibiotics that are related to ESBLs.
Statistical modelling for exposure measurement error with application to epidemiological data
Agogo, G.O. - \ 2016
Wageningen University. Promotor(en): Hendriek Boshuizen; Fred van Eeuwijk, co-promotor(en): Hilko van der Voet. - Wageningen : Wageningen University - ISBN 9789462576223 - 160
calibration - regression analysis - exposure assessment - validity - simulation models - statistical bias - epidemiology - kalibratie - regressieanalyse - blootstellingsbepaling - geldigheid - simulatiemodellen - statistische vertekening - epidemiologie

Background Measurement error in exposure variables is an important issue in epidemiological studies that relate exposures to health outcomes. Such studies, however, usually pay limited attention to the quantitative effects of exposure measurement error on estimated exposure-outcome associations. Therefore, the estimators for exposure-outcome associations are prone to bias. Existing methods to adjust for the bias in the associations require a validation study with multiple replicates of a reference measurement. Validation studies with multiple replicates are quite costly and therefore, in some cases only a single–replicate validation study is conducted besides the main study. For a study that does not include an internal validation study, the challenge in dealing with exposure measurement error is even bigger. The challenge is how to use external data from other similar validation studies to adjust for the bias in the exposure-outcome association. In accelerometry research, various accelerometer models have currently been developed. However, some of these new accelerometer models have not been properly validated in field situations. Despite the widely recognized measurement error in the accelerometer, some accelerometers have been used to validate other instruments, such as physical activity questionnaires, in measuring physical activity. Consequently, if an instrument is validated against the accelerometer, and the accelerometer itself has considerable measurement error, the observed validity in the instrument being validated will misrepresent the true validity.

Methodology In this thesis, we adapted regression calibration to adjust for exposure measurement error for a single-replicate validation study with zero-inflated reference measurements and assessed the adequacy of the adapted method in a simulation study. For the case where there is no internal validation study, we showed how to combine external data on validity for self-report instruments with the observed questionnaire data to adjust for the bias in the associations caused by measurement error in correlated exposures. In the last part, we applied a measurement error model to assess the measurement error in physical activity as measured by an accelerometer in free-living individuals in a recently concluded validation study.

Results The performance of the proposed two-part model was sensitive to the form of continuous independent variables and was minimally influenced by the correlation between the probability of a non-zero response and the actual non-zero response values. Reducing the number of covariates in the model seemed beneficial, but was not critical in large-sample studies. We showed that if the confounder is strongly linked with the outcome, measurement error in the confounder can be more influential than measurement error in the exposure in causing the bias in the exposure-outcome association, and that the bias can be in any direction. We further showed that when accelerometers are used to monitor the level of physical activity in free-living individuals, the mean level of physical activity would be underestimated, the associations between physical activity and health outcomes would be biased, and there would be loss of statistical power to detect associations.

Conclusion The following remarks were made from the work in this thesis. First, when only a single-replicate validation study with zero-inflated reference measurements is available, a correctly specified regression calibration can be used to adjust for the bias in the exposure-outcome associations. The performance of the proposed calibration model is influenced more by the assumption made on the form of the continuous covariates than the form of the response distribution. Second, in the absence of an internal validation study, carefully extracted validation data that is transportable to the main study can be used to adjust for the bias in the associations. The proposed method is also useful in conducting sensitivity analyses on the effect of measurement errors. Lastly, when “reference” instruments are themselves marred by substantial bias, the effect of measurement error in an instrument being validated can be seriously underestimated.

Transmission of antibiotic resistance from animals to humans : Broilers as a reservoir of ESBL-producing bacteria
Huijbers, P.M.C. - \ 2016
Wageningen University. Promotor(en): Mart de Jong; Lisette Graat; E. van Duijkeren. - Wageningen : Wageningen University - ISBN 9789462576216 - 156
broilers - man - disease transmission - antibiotic resistance - bacteria - enterobacteriaceae - poultry farming - epidemiology - vleeskuikens - mens - ziekteoverdracht - antibioticaresistentie - bacteriën - enterobacteriaceae - pluimveehouderij - epidemiologie

Huijbers, P.M.C. (2016). Transmission of antibiotic resistance from animals to humans: Broilers as a reservoir of ESBL-producing bacteria. PhD thesis, Wageningen University, Wageningen, the Netherlands.

Antibiotic resistance in animals becomes a public health issue when there is transmission of antibiotic resistant bacteria, or their resistance genes, from animals to humans. β-lactam antibiotics are critically important for the treatment of human bacterial infections. Resistance to this class of antibiotics, mediated by extended-spectrum β-lactamases (ESBL) has emerged. Broilers might contribute to transmission to humans due to the high prevalence of ESBL-producing Enterobacteriaceae among their intestinal biome, compared to other livestock species, companion animals, and wildlife. Transmission to humans might occur via the food chain, by direct contact or via the environment. The aim was to investigate transmission of antibiotic resistant bacteria between animals and humans, and more specifically transmission of ESBL-producing E. coli between broilers, and between broilers and humans in varying degrees of contact with these animals. Systematically collected and categorised evidence from literature showed that clinically relevant antibiotic resistant bacteria were present in the natural environment, that is in soil, water, air and wildlife. It was therefore hypothesised that humans in areas with high broiler densities might have an increased risk for carriage of ESBL-producing Enterobacteriaceae. This hypothesis was rejected, as the observed risk was lower for these individuals. The situation might be different for individuals living on broiler farms as ESBL-producing E. coli were detected on all investigated farms. Among broilers, the within farm prevalence approached 100%, and there was no difference between conventional and organic farms at five weeks, i.e. just before slaughter on conventional farms. On organic farms, the prevalence decreased to 80.0% at 70 days, i.e. slaughter age. Not only transmission to humans via the farm environment, but close physical contact with broilers might, therefore, lead to increased risk for carriage. Prevalence among farmers, their family members and employees on both conventional (19.1%) and organic (18.5%) broiler farms was higher compared to humans in the general population (5.1%). Moreover, people in close contact with live broilers showed the highest risk (27.1 vs. 14.3%). Evidence for clonal transmission of ESBL-producing E. coli between humans and broilers was found on conventional farms, and horizontal gene transfer was suspected on both conventional and organic farms. Even without selection pressure from antibiotics ESBL-producing E. coli were able to transmit and persist in an organic broiler flock, which shows that broilers form a reservoir of antibiotic resistance genes. This leads to an increased risk of carriage of humans on farms through direct contact with broilers and possibly via the direct farm environment. As only a very small percentage of the general population is exposed to live broilers, direct contact with broilers does not appear to be important for carriage in the general human population.

Bioeconomic modelling of foot and mouth disease and its control in Ethiopia
Jemberu, W.T. - \ 2016
Wageningen University. Promotor(en): Henk Hogeveen, co-promotor(en): Monique Mourits. - Wageningen : Wageningen University - ISBN 9789462576872 - 175
foot-and-mouth disease virus - economic models - mathematical models - epidemiology - animal diseases - cattle - cattle diseases - ethiopia - mond- en klauwzeervirus - economische modellen - wiskundige modellen - epidemiologie - dierziekten - rundvee - rundveeziekten - ethiopië

Keywords: Control, cost-benefit, economic impact, epidemiology, Ethiopia, Foot and mouth disease, intention, modelling, production system.

Bioeconomic Modelling of Foot and Mouth Disease and Its control in Ethiopia

Foot and mouth disease (FMD) is a highly contagious viral disease which affects cloven hoofed animals. FMD is endemic in Ethiopia with potential impact both on national and household economies because of its effect on production and trade. The general objective of this PhD research was to provide insight into the epidemiology and economics of FMD and its control in Ethiopia to support decision making in the control of the disease.

A study of the national incidence of FMD outbreak revealed that the disease is endemic in all regional states affecting more than a quarter of the country every year, with the highest frequency of outbreaks occurring in the central, southern and southeastern parts of the country. The type of production system, presence of a major livestock market and/or route, and adjacency to a national parks or wildlife sanctuary were associated with the risk of outbreaks in the districts.

Field outbreak study indicated that FMD morbidity rates of 85% and 95 % at herd level; and 74% and 61% at animal level in the affected herds in the crop–livestock mixed system (CLM) and pastoral system, respectively. The herd level economic loss estimates were on average USD 76 per affected herd in CLM and USD 174 per affected herd in the pastoral production system.

Study of motivation of farmers to implement FMD control, through the Health Belief Model (HBM) framework, revealed that almost all farmers had high intention to implement FMD vaccination free of charge, which decreases, especially in CLM system, if the vaccine is charged. Farmers in the pastoral and crop-livestock mixed production systems had low intention to implement herd isolation and animal movement restriction control measure. Among the HBM perception constructs perceived barrier was found to be the most important predictor of the intention to implement FMD control measures.

A modelling study on the national economic impact and cost-benefit analysis FMD control strategies showed that the annual cost of the disease is about 1,354 million birr. A stochastic cost-benefit analysis of three potential FMD control strategies indicated that all the strategies on average have a positive economic return but with variable degree of uncertainty including possibility of loss. Targeted vaccination strategy gives relatively the best economic return with relatively less risk of loss.

Dietary patterns, biomarkers of atherosclerosis, cardiovascular and all-cause mortality
Sijtsma, F.P.C. - \ 2015
Wageningen University. Promotor(en): Daan Kromhout; D.R. Jacobs, co-promotor(en): Sabita Soedamah-Muthu. - Wageningen : Wageningen University - ISBN 9789462575493 - 207
dieet - hart- en vaatziekten - atherosclerose - prognostische merkers - ziektemerkers - mortaliteit - classificatiesystemen - epidemiologie - longitudinaal onderzoek - diet - cardiovascular diseases - atherosclerosis - prognostic markers - disease markers - mortality - classification systems - epidemiology - longitudinal studies

Summary belonging to the thesis entitled ‘Dietary patterns, biomarkers of atherosclerosis, cardiovascular and all-cause mortality’

The long history of epidemiologic studies on diet and cardiovascular disease (CVD) has traditionally relied on analysis of specific nutrients or foods. Dietary patterns are multiple dietary components operationalized as a single exposure; they reflect the entire diet. In general, two methods are used to define dietary patterns: 1) theoretically, or a priori, defined dietary scores and 2) empirically, or a posteriori, derived dietary patterns. A priori dietary scores were developed to assess diet quality based on adherence to dietary patterns or recommendations. An example of an ‘a posteriori’ approach is factor analysis (e.g. principal components analysis (PCA)). Factor analysis reduces data into patterns based upon intercorrelations between nutrients or foods. The aim of this thesis was to create, examine and compare several dietary patterns and indices and assess these in relation to both early stage markers of CVD (markers of endothelial function and oxidative stress) and to mortality from CVD and all-causes.

In chapter 2 we described the creation of the A Priori Diet Quality Score, representing overall diet quality in the Coronary Artery Risk Development in Young Adults (CARDIA) study. The CARDIA study included 5115 black and white men and women, aged 18-30 at baseline (1985-86). Diet was assessed diet at baseline, year 7(1992-93) and 20 (2005-06) examinations. The A Priori Diet Quality Score summed 46 food groups rated by investigators as positive or negative on the basis of hypothesized health effects. In 2652 participants with 3 diet assessments, the mean (±SD) A Priori Diet Quality Score increased from 64.1± 13.0 at year 0 to 71.1 ± 12.6 at year 20, which was primarily attributable to increased age. However, the secular trend, which was estimated from differences of dietary quality scores across time at a fixed age (age matched time trend), decreased. The diet score was higher in whites than in blacks and in women than in men and increased with education, but demographic gaps in the score narrowed over 20 y. Consumption of positively rated food groups tended to increase and negatively rated food groups tended to decrease, and were similar in direction across demographic groups.

In chapter 3 we used the ‘A Priori Diet Quality Score’ and two dietary patterns derived using principal components analysis (PCA) the ‘Fruit and Vegetables’ dietary pattern and the ‘Meat’ dietary pattern in the CARDIA study. We studied prospective associations of the ‘A Priori Diet Quality Score’, the ‘Fruit and Vegetables’ dietary pattern and the ‘Meat’ dietary pattern with cellular adhesion molecules (CAMs). The ‘Fruit and Vegetables’ dietary pattern was characterized by high intakes of fruit, vegetables, and whole grains and the ‘Meat’ dietary pattern by high intakes of red meat, refined grain, and butter. The ‘A Priori Diet Quality Score’ was related to all CAMs. The ‘Fruit and Vegetables’ dietary pattern was related to E-selectin and sICAM-1 but not to P-selectin and VCAM. The ‘Meat’ dietary pattern was related to all CAMs except VCAM. Strongest associations were for the ‘Meat’ dietary pattern with E-selectin (effect size 28% of an SD (+3.9/13.7 ng/mL)) and P-selectin (effect size 37% of an SD (+4.1/11.2 ng/mL)) and the ‘A Priori Diet Quality Score’ with sICAM-1 (effect size 34% of an SD (-15.1/44.7 ng/mL)) and VCAM (effect size of 26% of an SD (-45.1/170.3 ng/mL)).

Chapter 4 described prospective associations of the A Priori Diet Quality Score, ‘Fruit and Vegetables’ dietary pattern and ‘Meat’ dietary pattern and a plasma biomarker of lipid peroxidation, F2-isoprostanes also in the CARDIA study. We estimated associations between each dietary pattern and plasma F2-isoprostanes cross-sectionally (at year 20, n=2736) and prospectively (year 0/7 average diet and year 15/20 average F2-isoprostanes, n=2718). In the cross-sectional analysis, the A Priori Diet Quality Score and the ‘Fruit and Vegetables’ dietary pattern were inversely, and the ‘Meat’ dietary pattern was positively, associated with F2-isoprostanes (all p values <0.001). These associations were also statistically significant in prospective analysis.

In chapter 5 we described a food classification system derived from the Food-based Dietary Guidelines in the Netherlands that can be used to systematically and objectively classify foods in relation to their effects on health. Classification criteria for each food group were developed based on presumed positive, neutral or negative effects on chronic diseases of five nutrients: four that likely increase (saturated fatty acids, mono-trans unsaturated fatty acids, sodium, and added sugar) and one that likely decreases (dietary fiber) the risk of chronic diseases. This classification system also provided a framework to create food-based dietary scores for epidemiologic research on diet and chronic disease relationships.

Chapter 6 describes the creation of two dietary scores the ‘Dutch Healthy Nutrient and Food Score’ and the ‘Dutch Undesirable Nutrient and Food Score’ based on the food classification system described in chapter 5 in the Alpha Omega Trial. The Alpha Omega Trial is a randomized controlled trial; however the current analyses were done from an observational prospective cohort perspective (with adjustment for intervention groups). We included 4307 cardiac patients aged 60-80 years and monitored mortality for 10 years. Patients in the highest quintile of the ‘Dutch Healthy Nutrient and Food Score’ had 30% (HR 0.70; 95% CI 0.55-0.91) lower CVD and 32% (HR 0.68; 95%CI 0.47-0.99) lower all-cause mortality risk compared to patients in the first quintile. The ‘Dutch Undesirable Nutrient and Food Score’ was unrelated to both CVD and all-cause mortality.

In Chapter 7 we also created a ‘Dutch Healthy Nutrient and Food Score’ and a ‘Dutch Undesirable Nutrient and Food Score’ in the Zutphen Elderly Study. We assessed the association of these scores with 25 year CVD and all-cause mortality and life-years gained. We divided the men (age 65-84 years) into those with (n=210) and without (n=616) cardiovascular-metabolic diseases at baseline in 1985. During a median follow-up of 10.6 years (IQR 5.8-15.9) 806 participants died, of whom 359 from CVD. Diet scores did not predict death in all men. Among men with cardiovascular-metabolic diseases, ‘Dutch Healthy Nutrient and Food Score’ was associated with lower CVD (HR: 0.57; 95%CI: 0.35-0.93) and all-cause mortality risk (HR: 0.64; 95% CI: 0.44-0.94) comparing highest vs. lowest tertiles of the score. Men with cardiovascular-metabolic diseases in the highest vs. lowest tertile of the ‘Dutch Healthy Nutrient and Food Score’ lived 2.5 year longer. The ‘Dutch Healthy Nutrient and Food Score’ was not associated with CVD and all-cause mortality in men without cardiovascular-metabolic diseases. The ‘Dutch Undesirable Nutrient and Food Score’ was not associated with any of the outcomes.

In Chapter 8 we summarized the main findings of this thesis and reflected on some methodological considerations. First, we discussed the different approaches to derive dietary scores and patterns and the advantages and disadvantages of these methods. Second, we reflected on important aspects for creating a priori dietary scores and on further research. Finally, the general conclusions and implications were presented.

From the results presented in this thesis we conclude that adherence to a healthy diet is inversely associated with early stage markers of CVD (markers of endothelial function and oxidative stress), CVD and all-cause mortality. In summary, a healthy diet consists of plenty of vegetables and fruit, legumes, whole grains, nuts and seeds, moderate intake of fish/poultry/lean meats and low fat dairy, and limited intake of processed meats, refined grains, sugar sweetened beverages, ready meals and snacks. However, this thesis also showed that a high quality dietary pattern can be achieved in several different ways, and may differ among populations.

Foot-and-mouth disease virus : the role of infection routes and species differences in the transmission of FMDV
Bravo De Rueda Cabrera, C. - \ 2015
Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Aldo Dekker; Phaedra Eble. - Wageningen : Wageningen University - ISBN 9789462573284 - 137
mond- en klauwzeervirus - mond- en klauwzeer - infectieziekten - ziekteoverdracht - ziektebestrijding - infectiebestrijding - soortverschillen - epidemiologie - diergeneeskunde - foot-and-mouth disease virus - foot and mouth disease - infectious diseases - disease transmission - disease control - infection control - species differences - epidemiology - veterinary science

ÁFoot-and-mouth disease is a contagious viral disease of cloven-hoofed animals (e.g. cattle, sheep, pigs) and can cause severe economic losses to the farm animal industries. The aim of this thesis was to quantify underlying mechanisms regarding transmission of FMDV. With data from past animal experiments we identified the factors which are associated with the amount of virus shed by infected animals and thus may be of importance for transmission of the virus. In an experimental study, the contribution of the environment on the transmission of FMDV was investigated by using a new mathematical model in which the contribution of the environment on transmission was incorporated. Roughly 44% of the transmission of FMDV occurred through the environment that was contaminated with se-excretions from FMDV infected animals. The role of the different species on the transmission of FMDV was investigated with a transmission study of FMDV between infected sheep and naïve cattle. Sheep were found to be less infectious than cattle but similarly susceptible. Using a so-called next-generation matrix, transmission of FMDV in mixed cattle-sheep populations (with different proportions of cattle and different proportions of vaccinated animals) was quantified and the effects of different vaccination strategies against FMDV were analysed. In mixed populations of cattle and sheep, transmission of FMDV is higher when more cattle are present. In populations with more than 14% cattle, targeting vaccination to cattle only can be sufficient to control FMDV.

The results of this thesis show that transmission of FMDV can occur via a contaminated environment, (without animal presence) and that sheep seem to play a limited role in the transmission of FMDV. These results can be used to improve the control measures to prevent and control FMDV in different animal populations.

Aziatisch vliegje zet fruitteelt op stelten
Sikkema, A. ; Helsen, H.H.M. - \ 2014
Resource: weekblad voor Wageningen UR 9 (2014)7. - ISSN 1874-3625 - p. 10 - 10.
drosophila suzukii - fruitteelt - insectenplagen - plantenplagen - epidemiologie - gewasbescherming - bestrijdingsmethoden - fruit growing - insect pests - plant pests - epidemiology - plant protection - control methods
De Suzuki-fruitvlieg uit Azië is een ramp voor de Nederlandse fruitsector: ‘We raken dit Aziatische vliegje nooit meer kwijt.’
Schmallenberg virus : technical and scientific studies
Poel, W.H.M. van der - \ 2014
Lelystad : Central Veterinary Institute of Wageningen UR - 67
dierpathologie - schmallenbergvirus - epidemiologie - pathogenese - transmissie - vectoren - diagnose - reverse transcriptase pcr - serologie - wilde dieren - huisdieren - kalveren - lammeren - koeien - schapen - animal pathology - schmallenberg virus - epidemiology - pathogenesis - transmission - vectors - diagnosis - serology - wild animals - domestic animals - calves - lambs - cows - sheep
Schmallenberg virus primarily infects domestic and wild ruminants. Cattle and sheep seem to be the most susceptible species. Goats, pigs and camelids seem to be less susceptible. In pregnant cattle and sheep, the virus can infect multiple organs of the un-borne fetus. However, this infection often does not cause major lesions and infrequently leads to malformations.
Mechanisms underlying disease transmission between spatially separated animals
Bunnik, B.A.D. van - \ 2014
Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Thomas Hagenaars; Gonnie Nodelijk. - Wageningen : Wageningen University - ISBN 9789461739537 - 150
dieren - vleeskuikens - infectieziekten - ziekteoverdracht - gastheren (dieren, mensen, planten) - wiskundige modellen - epidemiologie - diergeneeskunde - animals - broilers - infectious diseases - disease transmission - hosts - mathematical models - epidemiology - veterinary science

Transmission of infections between spatially separated hosts is a common problem, not only during major outbreaks of livestock diseases, but also in many other settings such as the transmission of infectious diseases between plants and crops or in healthcare settings. During the last major epidemics of livestock diseases in the Netherlands and abroad, disease transmission events occurred despite movement bans and other (bio-)security measures, implying that indirect transmission plays a major role. A better understanding of indirect transmission is necessary to put in place evidence based bio-security measures against neighbourhood (indirect) transmission. To gain more insight in the mechanisms underlying indirect transmission a series of experimental studies combined with mathematical modelling were conducted of which the results are presented in this thesis. First the effect of acidification of drinking water on the transmission parameters of direct and indirect transmission of Campylobacter jejuni (C. jejuni) between broilers was studied. It was shown that acidified drinking water has an effect on indirect transmission but not on direct transmission of C. jejuni between broilers. The sender and receiver sub-process of indirect transmission was then studied in more detail and it was shown that a significant negative interaction effect between acidification of the sender and receiver sub-processes exists, indicating that there is no additional effect of acidification of the drinking water on both sides of the transmission process compared to acidified drinking water only on one side. To study the transport of the pathogen in the environment in more detail, a series of indirect transmission experiments was carried out and a model framework was developed to study indirect transmission between spatially separated hosts. These studies showed that indirect transmission of C. jejuni between broilers is best described by a multistage environmental route from sending to receiving animal, suggesting that indirect transmission occurs through progressive (but slow) contamination of the environment surrounding the source. Indirect transmission experiments where repeated with both C. jejuni and Escherichia coli and the results showed that for C. jejuni it takes much longer for the first effective (viable) bacterium to cross the small distance of approximately 75 cm than it does for Escherichia coli. A new modelling approach to study indirect transmission was developed guided by these indirect transmission experiments. This model is capable of accurately describing the pathogen dispersal process by a diffusive transport mechanism which includes pathogen mortality. Lastly, a range of dose-response models were compared and tested how well these fitted to the data from a dose-response experiment. Here it was shown that for interpolation purposes two relatively simple models are best capable of describing the data from the dose-response experiment. For extrapolation purposes, however, it was shown that from the models that were studied a model that abides by the independent action hypothesis is best.

Epidemiologie en bestrijding van bacteriekanker bij pruimenbomen
Wenneker, M. ; Bruine, J.A. de - \ 2013
Randwijk : Praktijkonderzoek Plant en Omgeving, Bloembollen, Boomkwekerij & Fruit - 24
prunus domestica - pruimen - plantenziekteverwekkende bacteriën - bacterieziekten - pseudomonas syringae pv. morsprunorum - pseudomonas syringae pv. syringae - kanker (plantenziektekundig) - onderstammen - epidemiologie - ziektebestrijding - gewasbescherming - nederland - plums - plant pathogenic bacteria - bacterial diseases - cankers - rootstocks - epidemiology - disease control - plant protection - netherlands
De introductie van de zwakke onderstam VVA-1 heeft een nieuwe impuls gegeven aan de (intensieve) pruimenteelt in Nederland. Helaas blijkt het probleem van bacteriekanker, veroorzaakt door Pseudomonas syringae bacterie-soorten, een rem te zijn op de verdere ontwikkeling van de pruimenteelt in Nederland. De volgende conclusies en aanbevelingen volgen uit dit onderzoek: • Kwekerij handelingen kunnen van belang zijn bij het ontstaan van bacteriekanker (bijvoorbeeld inknippen van de bomen, opschonen en rooien). Deze activiteiten zijn standaard bij het opkweken van pruimenbomen. • De grootste invloed lijkt de onderstam VVA-1 te hebben. Onder Nederlandse omstandigheden kan er een zware infectiedruk zijn. Blijkbaar te groot voor VVA-1. • In het (Nederlandse) rassen- en veredelingsonderzoek voor pruimen én kersen moet resistentie tegen bacteriekanker prioriteit hebben. • Onderstam-ras combinaties moeten specifiek getoetst worden op gevoeligheid voor Pseudomonas syringae infecties. • Opvolgen van algemene beheersmaatregelen in de boomgaard om infectie (of verdere verspreiding) te voorkomen is aan te bevelen.
Characterization and epidemiology of members of the genus Torradovirus
Verbeek, M. - \ 2013
Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Rene van der Vlugt; Richard Kormelink. - S.l. : s.n. - ISBN 9789461736703 - 159
solanum lycopersicum - tomaten - plantenvirussen - picornaviridae - identificatie - epidemiologie - spanje - solanum lycopersicum - tomatoes - plant viruses - picornaviridae - identification - epidemiology - spain

The research described in this thesis focuses on the molecular and biological characterization of a new group of plant viruses. At the start of this research only a ‘torrado’ disease in tomato was known, which is recognised by necrosis on leaves and fruits, that eventually turn into its typical and devastating burnt-like symptoms. Using a wide range of available (virological) tools the causal agent was identified as a so-far unknown spherical virus of approximately 28 nm in diameter. Further analysis revealed that the virus contained a bi-partite RNA genome of which the entire nucleotide sequence was elucidated. The virus was named after the Spanish name of the disease, hence Tomato torrado virus (ToTV). Although this virus has been found mainly in Europe, it is emerging and meanwhile found in Central America and Australia.

After the discovery of ToTV, another disease suspected to be caused by a torrado-like virus was analysed. It was shown that this disease, which was found in tomatoes grown in Mexico, was caused by a similar but distinct torradovirus named Tomato marchitez virus (ToMarV). Its molecular and biological features, as analysed and described in this thesis, supported the proposal of a new genus denoted Torradovirus, named after its first representative. This genus was recognized and classified by the International Committee on Taxonomy of Viruses (ICTV) into the family Secoviridae (order Picornavirales). Currently, the genus Torradovirus harbours, besides the recognised species ToTV and ToMarV, also the tentative species Tomato chocolàte virus (ToChV), Tomato chocolate spot virus (ToChSV, analysed by another research group), and Lettuce necrotic leaf curl virus (LNLCV).

Elucidation of torradovirus genome sequences revealed that their RNA1 contained one open reading frame (ORF) that contains motifs typical for proteins involved in replication, i.e. helicase, protease and RNA-dependent RNA polymerase (RdRp). RNA2, on the other hand, contained two ORFs (RNA2-ORF1 and RNA2-ORF2) that coded for a small (~20 kDa) protein of unknown function, the putative movement protein, and the three coat proteins, respectively.

Considering the economic importance of torradoviruses and their emerging character, attempts were made to develop a diagnostic tool to detect the presence of these viruses. To this end generic PCR primer pairs (Torradovirus-1F/Torradovirus-1R and Torradovirus-2F/Torradovirus-2R) were developed against highly conserved regions in RNA1 and RNA2, respectively. Evaluation of these primer sets revealed that they supported detection of all currently known torradoviruses.

Limited information indicated that members of the genus Torradovirus were transmitted by whiteflies. By a detailed study using varying acquisition access periods and inoculation access periods, it was demonstrated that ToTV, ToMarV and ToChV are all transmitted by three whitefly species, namely Trialeurodes vaporariorum, Trialeurodes abutilonea and Bemisia tabaci. The mode of transmission was determined as semi-persistent, i.e. like viruses that enter and remain in the foregut until being transmitted to another plant host. However, localisation of the viral RNA within the whitefly vector confirmed the presence of virus in the stylets and thereby showed that torradoviruses represent the first spherical viruses transmitted by whiteflies in a semi-persistent and stylet-borne manner.

Mechanisms of Avian Influenza virus transmission between farms: combining data collection and mathematical modelling
Ssematimba, A. - \ 2013
Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Thomas Hagenaars. - S.l. : s.n. - ISBN 9789461734549 - 148
aviaire influenzavirussen - ziekteoverdracht - pluimveehouderij - wiskundige modellen - epidemiologie - diergeneeskunde - nederland - avian influenza viruses - disease transmission - poultry farming - mathematical models - epidemiology - veterinary science - netherlands

The lack of sufficient knowledge on the mechanisms of between-farm spread of livestock diseases hampers the development of much needed effective and fast control strategies. Some of the mechanisms responsible for pathogen spread can be deduced from epidemic tracing reports and literature while others can only be hypothesized from findings of studies on daily farm practices throughout the production round. For outbreaks without known/traced transmission routes, the concept of ‘neighbourhood’ infection is often adopted. This concept was founded based on the distance-dependence of the transmission risk with geographical proximity to an infectious farm being the key determinant of risk. Mathematical modelling plays an important role in obtaining quantitative insights into the contributions of the different mechanisms to disease spread. This can be by ranking the contributions of the individual transmission routes and/or obtaining a generic distance-dependent transmission risk. The models can guide the design of control strategies by providing a means to assess the efficacy of intervention strategies. In this thesis, modelling was used to assess the contributions of the wind-borne route and the other (traced) between-farm contacts to the transmission of highly pathogenic avian influenza during an epidemic in the Netherlands in 2003. It was found that these two routes together could only explain approximately 31% of the infections/cases. Visits by epidemic control teams were the least risky indicating the effectiveness of their biosecurity protocols in preventing transmission. New data on day-to-day farm practices and farmer opinion was collected in an attempt to generate hypotheses on transmission pathways and mechanisms that were yet to be appreciated. Indeed relevant unappreciated practices were found. They include irregularities in compliance to biosecurity as well as a broad category of neighbourhood-related risks. A new modelling approach to study neighbourhood transmission was developed guided by indirect transmission experiments. It involves the approximation of the pathogen dispersal process by a diffusive transport mechanism. Applying this diffusion model to the outbreak data of 2003, it was found that assuming delayed transmission, as opposed to instantaneous transmission, is an important phenomenon to be considered when modelling disease spread between locations. This modelling approach has the added advantage of availing an opportunity to assess the performance of intervention strategies without detailed mechanism-specific information.

Onderzoeksverslag 'Distributie van Clavibacter michiganensis subsp. michiganensis in tomatenplanten'
Wolf, J.M. van der; Zouwen, P.S. van der; Ludeking, D.J.W. ; Hamelink, R. ; Schenk, M.F. - \ 2012
Wageningen : Wageningen UR/Plant Research International/Wageningen UR Glastuinbouw (Rapport / Plant Research International 448) - 40
epidemiologie - zaadbesmetting - ziektedistributie - clavibacter michiganensis subsp. michiganensis - plantenziekten - plantenziekteverwekkende bacteriën - tomaten - glastuinbouw - infectie - solanum lycopersicum - in zaden overlevende bacteriën - epidemiology - seed contamination - disease distribution - plant diseases - plant pathogenic bacteria - tomatoes - greenhouse horticulture - infection - seedborne bacteria
Van 2009 tot 2011 werden kasproeven uitgevoerd om de kolonisatie van tomatenplanten met Clavibacter michiganensis subsp. michiganensis (Cmm) vanuit besmet zaad en de secundaire verspreiding van Cmm in een gewas te bestuderen.
Insect bite hypersensitivity in horses: genetic and epidemiological analysis
Schurink, A. - \ 2012
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Bart Ducro; Klaas Frankena. - S.l. : s.n. - ISBN 9789461733566 - 168
dierveredeling - overgevoeligheid - paarden - genetische analyse - epidemiologie - insectenbeten - nederland - fries (paardenras) - shetland pony - animal breeding - hypersensitivity - horses - genetic analysis - epidemiology - insect bites - netherlands - frisian (horse breed) - shetland pony

Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by bites of Culicoides spp. IBH reduces welfare of affected horses and at present no effective preventive measure or cure exists. Aim of our research was to increase knowledge of the genetic background of IBH in horse populations and to explore opportunities to reduce IBH prevalence through selection and breeding.

Data on Shetland pony and Friesian horse mares were gathered at obligatory inspections. IBH prevalence was 7.5% in Shetland pony mares and 18.2% in Friesian horse mares. Data were analyzed to identify risk factors. Combined effect of month and year of IBH scoring, region within the Netherlands and inspector were associated with IBH in both breeds. IBH prevalence significantly differed with coat colour and withers height category in Shetland pony mares. Moreover, prevalence was higher in Shetland pony mares with high body condition score (9.4%).

Quantitative genetic analyses revealed substantial genetic variation for IBH in both breeds. Heritability on the observed scale and on the underlying scale was 0.08 and 0.24 respectively in Shetland pony mares, 0.07 and 0.16 respectively in Friesian horse mares. Therefore, IBH is a heritable phenotype in both breeds. Repeatability was 0.30 in Shetland pony mares and 0.89 in Friesian horse mares. Maternal effect (0.17) was estimated in Friesian horse mares only.

To identify genomic regions contributing to the genetic variance, Shetland pony mares and Icelandic horses were selected according to a matched case-control design. Odds ratios of allele substitution effects of the unfavourable allele were between 1.94 and 5.95. Also, 13 and 28% of genetic variance was explained by all SNPs in respectively Shetland pony mares and Icelandic horses. Significant associated genomic regions across breeds suggest interesting candidate regions on ECA3, 7, 11, 20 and 23 contributing to genetic variance. Results support that ELA class II region on ECA20 is involved in IBH etiology, although follow-up studies are needed to confirm this and to identify genes in the other regions.

The general discussion explored possibilities to reduce IBH prevalence through breeding and discussed implications of using clinical symptoms or diagnostic test results. Simulated selection was based on EBV, which included own performance, progeny performance or genomic data. Selection on IBH clinical symptoms should be based on testing at least 10 but preferably more progeny, accompanying strict selection in sires to achieve reasonable genetic gain. Expected genetic gain per year in genomic selection outperformed other strategies, although implementation of genomic selection requires a considerable investment in a reference population. A diagnostic test for IBH (yet unfeasible to perform on a large sample) has the potential to increase genetic gain

Differences in leaf litter, ascospore production and infection of pear scab (Venturia pirina) in Dutch organic orchards
Timmermans, B.G.H. ; Jansonius, P.J. - \ 2012
In: Eco-fruit : 15th international conference on cultivation technique and phytopathological problems in organic fruit-growing and viticulture, 20-22 February 2012, Hohenheim. - Weinsberg : Foerdergemeinschaft Oekologischer Obstbau e.V. - p. 253 - 259.
venturia pyrina - peren - fruitteelt - epidemiologie - plantenziekteverwekkende schimmels - schimmelziekten - plantenziekten - biologische landbouw - analyse - ziektebestrijdende teeltmaatregelen - regen - ascosporen - pears - fruit growing - epidemiology - plant pathogenic fungi - fungal diseases - plant diseases - organic farming - analysis - cultural control - rain - ascospores
In 2010 and 2011 the amounts of leaf litter and ascospore production per unit of leaf litter area in 7 organic pear orchards throughout the Netherlands were measured. In one of the orchards, adapted managements strategies were implemented, being grass/clover that is grown as ground cover on the tree-strip, and organic cattle-manure that replaces chicken manure pellets, in order to stimulate the earthworm population and change the palatability of the leaf litter. First results indicate large differences between orchards in percentage of ground covered by dead leaves at the time of major ascospore infections, but also in number of ascospores per cm2 leaf litter and in resulting potential ascospore dose. These data, together with weather data (temperature, rainfall), were used in a simple multivariate analysis to gain insight in the dynamics of the system. The first results show that, to a limited degree, leaf litter was indeed important for the scab epidemic in 2011, whereas in 2010 the high amount of rainfall in the second part of the growing season must have led to a high conidial infection pressure. Surprisingly, in both years ascospore number per unit leaf area was of more importance than leaf litter area or potential ascospore dose.
Een aanpak om schade door slakken in aardappelen te voorkomen : monitoring van Zuid-Limburgse percelen om in de bodem levende slakken te signaleren en schadelijke populaties vast te stellen voor middelenonderzoek en advisering praktijk (2010-2011)
Rozen, K. van; Huiting, H.F. ; Meuffels, G.J.H.M. ; Wilms, J.A.M. ; Schiffelers, R. ; Crijns, S. - \ 2012
Lelystad : Praktijkonderzoek Plant & Omgeving B.V. - 35
naaktslakken - aardappelen - epidemiologie - arion hortensis - plantenplagen - gewasbescherming - akkerbouw - oogstschade - zuid-limburg - slanke wormnaaktslak - slugs - potatoes - epidemiology - plant pests - plant protection - arable farming - crop damage - boettgerilla pallens
Enkele slakkensoorten zijn verantwoordelijk voor vraatschade in aardappelen. Deze soorten behoren tot de wegslakken en de kielnaaktslakken. Van deze twee groepen slakken zijn in dit onderzoek vrijwel uitsluitend Zwarte wegslakken (Arion hortensis) in vooraf geselecteerde percelen aangetroffen. Dit zijn slakken die met het ingraven van een krop andijvie of kippenvoerprak afgedekt met slakkenmatjes in het najaar goed zijn vast te stellen. Met lokmiddel worden betrouwbaar hogere aantallen onder slakkenmatjes vastgesteld dan zonder lokmiddel. Deze slakken kunnen echter op gunstige momenten vroeg in de ochtend ook prima worden waargenomen. Dit in tegenstelling tot de kielnaaktslakken, die voornamelijk ondergronds actief zijn. Met de vallen zijn nauwelijks kielnaaktslakken aangetroffen, op de betreffende percelen werden deze slakken ook niet tijdens het doorzoeken van de grond waargenomen. Daarentegen werd een soort uit een andere groep in de bodem vastgesteld die niet eerder met vraatschade in de Nederlandse aardappelproductiepercelen in verband werd gebracht; de Slanke wormnaaktslak. Het doorzoeken van de grond leverde de hoogste aantallen op, met de geteste vallen zijn daarentegen in totaal maar twee wormnaaktslakken in de bodem vastgesteld. In het veld en in het lab werd vraatschade aan aardappelen door deze slakkensoort waargenomen. Of deze slakkensoort een bedreiging vormt voor de aardappelteelt is niet bekend. Dit onderzoek geeft aan dat het slakkenprobleem in aardappelen een sterk incidenteel karakter heeft. De uitdaging is om die percelen uit te selecteren waar slakkenschade in aardappelen tot afkeuring of prijskorting leidt, met als gevolg een financiële strop voor de individuele teler. In het proefveldonderzoek naar middelen ter bestrijding van ondergronds levende slakken werden zeer lage aantallen slakken waargenomen, dit leidde nauwelijks tot aangevreten knollen. Over de effectiviteit van de middelen kon hierdoor geen indicatie worden afgegeven.
CHIP: Commodity based Hazard Identification Protocol for emerging diseases in plants and animals
Bremmer, J. ; Swanenburg, M. ; Galen, M.A. van; Hoek, Maarten ; Rau, M.L. ; Hennen, W.H.G.J. ; Benninga, J. ; Ge, L. ; Breukers, M.L.H. - \ 2012
Wageningen : LEI Wageningen UR / EFSA (Supporting publications 2012 EN-327)
risicoschatting - risicoanalyse - plantenziekten - dierziekten - epidemiologie - gewasbescherming - diergezondheid - beslissingsmodellen - risk assessment - risk analysis - plant diseases - animal diseases - epidemiology - plant protection - animal health - decision models
This project comprised the development of a commodity-based hazard identification protocol for biological hazards in plants and animals as a decision support tree programmed in Excel. The content of the decision tree is based on the results of a systematic review of pest and pathogen characteristics, a review of risk assessment schemes and on expert judgement. Application of the protocol results in an indication of the level of likelihood of entry of animal and plant pathogens/pests in the area of destination associated with the commodity/pathway, and it guides the decision regarding potential actions to be undertaken in the search for existing and emerging pathogens/pests.
The relation between farming practices, ecosystem, and white spot in syndrome virus (WSSV) disease outbreaks in penaeus monodon farms in the Philippines
Tendencia Alapide, E. - \ 2012
Wageningen University. Promotor(en): Johan Verreth, co-promotor(en): Roel Bosma; J.H. Primavera. - S.l. : s.n. - ISBN 9789461733702 - 135
garnalen - witte-vlekken-syndroom-virus - garnalenteelt - uitbraken (ziekten) - epidemiologie - infectieziekten - dierziektepreventie - aquatische ecosystemen - fysicochemische eigenschappen - mangroves - filippijnen - shrimps - white spot syndrome virus - shrimp culture - outbreaks - epidemiology - infectious diseases - animal disease prevention - aquatic ecosystems - physicochemical properties - mangroves - philippines

The white spot syndrome virus (WSSV) affecting shrimp aquaculture in most producing countries has caused huge economic losses resulting in bankruptcy to both large and small farmers. Studies done on WSSV epidemiology were mostly tank-based and on species other than Penaeus monodon. There is a need to investigate WSSV epidemiology in P. monodon in on-farm situations, thus including both risk and protective factors. This thesis aimed to generate knowledge that can improve prevention against WSSV in shrimp culture through better farm husbandry by studying the epidemiology of WSSV in on-farm situations. To achieve this goal data from cross-sectional and case studies were analysed to identify on-farm WSSV risk and protective factors, and longitudinal studies were done to assess factors affecting water quality and causing WSSV infection to result in an outbreak.

The thesis identified the following WSSV risk factors related to the physico-chemical parameters of the water: low and fluctuating temperature, low and fluctuating salinity, and pH fluctuation. The risk of high temperature and high salinity for an outbreak of WSV disease may be related to fluctuations in these two parameters. Risk factors related to farm husbandry techniques were feeding with molluscs, sludge removal and its deposition on the dike, sharing water source with other farms and having the same receiving and intake water. Identified WSSV protective factors were high mangrove to pond area ratio, feeding with natural food or phytoplankton, and higher percentage of beneficial bacteria like the yellow colonies that grow on thiosulphate citrate bilesalt sucrose agar, a Vibrio selective medium.

Results of the longitudinal studies demonstrated that WSSV infection may not result in outbreaks in greenwater pond and in ponds with mangroves in the receiving environment. Our results did not provide explanations why the WSSV infection did not result in an outbreak in farms with mangroves in the receiving environment. In greenwater ponds, this was attributed to the better water and soil quality, higher plankton count, and higher heterotrophic bacterial count.

Interactie tussen diverse aaltjessoorten en verticillium in suikerbieten
Pepping, M. ; Raaijmakers, E. ; Hanse, B. ; Beers, T.G. van; Molendijk, L.P.G. - \ 2012
Kennisakker.nl 2012 (2012)2 juli.
suikerbieten - plantenparasitaire nematoden - verticillium dahliae - plantenziekten - oogstschade - aantasting - epidemiologie - gewasbescherming - akkerbouw - rasverschillen - sugarbeet - plant parasitic nematodes - plant diseases - crop damage - infestation - epidemiology - plant protection - arable farming - breed differences
Schade door verticillium wordt bevorderd door aaltjes, is de conclusie. Hoe meer aaltjes, hoe meer aantasting er zichtbaar was. Dit gold bij het voor verticillium gevoelige ras voor alle vier de aaltjessoorten (witte bietencysteaaltjes, gele bietencysteaaltjes, noordelijk wortelknobbelaaltjes en wortellesieaaltjes) en bij het tolerante ras alleen niet voor wortellesieaaltjes. Telers kunnen aantasting door verticillium reduceren door de hoeveelheden plantparasitaire aaltjes zo laag mogelijk te houden.
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