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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Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals : a systematic review
Köck, R. ; Daniels-Haardt, I. ; Becker, K. ; Mellmann, A. ; Friedrich, A.W. ; Mevius, D. ; Schwarz, S. ; Jurke, A. - \ 2018
Clinical Microbiology and Infection (2018). - ISSN 1198-743X
Antibiotic resistance - Carbapenemase - Enterobacteriales - Epidemiology - Livestock - Zoonosis
Objectives: The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans. Methods: We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities. Results: We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33–67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2–26% in Africa, and 1–15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16–19%. Conclusions: The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.
Intake of dietary saturated fatty acids and risk of type 2 diabetes in the European Prospective Investigation into Cancer and Nutrition-Netherlands cohort : associations by types, sources of fatty acids and substitution by macronutrients
Liu, Shengxin ; Schouw, Yvonne T. van der; Soedamah-Muthu, Sabita S. ; Spijkerman, Annemieke M.W. ; Sluijs, Ivonne - \ 2018
European Journal of Nutrition (2018). - ISSN 1436-6207 - p. 1 - 12.
Cohort study - Epidemiology - Nutrition - Saturated fatty acids - Type 2 diabetes
Purpose: The association between dietary saturated fatty acids (SFA) intake and type 2 diabetes (T2D) remains unclear. This study aimed at investigating the association between SFA intake and T2D risk based on (1) individual SFA (differing in carbon chain length), (2) food sources of SFA and (3) the substituting macronutrients. Methods: 37,421 participants from the European Prospective Investigation into Cancer and Nutrition-Netherlands (EPIC-NL) cohort were included in this study. Baseline dietary intake was assessed by a validated food frequency questionnaire. T2D risks were estimated by Cox regression models adjusted for non-dietary and dietary covariates. Results: 893 incident T2D cases were documented during 10.1-year follow-up. We observed no association between total SFA and T2D risk. Marginally inverse associations were found for lauric acid (HR per 1 SD of energy%, 95% CI 0.92, 0.85–0.99), myristic acid (0.89, 0.79–0.99), margaric acid (0.84, 0.73–0.97), odd-chain SFA (pentadecylic plus margaric acids; 0.88, 0.79–0.99), and cheese derived SFA (0.90, 0.83–0.98). Soft and liquid fats derived SFA was found related to higher T2D risk (1.08, 1.01–1.17). When substituting SFA by proteins, carbohydrates and polyunsaturated fatty acids, significantly higher risks of T2D were observed (HRs per 1 energy% ranging from 1.05 to 1.15). Conclusion: In this Dutch population, total SFA does not relate to T2D risk. Rather, the association may depend on the types and food sources of SFA. Cheese-derived SFA and individual SFA that are commonly found in cheese, were significantly related to lower T2D risks. We cannot exclude the higher T2D risks found for soft and liquid fats derived SFA and for substituting SFA with other macronutrients are influenced by residual confounding by trans fatty acids or limited intake variation in polyunsaturated fatty acids and vegetable protein.
Diet quality in childhood : the Generation R Study
Velde, Laura A. van der; Nguyen, Anh N. ; Schoufour, Josje D. ; Geelen, Anouk ; Jaddoe, Vincent W.V. ; Franco, Oscar H. ; Voortman, Trudy - \ 2018
European Journal of Nutrition (2018). - ISSN 1436-6207 - p. 1 - 11.
Determinants - Diet quality - Dietary patterns - Epidemiology - Tracking - Validation
Purpose: We aimed to evaluate diet quality of 8-year-old children in the Netherlands, to identify sociodemographic and lifestyle correlates of child diet quality, and to examine tracking of diet quality from early to mid-childhood. Methods: For 4733 children participating in a population-based cohort, we assessed dietary intake using a validated food-frequency questionnaire at a median age of 8.1 years (interquartile range 8.0–8.2) (2011–2014). Based on dietary guidelines, we developed and validated a food-based diet quality score for children consisting of ten components (score 0–10): sufficient intake of vegetables; fruit; whole grains; fish; legumes; nuts; dairy; oils and soft fats; and low intake of sugar-containing-beverages; and high-fat and processed meat. Results: We observed a mean (± SD) diet quality score of 4.5 (± 1.2) out of a maximum of 10. On average, intake of legumes, nuts, and oils or soft fats was below recommendations, whereas intake of sugar-containing beverages and high-fat or processed meat was higher than recommended. The main factors associated with higher diet quality were higher maternal educational level (β = 0.29, 95% CI 0.21, 0.37 versus low education), higher household income (β = 0.15, 95% CI 0.05, 0.25 versus low income), no maternal smoking (β = 0.13, 95% CI 0.02, 0.25 versus current smoking), and less screen time (β = 0.31, 95% CI 0.24, 0.38)—all independent of each other. For children with available dietary data at age 1 year (n = 2608), we observed only weak tracking of diet quality from early to mid-childhood (Pearson’s r = 0.19, k = 0.11 for extreme quartiles). Conclusion: Overall diet quality of 8-year-old children did not conform to dietary guidelines, especially for children having more screen time, children of lower educated or smoking mothers, or from lower-income households.
R0: Host Longevity Matters
Viljoen, L.M. ; Hemerik, L. ; Molenaar, J. - \ 2018
Acta Biotheoretica 66 (2018)1. - ISSN 0001-5342 - p. 1 - 16.
Duration of infection - Epidemiology - Fitness strategy - Host longevity - milker–killer dilemma - R
The basic reproduction ratio, R0, is a fundamental concept in epidemiology. It is defined as the total number of secondary infections brought on by a single primary infection, in a totally susceptible population. The value of R0 indicates whether a starting epidemic reaches a considerable part of the population and causes a lot of damage, or whether it remains restricted to a relatively small number of individuals. To calculate R0 one has to evaluate an integral that ranges over the duration of the infection of the host. This duration is, of course, limited by remaining host longevity. So, R0 depends on remaining host longevity and in this paper we show that for long-lived hosts this aspect may not be ignored for long-lasting infections. We investigate in particular how this epidemiological measure of pathogen fitness depends on host longevity. For our analyses we adopt and combine a generic within- and between-host model from the literature. To find the optimal strategy for a pathogen from an evolutionary point of view, we focus on the indicator (Formula presented.), i.e., the optimum of R0 as a function of its replication and mutation rates. These are the within-host parameters that the pathogen has at its disposal to optimize its strategy. We show that (Formula presented.) is highly influenced by remaining host longevity in combination with the contact rate between hosts in a susceptible population. In addition, these two parameters determine whether a killer-like or a milker-like strategy is optimal for a given pathogen. In the killer-like strategy the pathogen has a high rate of reproduction within the host in a short time span causing a relatively short disease, whereas in the milker-like strategy the pathogen multiplies relatively slowly, producing a continuous small amount of offspring over time with a small effect on host health. The present research allows for the determination of a bifurcation line in the plane of host longevity versus contact rate that forms the boundary between the milker-like and killer-like regions. This plot shows that for short remaining host longevities the killer-like strategy is optimal, whereas for very long remaining host longevities the milker-like strategy is advantageous. For in-between values of host longevity, the contact rate determines which of both strategies is optimal.
Informal value chain actors’ knowledge and perceptions about zoonotic diseases and biosecurity in Kenya and the importance for food safety and public health
Nyokabi, Simon ; Birner, Regina ; Bett, Bernard ; Isuyi, Linda ; Grace, Delia ; Güttler, Denise ; Lindahl, Johanna - \ 2018
Tropical Animal Health and Production 50 (2018)3. - ISSN 0049-4747 - p. 509 - 518.
Biosecurity measures - Disease prevention - Disease transmission - Epidemiology - Infectious disease - Livestock value chains - Veterinary public health - Zoonoses
Zoonotic diseases, transmitted from animals to humans, are a public health challenge in developing countries. Livestock value chain actors have an important role to play as the first line of defence in safeguarding public health. However, although the livelihood and economic impacts of zoonoses are widely known, adoption of biosecurity measures aimed at preventing zoonoses is low, particularly among actors in informal livestock value chains in low and middle-income countries. The main objective of this study was to investigate knowledge of zoonoses and adoption of biosecurity measures by livestock and milk value chain actors in Bura, Tana River County, in Kenya, where cattle, camels, sheep and goats are the main livestock kept. The study utilised a mixed methods approach, with a questionnaire survey administered to 154 value chain actors. Additional information was elicited through key informant interviews and participatory methods with relevant stakeholders outside the value chain. Our results found low levels of knowledge of zoonoses and low levels of adherence to food safety standards, with only 37% of milk traders knowing about brucellosis, in spite of a sero-prevalence of 9% in the small ruminants tested in this study, and no slaughterhouse worker knew about Q fever. Actors had little formal education (between 0 and 10%) and lacked training in food safety and biosecurity measures. Adoption of biosecurity measures by value chain actors was very low or non-existent, with only 11% of butchers wearing gloves. There was a gendered dimension, evidenced by markedly different participation in value chains and lower adoption rates and knowledge levels among female actors. Finally, cultural and religious practices were shown to play an important role in exposure and transmission of diseases, influencing perceptions and attitudes to risks and adoption of biosecurity measures.
High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses
Barry, A.F. ; Durães-Carvalho, R. ; Oliveira-Filho, Edmilson F. ; Alfieri, A. ; Poel, W.H.M. Van der - \ 2017
Infection, genetics and evolution 56 (2017). - ISSN 1567-1348 - p. 8 - 13.
Epidemiology - Phylogeny - Sapoviruses - Taxonomy - Zoonoses
The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses showed an increase in porcine SaV (PoSaV) population dynamics and genetic diversity between 1975 and 1982, resulting in a SaV gene flow and generation of new strains among porcine and human populations. Our results also show the contribution of different animal populations involved in SaV epidemiology and highlight zoonotic aspects, as exemplified by the crucial role that swine, dogs, mink and humans play in SaV spread. Additionally, phylogenetic analysis suggests that bats may play key role in SaV epidemiology. According to our hypothesis, these animals may act as reservoirs or intermediate host species, contributing to viral spread in zoonotic and other epidemiological scenarios and facilitating the generation of new SaV genogroups and genotypes through recombination events. Data from large-scale phylogeny partition based on patristic distance, did not show a correlation between transmission clusters on generation of SaV genogroups, nevertheless we present both important findings about SaV taxonomy and important considerations useful for further taxonomical studies.
Peste des Petits Ruminants (PPR) in Pakistan : Analysis of a national level serological data
Abubakar, Muhammad ; Zahur, Aamir Bin ; Afzal, Muhammad ; Ali, Qurban ; Gonzales Rojas, Jose - \ 2017
Small Ruminant Research 155 (2017). - ISSN 0921-4488 - p. 57 - 65.
Epidemiology - Pakistan - PPR - Serological data - Sheep and goats

The study was aimed to obtain baseline information about the presence and distribution of Peste des petits ruminants (PPR) in Pakistan by quantifying the sero-prevalence of this infection in all provinces/regions in the country. There are ongoing activities towards the progressive control and eventual eradication of PPR from Pakistan. To design a suitable control program and monitor its progress, baseline information on the occurrence of the disease in the target population is needed. Using a cluster sampling approach a total of 19575 serum samples from sheep and goat were collected from all provinces of the country. These samples were analyzed for the presence of antibodies against PPR virus using a competitive ELISA. Out of 19575 samples tested, 5389 were classified as sero-positive. The prevalence (95% confidence intervals (CI)) at the province level ranged 9.93% (0.027%–0.151%) in Azad Jammu & Kashmir to 38.16% (0.366%–0.466%) in Balochistan. Difference in sero-positivity could be attributed to animals’ movement, agro-climatic conditions of areas. Risk factors covered in the study were season as well as age and sex of the animals. PPR is endemic and it is distributed across all provinces in the country. This study provides basic information for the identification of disease hotspots for implementation of a control programme in Pakistan.

Campylobacter epidemiology-sources and routes of transmission for human infection
Newell, Diane G. ; Mughini-Gras, Lapo ; Kalupahana, R.S. ; Wagenaar, Jaap A. - \ 2017
In: Campylobacter: Features, Detection, and Prevention of Foodborne Disease / Klein, Günter, Elsevier Inc. Academic Press - ISBN 9780128036235 - p. 85 - 110.
Campylobacter - Environment - Epidemiology - Outbreak - Reservoir - Source attribution - Subtyping - Transmission route

The identification of the sources and routes of transmission of Campylobacter jejuni/coli is essential to the prevention and control of human campylobacteriosis. However, this has proved a significant challenge over the past 35 years because these organisms were so unlike other enteric bacteria, especially Escherichia coli and Salmonella spp. Our current understanding of Campylobacter epidemiology is derived from a range of approaches, including epidemiological studies, and microbiological subtyping. These approaches indicate that poultry is the primary reservoir for campylobacters causing human disease. However, although campylobacteriosis is generally considered a foodborne disease primarily acquired through the handling and consumption of poultry meat, discrepancies between source attribution data from case-control studies and those based on subtyping strongly suggest that transmission routes through environmental exposure may be as, if not more, important.

An increase in physical activity after colorectal cancer surgery is associated with improved recovery of physical functioning : A prospective cohort study
Zutphen, Moniek van; Winkels, Renate M. ; Duijnhoven, Fränzel J.B. van; Harten-Gerritsen, Suzanne A. van; Gils-Kok, Dieuwertje van; Duijvendijk, Peter van; Halteren, Henk K. van; Hansson, Bibi M.E. ; Kruyt, Flip M. ; Spillenaar Bilgen, Ernst J. ; Wilt, Johannes H.W. de; Dronkers, Jaap J. ; Kampman, Ellen - \ 2017
BMC Cancer 17 (2017)1. - ISSN 1471-2407
Colorectal cancer - Colorectal surgery - Epidemiology - Physical activity - Recovery of function - Rehabilitation
Background: The influence of physical activity on patient-reported recovery of physical functioning after colorectal cancer (CRC) surgery is unknown. Therefore, we studied recovery of physical functioning after hospital discharge by (a) a relative increase in physical activity level and (b) absolute activity levels before and after surgery. Methods: We included 327 incident CRC patients (stages I-III) from a prospective observational study. Patients completed questionnaires that assessed physical functioning and moderate-to-vigorous physical activity shortly after diagnosis and 6 months later. Cox regression models were used to calculate prevalence ratios (PRs) of no recovery of physical functioning. All PRs were adjusted for age, sex, physical functioning before surgery, stage of disease, ostomy and body mass index. Results: At 6 months post-diagnosis 54% of CRC patients had not recovered to pre-operative physical functioning. Patients who increased their activity by at least 60 min/week were 43% more likely to recover physical function (adjusted PR 0.57 95%CI 0.39-0.82), compared with those with stable activity levels. Higher post-surgery levels of physical activity were also positively associated with recovery (P for trend = 0.01). In contrast, activity level before surgery was not associated with recovery (P for trend = 0.24). Conclusions: At 6 month post-diagnosis, about half of CRC patients had not recovered to preoperative functioning. An increase in moderate-to-vigorous physical activity after CRC surgery was associated with enhanced recovery of physical functioning. This benefit was seen regardless of physical activity level before surgery. These associations provide evidence to further explore connections between physical activity and recovery from CRC surgery after discharge from the hospital.
Mutations in the haemagglutinin protein and their effect in transmission of highly pathogenic avian influenza (HPAI) H5N1 virus in sub-optimally vaccinated chickens
Sitaras, Ioannis ; Rousou, Xanthoula ; Peeters, Ben ; Jong, Mart C.M. de - \ 2016
Vaccine 34 (2016)46. - ISSN 0264-410X - p. 5512 - 5518.
Epidemiology - H5N1 - HA - Influenza - Mutations - Transmission - Vaccination

Background Transmission of highly pathogenic avian influenza (HPAI) viruses in poultry flocks is associated with huge economic losses, culling of millions of birds, as well as human infections and deaths. In the cases where vaccination against avian influenza is used as a control measure, it has been found to be ineffective in preventing transmission of field strains. Reports suggest that one of the reasons for this is the use of vaccine doses much lower than the ones recommended by the manufacturer, resulting in very low levels of immunity. In a previous study, we selected for immune escape mutants using homologous polyclonal sera and used them as vaccines in transmission experiments. We concluded that provided a threshold of immunity is reached, antigenic distance between vaccine and challenge strains due to selection need not result in vaccine escape. Here, we evaluate the effect that the mutations in the haemagglutinin protein of our most antigenically-distant mutant may have in the transmission efficiency of this mutant to chickens vaccinated against the parent strain, under sub-optimal vaccination conditions resembling those often found in the field. Methods In this study we employed reverse genetics techniques and transmission experiments to examine if the HA mutations of our most antigenically-distant mutant affect its efficiency to transmit to vaccinated chickens. In addition, we simulated sub-optimal vaccination conditions in the field, by using a very low vaccine dose. Results We find that the mutations in the HA protein of our most antigenically-distant mutant are not enough to allow it to evade even low levels of vaccination-induced immunity. Discussion Our results suggest that – for the antigenic distances we investigated – vaccination can reduce transmission of an antigenically-distant strain compared to the unvaccinated groups, even when low vaccine doses are used, resulting in low levels of immunity.

Natural and human induced factors influencing the abundance of Schistosoma host snails in Zambia
Monde, Concillia ; Syampungani, Stephen ; Brink, Paul J. van den - \ 2016
Environmental Monitoring and Assessment 188 (2016)6. - ISSN 0167-6369
Epidemiology - Host snails - Malacological - Schistosomiasis

Schistosomiasis remains a global public health problem affecting about 240 million people. In Zambia, 2 million are infected while 3 million live with the risk of getting infected. Research and interventions relating to schistosomiasis are mainly linked to disease epidemiology. Malacological and ecological aspects of the disease are superficially understood. Developing effective control measures requires an understanding of interacting environmental and socioeconomic factors of host snails vis-a-vis schistosomiasis. Therefore, the present work involved collecting social and environmental data in a large field study in two zones in Zambia that are different in terms of temperature and rainfall amounts. Social data collected through questionnaires included demographic, educational and knowledge of schistosomiasis disease dynamics. Environmental data included physicochemical factors, aquatic plants and snails. Gender (P <0.001) significantly influences livelihood strategies, while age (P = 0.069) and level of education (P = 0.086) have a moderate influence in zone I. In zone III, none of these factors (age, P = 0.378; gender, P = 0.311; education, P = 0.553) play a significant role. Environmental parameters explained 43 and 41 % variation in species composition for zones I and III, respectively. Most respondents’ (52 %, 87 %) perception is that there are more cases of bilharzia in hot season than in other seasons (rainy season 23 %, 7 %; cold season 8 %, 0 % and year round 17 %, 6 %) for zone I and zone III, respectively.

Co-housing of Rift Valley fever virus infected lambs with immunocompetent or immunosuppressed lambs does not result in virus transmission
Wichgers Schreur, Paul J. ; Keulen, Lucien Van; Kant, Jet ; Oreshkova, Nadia ; Moormann, Rob J.M. ; Kortekaas, Jeroen - \ 2016
Frontiers in Microbiology 7 (2016). - ISSN 1664-302X
Contact-exposure - Epidemiology - Horizontal transmission - Rift Valley fever virus - Risk assessment - Transmission

Rift Valley fever virus (RVFV) is transmitted among susceptible animals by mosquito vectors. Although the virus can be isolated from nasal and oral swabs of infected animals and is known to be highly infectious when administered experimentally via oral or respiratory route, horizontal transmission of the virus is only sporadically reported in literature. We considered that immunosuppression resulting from stressful conditions in the field may increase the susceptibility to horizontally transmitted RVFV. Additionally, we reasoned that horizontal transmission may induce immune responses that could affect the susceptibility of contact-exposed animals to subsequent infection via mosquito vectors. To address these two hypotheses, viremic lambs were brought into contact with sentinel lambs. One group of sentinel lambs was treated with the immunosuppressive synthetic glucocorticosteroid dexamethasone and monitored for signs of disease and presence of virus in the blood and target organs. Another group of contact-exposed sentinel lambs remained untreated for three weeks and was subsequently challenged with RVFV. We found that none of the dexamethasone-treated contact-exposed lambs developed detectable viremia, antibody responses or significant increases in cytokine mRNA levels. Susceptibility of immunocompetent lambs to RVFV infection was not influenced by previous contact-exposure. Our results are discussed in light of previous findings.

Decision-making for foot-and-mouth disease control : Objectives matter
Probert, William J.M. ; Shea, Katriona ; Fonnesbeck, Christopher J. ; Runge, Michael C. ; Carpenter, Tim E. ; Dürr, Salome ; Garner, M.G. ; Harvey, Neil ; Stevenson, Mark A. ; Webb, Colleen T. ; Werkman, Marleen ; Tildesley, Michael J. ; Ferrari, Matthew J. - \ 2016
Epidemics 15 (2016). - ISSN 1755-4365 - p. 10 - 19.
Decision making - Epidemiology - Foot-and-mouth disease - Management - Objectives - Optimisation

Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.

Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi
Murithi, H.M. ; Beed, F. ; Tukamuhabwa, P. ; Thomma, B.P.H.J. ; Joosten, M.H.A.J. - \ 2016
Plant Pathology 65 (2016)2. - ISSN 0032-0862 - p. 176 - 188.
Control - Epidemiology - Genetic composition - Pathogenicity - Soybean demand - Virulence

Soybean is a major source of oil and proteins worldwide. The demand for soybean has increased in Africa, driven by the growing feed industry for poultry, aquaculture and home consumption in the form of processed milk, baked beans and for blending with maize and wheat flour. Soybean, in addition to being a major source of cooking oil, is also used in other industrial processes such as in the production of paints and candle wax. The demand for soybean in Africa so far outweighs the supply, hence the deficit is mainly covered through imports of soybean products such as soybean meal. The area under soybean production has increased in response to the growing demand, a trend that is expected to continue in the coming years. As the production area increases, diseases and insect pests, declining soil fertility and other abiotic factors pose a major challenge. Soybean rust disease, caused by the fungus Phakopsora pachyrhizi, presents one of the major threats to soybean production in Africa due to its rapid spread as a result of the ease by which its spores are dispersed by the wind. Disease control by introducing resistant soybean varieties has been difficult due to the presence of different populations of the fungus that vary in pathogenicity, virulence and genetic composition. Improved understanding of the dynamics of rust ecology, epidemiology and population genetics will enhance the effectiveness of targeted interventions that, in turn, will safeguard soybean productivity.

Efficacy of antibiotic treatment and test-based culling strategies for eradicating brucellosis in commercial swine herds
Dieste-Pérez, L. ; Frankena, K. ; Blasco, J.M. ; Muñoz, P.M. ; Jong, M.C.M. de - \ 2016
Preventive Veterinary Medicine 126 (2016). - ISSN 0167-5877 - p. 105 - 110.
Antibiotherapy - Brucella suis - Epidemiology - Eradication - Pigs - Reproduction ratio

Swine brucellosis caused by Brucella suis biovar 2 is an emerging disease in continental Europe. Without effective vaccines being available, the European Food Safety Authority (EFSA) recommends the full depopulation of infected herds as the only strategy to eradicate B. suis outbreaks. Using data collected from 8 herds suffering natural swine brucellosis outbreaks, we assessed the efficacy of four control strategies: (i) oxytetracycline treatment only, as a default scenario, (ii) oxytetracycline treatment combined with skin testing and removal of positive animals, (iii) oxytetracycline treatment combined with serological testing (Rose Bengal test-RBT-and indirect ELISA -iELISA-) and removal of seropositive animals and (iv) oxytetracycline treatment combined with both serological (RBT/iELISA) and skin testing and removal of positive animals. A Susceptible-Infectious-Removal model was used to estimate the reproduction ratio (R) for each strategy. According to this model, the oxytetracycline treatment alone was not effective enough to eradicate the infection. However, this antibiotic treatment combined with diagnostic testing at 4-monthly intervals plus immediate removal of positive animals showed to be effective to eradicate brucellosis independent of the diagnostic test strategy used in an acceptable time interval (1-2 years), depending on the initial number of infected animals.

Carriage of extended-spectrum β-lactamases in pig farmers is associated with occurrence in pigs
Dohmen, W. ; Bonten, M.J.M. ; Bos, M.E.H. ; Marm, S. van; Scharringa, J. ; Wagenaar, J.A. ; Heederik, D.J.J. - \ 2015
Clinical Microbiology and Infection 21 (2015)10. - ISSN 1198-743X - p. 917 - 923.
Animal reservoirs - Animals - Antimicrobial resistance - CTX-M - Epidemiology - Escherichia coli - Zoonosis

Livestock may serve as a reservoir for extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE). The objectives of this study were to determine the prevalence of carriage with ESBL-PE in pig farmers, family members and employees, and its association with carriage in pigs. Rectal swabs were taken from 2388 pigs (398 pooled samples) on 40 pig farms and faecal samples were obtained from 142 humans living or working on 34 of these farms. Presence of ESBL-PE was determined by selective plating (agar). ESBL genes were analysed by PCR or microarray analysis, and gene sequencing. Genotypes and plasmids were determined by multilocus sequence typing and PCR-based replicon typing for selected isolates. ESBL genes were detected in Escherichia coli from eight humans (6%) (blaCTX-M-1, n = 6; blaTEM-52, n = 1 and blaCTX-M-14, n = 1) on six farms. In 157 pig isolates (107 pooled samples) on 18 farms (45%) ESBL genes were detected (blaCTX-M-1, n = 12; blaTEM-52, n = 6; and blaCTX-M-14, n = 3). Human and pig isolates within the same farm harboured similar ESBL gene types and had identical sequence and plasmid types on two farms (e.g. E. coli ST-453, blaCTX-M-1, IncI1), suggesting clonal transmission. For the remaining farms, sequence types, but not plasmid types, differed. Human ESBL carriage was associated with average number of hours working on the farm per week (OR = 1.04, 95% CI 1.02-1.06) and presence of ESBLs in pigs (OR = 12.5, 95% CI 1.4-111.7). Daily exposure to pigs carrying ESBL-PE is associated with ESBL carriage in humans.

Mathematical Modelling of Leprosy and Its Control
Blok, D.J. ; Vlas, S.J. de; Fischer, E.A.J. ; Richardus, Jan Hendrik - \ 2015
Advances in Parasitology 87 (2015). - ISSN 0065-308X - p. 33 - 51.
Disease control - Epidemiology - Leprosy - Mathematical modelling

Leprosy or Hansen's disease is an infectious disease caused by the bacterium Mycobacterium leprae. The annual number of new leprosy cases registered worldwide has remained stable over the past years at over 200,000. Early case finding and multidrug therapy have not been able interrupt transmission completely. Elimination requires innovation in control and sustained commitment. Mathematical models can be used to predict the course of leprosy incidence and the effect of intervention strategies. Two compartmental models and one individual-based model have been described in the literature. Both compartmental models investigate the course of leprosy in populations and the long-term impact of control strategies. The individual-based model focusses on transmission within households and the impact of case finding among contacts of new leprosy patients. Major improvement of these models should result from a better understanding of individual differences in exposure to infection and developing leprosy after exposure. Most relevant are contact heterogeneity, heterogeneity in susceptibility and spatial heterogeneity. Furthermore, the existing models have only been applied to a limited number of countries. Parameterization of the models for other areas, in particular those with high incidence, is essential to support current initiatives for the global elimination of leprosy. Many challenges remain in understanding and dealing with leprosy. The support of mathematical models for understanding leprosy epidemiology and supporting policy decision making remains vital.

Torradoviruses
Vlugt, R.A.A. Van Der; Verbeek, Martin ; Dullemans, A.M. ; Wintermantel, W.M. ; Cuellar, W.J. ; Fox, Adrian ; Thompson, J.R. - \ 2015
Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 485 - 512.
Emerging plant virus - Epidemiology - Picornavirales - Secoviridae - Vector transmission - Virus taxonomy

Torradoviruses are an example of a group of recently discovered plant viruses. The first description of Tomato torrado virus, now the type member of the newly established genus Torradovirus within the family Secoviridae, was published in 2007 and was quickly followed by findings of other torradoviruses, initially all on tomato. Their characterization led to the development of tools that allowed recognition of still other torradoviruses, only very recently found on non-tomato crops, which indicates these viruses have a much wider host range and diversity than previously believed. This review describes the characteristics of this newly emerged group of plant viruses. It looks in detail at taxonomic relationships and specific characteristics in their genomes and encoded proteins. Furthermore, it discusses their epidemiology, including host range, semipersistent transmission by whitefly vectors, and impact on diverse cropping systems.

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