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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Improving predictive performance on survival in dairy cattle using an ensemble learning approach
    Heide, E.M.M. van der; Kamphuis, C. ; Veerkamp, R.F. ; Athanasiadis, I.N. ; Azzopardi, G. ; Pelt, M.L. van; Ducro, B.J. - \ 2020
    Computers and Electronics in Agriculture 177 (2020). - ISSN 0168-1699
    Dairy cow - Ensemble - Machine learning - Survival

    Cow survival is a complex trait that combines traits like milk production, fertility, health and environmental factors such as farm management. This complexity makes survival difficult to predict accurately. This is probably the reason why few studies attempted to address this problem and no studies are published that use ensemble methods for this purpose. We explored if we could improve prediction of cow survival to second lactation, when predicted at five different moments in a cow's life, by combining the predictions of multiple (weak) methods in an ensemble method. We tested four ensemble methods: majority voting rule, multiple logistic regression, random forest and naive Bayes. Precision, recall, balanced accuracy, area under the curve (AUC) and gains in proportion of surviving cows in a scenario where the best 50% were selected were used to evaluate the ensemble model performance. We also calculated correlations between the ensemble models and obtained McNemar's test statistics. We compared the performance of the ensemble methods against those of the individual methods. We also tested if there was a difference in performance metrics when continuous (from 0 to 1) and binary (0 or 1) prediction outcomes were used. In general, using continuous prediction output resulted in higher performance metrics than binary ones. AUCs for models ranged from 0.561 to 0.731, with generally increasing performance at moments later in life. Precision, AUC and balanced accuracy values improved significantly for the naive Bayes and multiple logistic regression ensembles in at least one data set, although performance metrics did remain low overall. The multiple logistic regression ensemble method resulted in equal or better precision, AUC, balanced accuracy and proportion of animals surviving on all datasets and was significantly different from the other ensembles in three out of five moments. The random forest ensemble method resulted in the least significant improvement over the individual methods.

    A comparative analysis of human adult testicular cells expressing stem Leydig cell markers in the interstitium, vasculature, and peritubular layer
    Eliveld, Jitske ; Daalen, Saskia K.M. van; Winter-Korver, Cindy M. de; Veen, Fulco van der; Repping, Sjoerd ; Teerds, Katja ; Pelt, Ans M.M. van - \ 2020
    Andrology 8 (2020)5. - ISSN 2047-2919 - p. 1265 - 1276.
    human testis - markers - propagation - stem Leydig cells

    Background: Origin of human adult Leydig cells (ALCs) is not well understood. This might be partly due to limited data available on the identification and location of human precursor and stem Leydig cells (SLCs) which hampers the study on the development of ALCs. Objectives: The aim of the present study was to investigate whether described human (PDGFRα, NGFR) and rodent (NES, PDGFRα, THY1, NR2F2) SLC markers are expressed by a common cell population within human adult testicular interstitial cells in vivo and before and after in vitro propagation. Materials and methods: Immunohistochemical analyses were used to identify localization of human adult testicular interstitial cells expressing described SLC markers. Next, interstitial cells were isolated and cultured. The percentage of cells expressing one or more SLC markers was determined before and after culture using flow cytometry. Results: NR2F2 and PDGFRα were present in peritubular, perivascular, and Leydig cells, while THY1 was expressed in peritubular and perivascular cells. Although NES and NGFR were expressed in endothelial cells, co-localization with PDGFRα was found for both in vitro, although for NGFR only after culture. All marker positive cells were able to undergo propagation in vitro. Discussion: The partly overlap in localization and overlap in expression in human testicular cells indicate that PDGFRα, NR2F2, and THY1 are expressed within the same ALC developmental lineage from SLCs. Based on the in vitro results, this is also true for NES and after in vitro propagation for NGFR. Conclusion: Our results that earlier described SLC markers are expressed in overlapping human interstitial cell population opens up further research strategies aiming for a better insight in the Leydig cell lineage and will be helpful for development of strategies to cure ALC dysfunction.

    Marine stepping‐stones: Connectivity of Mytilus edulis populations between offshore energy installations
    Coolen, Joop W.P. ; Boon, Arjen R. ; Crooijmans, Richard ; Pelt, Hilde Van; Kleissen, Frank ; Gerla, Daan ; Beermann, Jan ; Birchenough, Silvana N.R. ; Becking, Leontine E. ; Luttikhuizen, Pieternella C. - \ 2020
    Molecular Ecology 29 (2020)4. - ISSN 0962-1083 - p. 686 - 703.
    Stepping-stones - Mytilus edulis - particle tracking models - North Sea - connectivity - offshore installations
    Recent papers postulate that epifaunal organisms use artificial structures as stepping-stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the Blue mussel, Mytilus edulis was expected to follow a pattern predicted by particle tracking models (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. eduliswere found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal sub-populations. Fixation coefficient FST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did notshow a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping-stone effect is obviously important for the distribution of M. edulis in the North Sea and it mayinfluence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters. Although we found an indication that FST was lower between connected locations, isolation by distance analysis showed noincrease in isolation with increasing distance. Finally, we did not find clear structure among the populations.
    Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household
    Bunt, G. van den; Fluit, A.C. ; Spaninks, M.P. ; Timmerman, A.J. ; Geurts, Y. ; Kant, A. ; Scharringa, J. ; Mevius, D. ; Wagenaar, J.A. ; Bonten, M.J.M. ; Pelt, W. van; Hordijk, J. - \ 2020
    Journal of Antimicrobial Chemotherapy 75 (2020)2. - ISSN 0305-7453 - p. 342 - 350.

    BACKGROUND: ESBL-producing Enterobacteriaceae (ESBL-E) are observed in many reservoirs. Pets might play an important role in the dissemination of ESBL-E to humans since they live closely together. OBJECTIVES: To identify prevalence, risk factors, molecular characteristics, persistence and acquisition of ESBL-E in dogs and cats, and co-carriage in human-pet pairs belonging to the same household. METHODS: In a nationwide study, one person per household was randomly invited to complete a questionnaire and to submit a faecal sample. Dog and cat owners were invited to also submit a faecal sample from their pet. Repeated sampling after 1 and 6 months was performed in a subset. ESBL-E were obtained through selective culture and characterized by WGS. Logistic regression analyses and random forest models were performed to identify risk factors. RESULTS: The prevalence of ESBL-E carriage in these cohorts was 3.8% (95% CI: 2.7%-5.4%) for human participants (n=550), 10.7% (95% CI: 8.3%-13.7%) for dogs (n=555) and 1.4% (95% CI: 0.5%-3.8%) for cats (n=285). Among animals, blaCTX-M-1 was most abundant, followed by blaCTX-M-15. In dogs, persistence of carriage was 57.1% at 1 month and 42.9% at 6 months. Eating raw meat [OR: 8.8, 95% CI: 4.7-16.4; population attributable risk (PAR): 46.5%, 95% CI: 41.3%-49.3%] and dry food (OR: 0.2, 95% CI: 0.1-0.5; PAR: 56.5%, 95% CI: 33.2%-66.6%) were predictors for ESBL-E carriage in dogs. Human-dog co-carriage was demonstrated in five households. Human-cat co-carriage was not observed. CONCLUSIONS: ESBL-E prevalence was higher in dogs than in humans and lowest in cats. The main risk factor for ESBL-E carriage was eating raw meat. Co-carriage in dogs and household members was uncommon.

    Exploration of variance, autocorrelation, and skewness of deviations from lactation curves as resilience indicators for breeding
    Poppe, M. ; Veerkamp, R.F. ; Pelt, M.L. van; Mulder, H.A. - \ 2020
    Journal of Dairy Science 103 (2020)2. - ISSN 0022-0302 - p. 1667 - 1684.
    automatic milking system - dairy cow - milk yield - resilience - variance

    The ability of a cow to cope with environmental disturbances, such as pathogens or heat waves, is called resilience. To improve resilience through breeding, we need resilience indicators, which could be based on the fluctuation patterns in milk yield resulting from disturbances. The aim of this study was to explore 3 traits that describe fluctuations in milk yield as indicators for breeding resilient cows: the variance, autocorrelation, and skewness of the deviations from individual lactation curves. We used daily milk yield records of 198,754 first-parity cows, recorded by automatic milking systems. First, we estimated a lactation curve for each cow using 4 different methods: moving average, moving median, quantile regression, and Wilmink curve. We then calculated the log-transformed variance (LnVar), lag-1 autocorrelation (rauto), and skewness (Skew) of the daily deviations from these curves as resilience indicators. A genetic analysis of the resilience indicators was performed, and genetic correlations between resilience indicators and health, longevity, fertility, metabolic, and production traits were estimated. The heritabilities differed between LnVar (0.20 to 0.24), rauto (0.08 to 0.10), and Skew (0.01 to 0.02), and the genetic correlations among the indicators were weak to moderate. For rauto and Skew, genetic correlations with health, longevity, fertility, and metabolic traits were weak or the opposite of what we expected. Therefore, rauto and Skew have limited value as resilience indicators. However, lower LnVar was genetically associated with better udder health (genetic correlations from −0.22 to −0.32), better longevity (−0.28 to −0.34), less ketosis (−0.27 to −0.33), better fertility (−0.06 to −0.17), higher BCS (−0.29 to −0.40), and greater dry matter intake (−0.53 to −0.66) at the same level of milk yield. These correlations support LnVar as an indicator of resilience. Of all 4 curve-fitting methods, LnVar based on quantile regression systematically had the strongest genetic correlations with health, longevity, and fertility traits. Thus, quantile regression is considered the best curve-fitting method. In conclusion, LnVar based on deviations from a quantile regression curve is a promising resilience indicator that can be used to breed cows that are better at coping with disturbances.

    Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information
    Heide, E.M.M. van der; Veerkamp, R.F. ; Pelt, M.L. van; Kamphuis, C. ; Ducro, B.J. - \ 2020
    Journal of Dairy Science 103 (2020)1. - ISSN 0022-0302 - p. 556 - 571.
    dairy cow - individual prediction - longevity - survival

    Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

    Advances in dairy cattle breeding to improve longevity
    Veerkamp, Roel ; Pelt, Mathijs van - \ 2019
    In: Advances in breeding of dairy cattle / van der Werf, J., Pryce, J., Burleigh Dodds Science Publishing Limited - ISBN 9781786762962 - p. 337 - 354.
    Improving longevity of dairy cows has long been of economic interest. There is also a societal interest in improving longevity and evidence suggests it is an important factor in mitigating greenhouse gases. Longevity is a complex trait to record and to improve genetically, despite considerable genetic variation being present. In most cases the farmer decides to cull a cow, and it is often for a number of reasons. Also, for animal breeders it takes too long for daughters of a bull to be culled before bull selection can take place. This chapter looks at recent advances in dairy cattle breeding to improve longevity. The importance and challenges of phenotype longevity are first explored followed by sections on the genetics of longevity and selection of animals before lifespan is known. Genetic evaluation and selection for longevity are then discussed. The chapter concludes with a case study on breeding of dairy cattle for productive lifespan in the Netherlands.
    Bridging the Think-Do Gap
    Pelt, Blair van - \ 2019
    Primary human testicular PDGFRα+ cells are multipotent and can be differentiated into cells with Leydig cell characteristics in vitro
    Eliveld, J. ; Berg, E.A. van den; Chikhovskaya, J.V. ; Daalen, S.K.M. van; Winter-Korver, C.M. de; Veen, F. van der; Repping, S. ; Teerds, K. ; Pelt, A.M.M. van - \ 2019
    Human Reproduction 34 (2019)9. - ISSN 0268-1161 - p. 1621 - 1631.
    mesenchymal stromal cell - PDGFRα - stem Leydig cell - steroidogenesis - testis

    STUDY QUESTION: Is it possible to differentiate primary human testicular platelet-derived growth factor receptor alpha positive (PDGFRα+) cells into functional Leydig cells? SUMMARY ANSWER: Although human testicular PDGFRα+ cells are multipotent and are capable of differentiating into steroidogenic cells with Leydig cell characteristics, they are not able to produce testosterone after differentiation. WHAT IS KNOWN ALREADY: In rodents, stem Leydig cells (SLCs) that have been identified and isolated using the marker PDGFRα can give rise to adult testosterone-producing Leydig cells after appropriate differentiation in vitro. Although PDGFRα+ cells have also been identified in human testicular tissue, so far there is no evidence that these cells are true human SLCs that can differentiate into functional Leydig cells in vitro or in vivo. STUDY DESIGN, SIZE, DURATION: We isolated testicular cells enriched for interstitial cells from frozen-thawed fragments of testicular tissue from four human donors. Depending on the obtained cell number, PDGFRα+-sorted cells of three to four donors were exposed to differentiation conditions in vitro to stimulate development into adipocytes, osteocytes, chondrocytes or into Leydig cells. We compared their cell characteristics with cells directly after sorting and cells in propagation conditions. To investigate their differentiation potential in vivo, PDGFRα+-sorted cells were transplanted in the testis of 12 luteinizing hormone receptor-knockout (LuRKO) mice of which 6 mice received immunosuppression treatment. An additional six mice did not receive cell transplantation and were used as a control. PARTICIPANTS/MATERIALS, SETTING, METHODS: Human testicular interstitial cells were cultured to Passage 3 and FACS sorted for HLA-A,B,C+/CD34-/PDGFRα+. We examined their mesenchymal stromal cell (MSC) membrane protein expression by FACS analyses. Furthermore, we investigated lineage-specific staining and gene expression after MSC trilineage differentiation. For the differentiation into Leydig cells, PDGFRα+-sorted cells were cultured in either proliferation or differentiation medium for 28 days, after which they were stimulated either with or without hCG, forskolin or dbcAMP for 24 h to examine the increase in gene expression of steroidogenic enzymes using qPCR. In addition, testosterone, androstenedione and progesterone levels were measured in the culture medium. We also transplanted human PDGFRα+-sorted testicular interstitial cells into the testis of LuRKO mice. Serum was collected at several time points after transplantation, and testosterone was measured. Twenty weeks after transplantation testes were collected for histological examination. MAIN RESULTS AND THE ROLE OF CHANCE: From primary cultured human testicular interstitial cells at Passage 3, we could obtain a population of HLA-A,B,C+/CD34-/PDGFRα+ cells by FACS. The sorted cells showed characteristics of MSC and were able to differentiate into adipocytes, chondrocytes and osteocytes. Upon directed differentiation into Leydig cells in vitro, we observed a significant increase in the expression of HSD3B2 and INSL3. After 24 h stimulation with forskolin or dbcAMP, a significantly increased expression of STAR and CYP11A1 was observed. The cells already expressed HSD17B3 and CYP17A1 before differentiation but the expression of these genes were not significantly increased after differentiation and stimulation. Testosterone levels could not be detected in the medium in any of the stimulation conditions, but after stimulation with forskolin or dbcAMP, androstenedione and progesterone were detected in culture medium. After transplantation of the human cells into the testes of LuRKO mice, no significant increase in serum testosterone levels was found compared to the controls. Also, no human cells were identified in the interstitium of mice testes 20 weeks after transplantation.N/A. LIMITATIONS, REASONS FOR CAUTION: This study was performed using tissue from only four donors because of limitations in donor material. Because of the need of sufficient cell numbers, we first propagated cells to passage 3 before FACS of the desired cell population was performed. We cannot rule out this propagation of the cells resulted in loss of stem cell properties. WIDER IMPLICATIONS OF THE FINDINGS: A lot of information on Leydig cell development is obtained from rodent studies, while the knowledge on human Leydig cell development is very limited. Our study shows that human testicular interstitial PDGFRα+ cells have different characteristics compared to rodent testicular PDGFRα+ cells in gene expression levels of steroidogenic enzymes and potential to differentiate in adult Leydig cells under comparable culture conditions. This emphasizes the need for confirming results from rodent studies in the human situation to be able to translate this knowledge to the human conditions, to eventually contribute to improvements of testosterone replacement therapies or establishing alternative cell therapies in the future, potentially based on SLCs. STUDY FUNDING/COMPETING INTEREST(S): This study was funded by Amsterdam UMC, location AMC, Amsterdam, the Netherlands. All authors declare no competing interests.

    Comparing regression, naive Bayes, and random forest methods in the prediction of individual survival to second lactation in Holstein cattle
    Heide, E.M.M. van der; Veerkamp, R.F. ; Pelt, M.L. van; Kamphuis, C. ; Athanasiadis, I. ; Ducro, B.J. - \ 2019
    Journal of Dairy Science 102 (2019)10. - ISSN 0022-0302 - p. 9409 - 9421.
    machine learning - naive Bayes - phenotypic prediction - random forest - regression

    In this study, we compared multiple logistic regression, a linear method, to naive Bayes and random forest, 2 nonlinear machine-learning methods. We used all 3 methods to predict individual survival to second lactation in dairy heifers. The data set used for prediction contained 6,847 heifers born between January 2012 and June 2013, and had known survival outcomes. Each animal had 50 genomic estimated breeding values available at birth and up to 65 phenotypic variables that accumulated over time. Survival was predicted at 5 moments in life: at birth, at 18 mo, at first calving, at 6 wk after first calving, and at 200 d after first calving. The data sets were randomly split into 70% training and 30% testing sets to evaluate model performance for 20-fold validation. The methods were compared for accuracy, sensitivity, specificity, area under the curve (AUC) value, contrasts between groups for the prediction outcomes, and increase in surviving animals in a practical scenario. At birth and 18 mo, all methods had overlapping performance; no method significantly outperformed the other. At first calving, 6 wk after first calving, and 200 d after first calving, random forest and naive Bayes had overlapping performance, and both machine-learning methods outperformed multiple logistic regression. Overall, naive Bayes has the highest average AUC at all decision points up to 200 d after first calving. Random forest had the highest AUC at 200 d after first calving. All methods obtained similar increases in survival in the practical scenario. Despite this, the methods appeared to predict the survival of individual heifers differently. All methods improved over time, but the changes in mean model outcomes for surviving and non-surviving animals differed by method. Furthermore, the correlations of individual predictions between methods ranged from r = 0.417 to r = 0.700; the lowest correlations were at first calving for all methods. In short, all 3 methods were able to predict survival at a population level, because all methods improved survival in a practical scenario. However, depending on the method used, predictions for individual animals were quite different between methods.

    Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes: a population-based modelling study
    Mughini-Gras, Lapo ; Dorado-García, Alejandro ; Duijkeren, Engeline van; Bunt, Gerrita van den; Dierikx, Cindy M. ; Bonten, Marc J.M. ; Bootsma, Martin C.J. ; Schmitt, Heike ; Hald, Tine ; Evers, Eric G. ; Koeijer, Aline de; Pelt, Wilfrid van; Franz, Eelco ; Mevius, Dik J. ; Heederik, Dick J.J. - \ 2019
    The Lancet Planetary Health 3 (2019)8. - ISSN 2542-5196 - p. e357 - e369.

    Background: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC), plasmid-mediated AmpC-producing E coli (pAmpC-EC), and other bacteria are resistant to important β-lactam antibiotics. ESBL-EC and pAmpC-EC are increasingly reported in animals, food, the environment, and community-acquired and health-care-associated human infections. These infections are usually preceded by asymptomatic carriage, for which attributions to animal, food, environmental, and human sources remain unquantified. Methods: In this population-based modelling study, we collected ESBL and pAmpC gene data on the Netherlands population for 2005–17 from published datasets of gene occurrences in E coli isolates from different sources, and from partners of the ESBL Attribution Consortium and the Dutch National Antimicrobial Surveillance System. Using these data, we applied an established source attribution model based on ESBL-EC and pAmpC-EC prevalence and gene data for humans, including high-risk populations (ie, returning travellers, clinical patients, farmers), farm and companion animals, food, surface freshwater, and wild birds, and human exposure data, to quantify the overall and gene-specific attributable sources of community-acquired ESBL-EC and pAmpC-EC intestinal carriage. We also used a simple transmission model to determine the basic reproduction number (R0) in the open community. Findings: We identified 1220 occurrences of ESBL-EC and pAmpC-EC genes in humans, of which 478 were in clinical patients, 454 were from asymptomatic carriers in the open community, 103 were in poultry and pig farmers, and 185 were in people who had travelled out of the region. We also identified 6275 occurrences in non-human sources, including 479 in companion animals, 4026 in farm animals, 66 in wild birds, 1430 from food products, and 274 from surface freshwater. Most community-acquired ESBL-EC and pAmpC-EC carriage was attributed to human-to-human transmission within or between households in the open community (60·1%, 95% credible interval 40·0–73·5), and to secondary transmission from high-risk groups (6·9%, 4·1–9·2). Food accounted for 18·9% (7·0–38·3) of carriage, companion animals for 7·9% (1·4–19·9), farm animals (non-occupational contact) for 3·6% (0·6–9·9), and swimming in freshwater and wild birds (ie, environmental contact) for 2·6% (0·2–8·7). We derived an R0 of 0·63 (95% CI 0·42–0·77) for intracommunity transmission. Interpretation: Although humans are the main source of community-acquired ESBL-EC and pAmpC-EC carriage, the attributable non-human sources underpin the need for longitudinal studies and continuous monitoring, because intracommunity ESBL-EC and pAmpC-EC spread alone is unlikely to be self-maintaining without transmission to and from non-human sources. Funding: 1Health4Food, Dutch Ministry of Economic Affairs, and the EU's Horizon-2020 through One-Health European Joint Programme.

    Attribution of human infections with Shiga toxin-producing Escherichia coli (STEC) to livestock sources and identification of source-specific risk factors, The Netherlands (2010–2014)
    Mughini-Gras, L. ; Pelt, W. van; Voort, M. van der; Heck, M. ; Friesema, I. ; Franz, E. - \ 2018
    Zoonoses and Public Health 65 (2018)1. - ISSN 1863-1959 - p. e8 - e22.
    animal reservoirs - E. coli - risk factors - shiga toxin-producing Escherichia coli - source attribution - transmission routes

    Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of public health concern whose sources and transmission routes are difficult to trace. Using a combined source attribution and case–control analysis, we determined the relative contributions of four putative livestock sources (cattle, small ruminants, pigs, poultry) to human STEC infections and their associated dietary, animal contact, temporal and socio-econo-demographic risk factors in the Netherlands in 2010/2011–2014. Dutch source data were supplemented with those from other European countries with similar STEC epidemiology. Human STEC infections were attributed to sources using both the modified Dutch model (mDM) and the modified Hald model (mHM) supplied with the same O-serotyping data. Cattle accounted for 48.6% (mDM) and 53.1% (mHM) of the 1,183 human cases attributed, followed by small ruminants (mDM: 23.5%; mHM: 25.4%), pigs (mDM: 12.5%; mHM: 5.7%) and poultry (mDM: 2.7%; mHM: 3.1%), whereas the sources of the remaining 12.8% of cases could not be attributed. Of the top five O-serotypes infecting humans, O157, O26, O91 and O103 were mainly attributed to cattle (61%–75%) and O146 to small ruminants (71%–77%). Significant risk factors for human STEC infection as a whole were the consumption of beef, raw/undercooked meat or cured meat/cold cuts. For cattle-attributed STEC infections, specific risk factors were consuming raw meat spreads and beef. Consuming raw/undercooked or minced meat were risk factors for STEC infections attributed to small ruminants. For STEC infections attributed to pigs, only consuming raw/undercooked meat was significant. Consuming minced meat, raw/undercooked meat or cured meat/cold cuts were associated with poultry-attributed STEC infections. Consuming raw vegetables was protective for all STEC infections. We concluded that domestic ruminants account for approximately three-quarters of reported human STEC infections, whereas pigs and poultry play a minor role and that risk factors for human STEC infection vary according to the attributed source.

    Validation of genetic evaluation for longevity with a random regression model
    Pelt, M.L. van; Jong, G. de; Veerkamp, R.F. - \ 2018
    In: World Congress on Genetics Applied to Livestock Production. - - 6 p.
    Preantral follicular atresia occurs mainly through autophagy, while antral follicles degenerate mostly through apoptosis
    Meng, Li ; Jan, Sabrina Z. ; Hamer, Geert ; Pelt, Ans M. van; Stelt, Inge van der; Keijer, Jaap ; Teerds, Katja J. - \ 2018
    Biology of Reproduction 99 (2018)4. - ISSN 0006-3363 - p. 853 - 863.

    There is a general agreement that granulosa cell apoptosis is the cause of antral follicle attrition. Less clear is whether this pathway is also activated in case of preantral follicle degeneration, as several reports mention that the incidence of granulosa cell apoptosis in preantral follicles is negligible. Our objective is therefore to determine which cell-death pathways are involved in preantral and antral follicular degeneration.Atretic preantal and antral follicles were investigated using immunohistochemistry and laser-capture microdissection followed by quantitative real-time reverse transcription polymerase chain reaction. Microtubule-associated light-chain protein 3 (LC3), sequestosome 1 (SQSTM1/P62), Beclin1, autophagy-related protein 7 (ATG7), and cleaved caspase 3 (cCASP3) were used as markers for autophagy and apoptosis, respectively. P62 immunostaining was far less intense in granulosa cells of atretic compared to healthy preantral follicles, while no difference in LC3 and BECLIN1 immunostaining intensity was observed. This difference in P62 immunostaining was not observed in atretic antral follicles. mRNA levels of LC3 and P62 were not different between healthy and atretic (pre)antral follicles. ATG7 immunostaining was observed in granulosa cells of preantral atretic follicles, not in granulosa cells of degenerating antral follicles. The number of cCASP3-positive cells was negligible in preantral atretic follicles, while numerous in atretic antral follicles. Taken together, we conclude that preantral and antral follicular atresia is the result of activation of different cell-death pathways as antral follicular degeneration is initiated by massive granulosa cell apoptosis, while preantral follicular atresia occurs mainly via enhanced granulosa cell autophagy.

    Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis
    Proietti, Silvia ; Caarls, Lotte ; Coolen, Silvia ; Pelt, Johan A. van; Wees, Saskia C.M. van; Pieterse, Corné M.J. - \ 2018
    Plant, Cell & Environment 41 (2018)10. - ISSN 0140-7791 - p. 2342 - 2356.
    Jasmonic acid (JA) regulates plant defenses against necrotrophic pathogens and insect herbivores. Salicylic acid (SA) and abscisic acid (ABA) can antagonize JA‐regulated defenses, thereby modulating pathogen or insect resistance. We performed a genome‐wide association (GWA) study on natural genetic variation in Arabidopsis thaliana for the effect of SA and ABA on the JA pathway. We treated 349 Arabidopsis accessions with methyl JA (MeJA), or a combination of MeJA and either SA or ABA, after which expression of the JA‐responsive marker gene PLANT DEFENSIN1.2 (PDF1.2) was quantified as a readout for GWA analysis. Both hormones antagonized MeJA‐induced PDF1.2 in the majority of the accessions but with a large variation in magnitude. GWA mapping of the SA‐ and ABA‐affected PDF1.2 expression data revealed loci associated with crosstalk. GLYI4 (encoding a glyoxalase) and ARR11 (encoding an Arabidopsis response regulator involved in cytokinin signalling) were confirmed by T‐DNA insertion mutant analysis to affect SA–JA crosstalk and resistance against the necrotroph Botrytis cinerea. In addition, At1g16310 (encoding a cation efflux family protein) was confirmed to affect ABA–JA crosstalk and susceptibility to Mamestra brassicae herbivory. Collectively, this GWA study identified novel players in JA hormone crosstalk with potential roles in the regulation of pathogen or insect resistance.
    Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment : a pooled analysis
    Dorado-Garcia, Alejandro ; Smid, J.H. ; Pelt, Wilfrid Van; Bonten, M.J.M. ; Fluit, A.C. ; Bunt, Gerrita van den; Wagenaar, J.A. ; Hordijk, J. ; Dierikx, C.M. ; Veldman, K.T. ; Koeijer, A.A. de; Dohmen, W. ; Schmitt, H. ; Liakopoulos, A. ; Pacholewicz, Ewa ; Lam, T.J.G.M. ; Velthuis, Annet ; Heuvelink, A. ; Gonggrijp, Maaike ; Duijkeren, E. van; Hoek, A.H.A.M. van; Roda Husman, A.N. de; Blaak, H. ; Havelaar, A.H. ; Mevius, D.J. ; Heederik, D.J.J. - \ 2018
    Journal of Antimicrobial Chemotherapy 73 (2018)2. - ISSN 0305-7453 - p. 339 - 347.
    Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.
    Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.
    Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).
    Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.
    Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.
    High prevalence of intra-familial co-colonization by extended-spectrum cephalosporin resistant Enterobacteriaceae in preschool children and their parents in Dutch households
    Liakopoulos, Apostolos ; Bunt, Gerrita van den; Geurts, Yvon ; Bootsma, Martin C.J. ; Toleman, Mark ; Ceccarelli, Daniela ; Pelt, Wilfrid van; Mevius, Dik J. - \ 2018
    Frontiers in Microbiology 9 (2018)FEB. - ISSN 1664-302X
    Co-carriage - ESBL/AmpC - Escherichia coli - Household - Insertion sequence - Netherlands - Plasmid
    Extended-spectrum cephalosporin-resistant (ESCR) Enterobacteriaceae pose a serious infection control challenge for public health. The emergence of the ESCR phenotype is mostly facilitated by plasmid-mediated horizontal extended-spectrum β-lactamases (ESBLs) and AmpC gene transfer within Enterobacteriaceae. Current data regarding the plasmid contribution to this emergence within the Dutch human population is limited. Hence, the aim of this study was to gain insight into the role of plasmids in the dissemination of ESBL/AmpC genes inside Dutch households with preschool children and precisely delineate co-colonization. In 87 ESCR Enterobacteriaceae from fecal samples of parents and preschool children within 66 Dutch households, genomic localization, plasmid type and insertion sequences linked to ESBL/AmpC genes were determined. Chromosomal location of ESBL/AmpC genes was confirmed when needed. An epidemiologically relevant subset of the isolates based on household co-carriage was assessed by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis for genetic relatedness. The narrow-host range I1a and F plasmids were the major facilitators of ESBL/AmpC-gene dissemination. Interestingly, we documented a relatively high occurrence of chromosomal integration of typically plasmid-encoded ESBL/AmpC-genes. A high diversity of non-epidemic Escherichia coli sequence types (STs) was revealed; the predominant STs belonged to the pandemic lineages of extraintestinal pathogenic E. coli ST131 and ST69. Intra-familiar co-carriage by identical ESCR Enterobacteriaceae was documented in 7 households compared to 14 based on sole gene typing, as previously reported. Co-carriage was more frequent than expected based on pure chance, suggesting clonal transmission between children and parents within the household.
    Samenvatting ESBL-Attributieanalyse (ESBLAT) : Op zoek naar de bronnen van antibioticaresistentie bij de mens
    Mevius, Dik ; Heederik, Dick ; Duijkeren, Engeline ; Veldman, Kees ; Essen, Alieda van; Kant, Arie ; Liakopoulos, Apostolos ; Geurts, Yvon ; Pelt, Wilfrid van; Mughini Gras, Lapo ; Schmitt, Heike ; Dierikx, Cindy ; Hoek, Angela van; Evers, Eric ; Roda Husman, Annemaria de; Blaak, Hetty ; Dissel, Jaap van; Smid, Joost ; Dohmen, Wietske ; Dorado-Garcia, Alejandro ; Havelaar, Arie ; Hordijk, Joost ; Wagenaar, Jaap ; Fluit, Ad ; Bunt, Gerrita van den; Bonten, Marc ; Velthuis, Annet ; Heuvelink, Annet ; Buter, Rianne ; Gonggrijp, Maaike ; Santman-Berends, Inge ; Lam, Theo ; Urlings, Bert ; Heres, Lourens ; Bouwknecht, Martijn ; Groot, Jacques de - \ 2018
    Netherlands : De Stichting TKI Agri&Food (TKI) - 11 p.
    Rapport ESBL-Attributieanalyse (ESBLAT) : Op zoek naar de bronnen van antibioticaresistentie bij de mens
    Mevius, Dik ; Heederik, Dick ; Duijkeren, Engeline ; Veldman, Kees ; Essen, Alieda van; Kant, Arie ; Liakopoulos, Apostolos ; Geurts, Yvon ; Pelt, Wilfrid van; Mughini Gras, Lapo ; Schmitt, Heike ; Dierikx, Cindy ; Hoek, Angela van; Evers, Eric ; Roda Husman, Annemaria de; Blaak, Hetty ; Dissel, Jaap van; Smid, Joost ; Dohmen, Wietske ; Dorado-Garcia, Alejandro ; Havelaar, Arie ; Hordijk, Joost ; Wagenaar, Jaap ; Fluit, Ad ; Bunt, Gerrita van den; Bonten, Marc ; Velthuis, Annet ; Heuvelink, Annet ; Buter, Rianne ; Gonggrijp, Maaike ; Santman-Berends, Inge ; Lam, Theo ; Urlings, Bert ; Heres, Lourens ; Bouwknecht, Martijn ; Groot, Jacques de - \ 2018
    Netherlands : De Stichting TKI Agri&Food (TKI) - 73
    RECON: Reef effect structures in the North Sea, islands or connections? : Summary report
    Coolen, J.W.P. ; Jak, R.G. ; Weide, B.E. van der; Cuperus, J. ; Luttikhuizen, P. ; Schutter, M. ; Dorenbosch, M. ; Driessen, F. ; Lengkeek, W. ; Blomberg, M. ; Moorsel, G. van; Faasse, M.A. ; Bos, O.G. ; Dias, I.M. ; Spierings, M. ; Glorius, S.G. ; Becking, L.E. ; Schol, T. ; Crooijmans, R. ; Boon, A.R. ; Pelt, H. van; Kleissen, F. ; Gerla, D. ; Degraer, S. ; Lindeboom, H.J. - \ 2018
    Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C074/17A) - 33
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