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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    The vertical transmission of antibiotic residues from parent hens to broilers
    Jansen, Larissa J.M. ; Berentsen, Ron J. ; Arends, Maura ; Berendsen, Bjorn J.A. - \ 2020
    Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 37 (2020)5. - ISSN 1944-0049 - p. 783 - 792.
    antibiotics - egg - feather - LC-MS - Vertical transmission

    Imprudent and superfluous use of antibiotics contributes to the selection of resistant bacteria, which is a large threat to human health. Therefore analytical procedures have been implemented in the poultry production sector to check if antibiotic treatments are registered, aiming to achieve more prudent use of antibiotics. These methods rely on the analysis of feathers, a matrix in which antibiotic residues persist. However, other routes besides direct administration, through which poultry feathers could contain antibiotic residues, should also be taken into account. In this research the vertical transmission from parent hen to broiler was investigated through a controlled animal study for the antibiotics enrofloxacin, doxycycline and sulfachlorpyridazine. Vertical transmission was observed for all antibiotics to both egg and egg shell. Also it is demonstrated that the transferred antibiotics from parent hen to chick are subsequently excreted via the chick’s droppings. Through this route, the broilers’ environment is contaminated. If eggs are hatched that were taken during treatment of the parent hen, this indirect route and/or the direct vertical transmission can eventually result in the detection of low concentrations of antibiotic residues in the broilers’ feathers at greater age: <50 µg kg−1 for freely extractable residues and <10 µg kg−1 for non-freely extractable residues. No antibiotics were detected in the broilers’ muscle or kidney from 4 weeks of age. This research provides relevant information regarding the possible amount of residues originating from vertical transmission when monitoring matrices such as feathers and broiler droppings in order to stimulate correct use and registration of antibiotics in the poultry sector.

    A European questionnaire-based study on population awareness and risk perception of antimicrobial resistance
    Alexa Oniciuc, Elena Alexandra ; Likotrafiti, Eleni ; Garre, Alberto ; Ruiz, Lorena ; Prieto, Miguel ; Alvarez-Ordóñez, Avelino - \ 2019
    FEMS Microbiology Letters 366 (2019)17. - ISSN 0378-1097
    antibiotics - antimicrobial resistance - awareness - consumption - knowledge - risk perception

    To tackle antimicrobial resistance (AMR) is of outmost importance for the general population to understand the severity and the relevance of different routes of transmission. Respondents of different age groups, educational and occupational backgrounds, area of living, diet and household composition participated in an online survey with questions concerning socio-demographics, personal use of antibiotics, awareness, general knowledge, sources of information, behavior and attitude toward antibiotics, and risk perception on antibiotics and AMR. Descriptive and logistic regression analyses were carried out. A total of 1252 respondents, mainly from EU, participated in the survey. About 57.7% declared they consumed antibiotics in the last year and some misguided behaviors were identified, especially for those not having a food- or health-related background, who more frequently failed in giving the right answer to uncontroversial true/false questions (ANOVA, P < 0.05). The youngest respondents were less confident on the information received from traditional media (OR = 0.425), the national government (OR = 0.462), and consumer organizations (OR = 0.497), while they frequently obtained information from social networks and online media, which could therefore be exploited as a channel for educational campaigns targeting this population group. New measures, strategies and policy agenda at a European level aimed at improving awareness on AMR among targeted community groups must be taken into consideration.

    Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular Mycobacterium tuberculosis
    Rienksma, Rienk A. ; Schaap, Peter J. ; Martins Dos Santos, Vitor A.P. ; Suarez-Diez, Maria - \ 2019
    Frontiers in Cellular and Infection Microbiology 9 (2019). - ISSN 2235-2988 - 1 p.
    antibiotics - drug response - flux balance analysis - host-pathogen interaction - metabolic model - Mycobacterium tuberculosis

    Little is known about the metabolic state of Mycobacterium tuberculosis (Mtb) inside the phagosome, a compartment inside phagocytes for killing pathogens and other foreign substances. We have developed a combined model of Mtb and human metabolism, sMtb-RECON and used this model to predict the metabolic state of Mtb during infection of the host. Amino acids are predicted to be used for energy production as well as biomass formation. Subsequently we assessed the effect of increasing dosages of drugs targeting metabolism on the metabolic state of the pathogen and predict resulting metabolic adaptations and flux rerouting through various pathways. In particular, the TCA cycle becomes more important upon drug application, as well as alanine, aspartate, glutamate, proline, arginine and porphyrin metabolism, while glycine, serine, and threonine metabolism become less important. We modeled the effect of 11 metabolically active drugs. Notably, the effect of eight could be recreated and two major profiles of the metabolic state were predicted. The profiles of the metabolic states of Mtb affected by the drugs BTZ043, cycloserine and its derivative terizidone, ethambutol, ethionamide, propionamide, and isoniazid were very similar, while TMC207 is predicted to have quite a different effect on metabolism as it inhibits ATP synthase and therefore indirectly interferes with a multitude of metabolic pathways.

    Investing in antibiotics to alleviate future catastrophic outcomes: What is the value of having an effective antibiotic to mitigate pandemic influenza?
    Megiddo, Itamar ; Drabik, D. ; Bedford, Tim ; Morton, Alec ; Wesseler, J.H.H. ; Laxminarayan, Ramanan - \ 2019
    Health Economics 28 (2019)4. - ISSN 1057-9230 - p. 556 - 571.
    antibiotics - antibiotics resistance - insurance value - pandemic influenza - real options analysis - secondary bacterial infections
    Over 95% of post‐mortem samples from the 1918 pandemic, which caused 50
    to 100 million deaths, showed bacterial infection complications. The introduc-
    tion of antibiotics in the 1940s has since reduced the risk of bacterial infections,
    but growing resistance to antibiotics could increase the toll from future
    influenza pandemics if secondary bacterial infections are as serious as in
    1918, or even if they are less severe. We develop a valuation model of the
    option to withhold wide use of an antibiotic until significant outbreaks such
    as pandemic influenza or foodborne diseases are identified. Using real options
    theory, we derive conditions under which withholding wide use is beneficial,
    and calculate the option value for influenza pandemic scenarios that lead to
    secondary infections with a resistant Staphylococcus aureus strain. We find that
    the value of withholding an effective novel oral antibiotic can be positive and
    significant unless the pandemic is mild and causes few secondary infections
    with the resistant strain or if most patients can be treated intravenously.
    Although the option value is sensitive to parameter uncertainty, our results
    suggest that further analysis on a case‐by‐case basis could guide investment
    in novel agents as well as strategies on how to use them.
    Antibiotics-induced monodominance of a novel gut bacterial order
    Hildebrand, Falk ; Moitinho-Silva, Lucas ; Blasche, Sonja ; Jahn, Martin Thomas Thomas ; Gossmann, Toni Ingolf ; Heuerta Cepas, Jaime ; Hercog, Rajna ; Luetge, Mechthild ; Bahram, Mohammad ; Pryszlak, Anna ; Alves, Renato J. ; Waszak, Sebastian M. ; Zhu, Ana ; Ye, Lumeng ; Costea, Paul Igor ; Aalvink, Steven ; Belzer, Clara ; Forslund, Sofia K. ; Sunagawa, Shinichi ; Hentschel, Ute ; Merten, Christoph ; Patil, Kiran Raosaheb ; Benes, Vladimir ; Bork, Peer - \ 2019
    Gut 68 (2019)10. - ISSN 0017-5749
    antibiotics - bacterial overgrowth - intestinal microbiology - molecular genetics

    Objective: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. Design: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. Results: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. Conclusion: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.

    Non-targeted workflow for identification of antimicrobial compounds in animal feed using bioassay-directed screening in combination with liquid chromatography-high resolution mass spectrometry
    Wegh, Robin S. ; Berendsen, Bjorn J.A. ; Driessen-Van Lankveld, Wilma D.M. ; Pikkemaat, Mariël G. ; Zuidema, Tina ; Ginkel, Leen A. Van - \ 2017
    Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 34 (2017)11. - ISSN 1944-0049 - p. 1935 - 1947.
    animal feed - antibiotics - Antimicrobials - bioassay - LC-MS
    A non-targeted workflow is reported for the isolation and identification of antimicrobial active compounds using bioassay-directed screening and LC coupled to high-resolution MS. Suspect samples are extracted using a generic protocol and fractionated using two different LC conditions (A and B). The behaviour of the bioactive compound under these different conditions yields information about the physicochemical properties of the compound and introduces variations in co-eluting compounds in the fractions, which is essential for peak picking and identification. The fractions containing the active compound(s) obtained with conditions A and B are selected using a microbiological effect-based bioassay. The selected bioactive fractions from A and B are analysed using LC combined with high-resolution MS. Selection of relevant signals is automatically carried out by selecting all signals present in both bioactive fractions A and B, yielding tremendous data reduction. The method was assessed using two spiked feed samples and subsequently applied to two feed samples containing an unidentified compound showing microbial growth inhibition. In all cases, the identity of the compound causing microbiological inhibition was successfully confirmed.
    Antibiotic residues and resistance in the environment
    Pikkemaat, M.G. ; Yassin, H. ; Fels-Klerx, H.J. ; Berendsen, B.J.A. - \ 2016
    Wageningen : RIKILT Wageningen UR (RIKILT-report 2016.009) - 31
    antibiotic residues - antibiotic resistance - antibiotics - environment - antibioticumresiduen - antibioticaresistentie - antibiotica - milieu
    Antibiotic usage has benefited the animal industry and helped providing affordable animal proteins to the growing human population. However, since extensive use of antibiotics results in the inhibition of susceptible organisms while selecting for the resistant ones, agricultural use is contributing substantially to the emergence and spread of antibiotic resistance in the environment. So far, scientific focus has predominantly been on the emergence and spread of resistant bacteria and genes into the environment as a result of veterinary treatment, in particular through manure but also through food products and direct animal contact. However, environmental contamination with antibiotic residues could also be an important factor in the selection and dissemination of antibiotic resistant bacteria. The persistence of antibiotics in the environment depends on factors like soil type and climate, but also on physical-chemical characteristics of the different types of antibiotics. Monitoring studies showed that substantial concentrations of antibiotic residues can occur in soil and water, in particular at locations close to intensive animal farming. Little is known about the concentrations that will exert selective pressure on environmental microorganisms and promote persistence or even enrichment of the environmental resistance gene pool. Traditionally, it was assumed that resistance is only induced at concentrations above the minimum inhibitory concentration (MIC). However, recently, evidence is accumulating that selective environments may occur at concentrations down to several hundred-folds below the MIC. However, for most of the antibiotics and environmental conditions, the minimal threshold concentrations that will induce or support propagation of antibiotic resistance in environmental microbes are still undefined. Therefore, more research is needed into the relationship between the concentrations of antibiotic residues in the environment and the prevalence and persistency of environmental antibiotic resistance. First, additional research is needed to determine what antibiotic concentrations still exert pressure on bacteria and can cause persistence or enrichment of resistant bacteria. Furthermore, the fate of antibiotics in the main reservoirs (manure, soil, water) should be studied, including antimicrobially active metabolites and their bioavailability. Finally, transmission of antibiotic compounds between reservoirs should be studied to identify the main reservoirs of interest and define intervening measures.
    Mining the human intestinal microbiota for biomarkers associated with metabolic disorders
    Hermes, Gerben - \ 2016
    Wageningen University. Promotor(en): Hauke Smidt; Erwin Zoetendal. - Wageningen : Wageningen University - ISBN 9789462579514 - 205
    gastrointestinal microbiota - metabolic disorders - biomarkers - obesity - intestinal microorganisms - antibiotics - dna sequencing - rna - ribosomal rna - microbiota van het spijsverteringskanaal - stofwisselingsstoornissen - biomarkers - obesitas - darmmicro-organismen - antibiotica - dna-sequencing - rna - ribosomaal rna

    After birth, our gastrointestinal (GI) tract is colonized by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develop intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or even new therapeutic target. Nevertheless, it is currently still unclear which bacterial groups play a role in the development of the metabolic syndrome in humans. This might partly be explained by: 1. Biological factors such as the heterogeneity in genotype, lifestyle, diet; and the often complex aetiology of human disease of which the metabolic syndrome is no exception. 2. Technological factors, such as the use of miscellaneous incompatible methods to assess the gut microbiota, often enumerating specific groups rather than using broad 16S rRNA gene surveys or metagenomics. 3. Studies vary greatly in the populations considered, their designs, and the degree of control for potential confounding factors such as lifestyle and diet. Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, based on stricter control over variables such age range or through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define groups.

    Perturbations in microbial diversity and community structure in adults with overweight and obesity may be partly due to long-term dietary habits or physiological changes in these subjects. As such, exploring the association between the gut microbiota and variation in BMI and weight in early life, prior to or close to the onset of overweight, might provide additional insights into these processes. Therefore, we studied the fecal microbiota of 295 six-seven year old children from the KOALA Birth Cohort, living in the south of the Netherlands. This age range is relatively uncharted microbiota territory. We found that its composition seems to conform to tot same ecosystem rules as that of adults. The bimodal distribution pattern of several bacterial groups as well as their co-correlating groups that were reported previously, including Uncultured Clostridiales II (UCII), Prevotella spp. and Dialister were confirmed. Furthermore, one of the previously described bimodal groups (Uncultured Clostridiales I) was shown before to exhibit very clear shifting state probabilities associated with ageing, where the high abundance state was mainly observed above 40 years of age. This was corroborated as no support for bimodality of this group was observed in the children included in the study described here. A large part of the variation in microbiota composition was explained by the abundance of aforementioned groups in contrast to the anthropometric outcomes, suggesting that in this group of healthy children within a relatively normal weight range, weight and associated parameters were not major drivers of overall genus-level microbial composition or vice versa. Hereafter, multiple linear and logistic regression models with rigorous adjustment for confounders were applied to investigate individual microbiota features association with weight related anthropometric outcomes. Previously reported parameters such as diversity, richness and Bacteroidetes to Firmicutes ratio, were not significantly associated with any of the outcomes. Nevertheless, the abundance of several specific bacterial taxa; Akkermansia, Sutterella wadsworthia et rel. and Bryantella formatexigens et rel. and the dichotomous abundance state of the bi-modally distributed UCII was consistently associated with weight-related outcomes.

    Other biochemical features of the metabolic syndrome have been associated with the gut microbiome. Mainly rodent studies have indicated that antibiotic treatment may improve glucose homeostasis and metabolic impairments. Therefore, the effects of gut microbiota manipulation by antibiotics (7d administration of amoxicillin, vancomycin or a placebo) on tissue-specific insulin sensitivity, energy metabolism, gut permeability and inflammation in 57 obese, pre-diabetic men from the same geographical region, were investigated. Vancomycin decreased bacterial diversity and significantly reduced well known butyrate- producing Firmicutes from Clostridium clusters IV and XIVa and bacterial groups involved in bile acid metabolism. These changes occurred concomitantly with altered plasma and fecal concentrations of these metabolites. In adipose tissue, gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. However, antibiotic treatment had no significant effects on tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability and adipocyte size. Importantly, despite a still considerably altered microbial composition at eight weeks follow-up, energy harvesting, adipocyte size and whole-body insulin sensitivity (HOMA-IR) remained unaltered. Overall these data indicate that interference with adult microbiota by antibiotic treatment for 7 days had no clinically relevant impact on metabolic health in obese humans. These data are in contrast with several rodent studies as well as a human intervention. The present study, which was well-powered and placebo-controlled, indicates that the previously reported vancomycin-induced effects on human peripheral insulin sensitivity are probably of minor physiological significance.

    The aforementioned group that was relatively homogeneous with regards to phenotype was combined with another cohort with similar phenotypical characteristics (obese, male and pre-diabetic) from another region of the Netherlands, to investigate whether tissue specific insulin sensitivity, as measured by the golden standard hyperinsulinemic-euglycemic clamp technique, is related to a specific microbial pattern. Remarkably, despite the fact that both cohorts were constructed based on comparable recruitment strategies, the average microbiota composition in both cohorts showed pronounced differences. Firstly, we found no consistent and significant association between liver, adipose tissue or skeletal muscle insulin sensitivity and the microbiota in both cohorts. Nevertheless, Random Forests classifiers using microbiota composition as predictors revealed taxa associated with fasting glucose concentrations and HbAc1 but only in one cohort. The top microbial features distinguishing classes were different Proteobacteria and groups involved in butyrogenesis, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Eubacterium rectale and related species, for fasting glucose levels. For HbAc1 these taxa were Oscillospira guillermondii, Sporobacter termitidis, Lactobacillus gasseri and Peptococcus niger and related species. The striking cohort-specific observations suggest that the relation between microbiota composition and type 2 diabetes mellitus as well as other characteristics of the metabolic syndrome is very dependent on the selected cohort of patients and their respective baseline microbiota composition. Similar observations have been made by other researchers as well. It could be that differences in microbiota composition are not associated with the insulin resistance phenotype when the overweight and/or obese state of the patient is already established, as is the case for our metabolic syndrome patients. In the latter case we cannot exclude that the composition of the fecal microbiota may play a role in the worsening of insulin sensitivity in an early stage in the development from a lean towards an overweight/obese phenotype. Furthermore, the observation of a subgroup- specific microbiota only observed in one of the cohorts might indicate an alternative state of microbiota composition driven by yet unknown forces. Nevertheless, this study clearly demonstrated that cohort-specific microbiota differences hamper finding a consensus biological interpretation between cross-sectional studies. This, combined with the complexity of individual disease pathogenesis, as well as the individual-specific differences in microbiota composition, may explain the inconsistency in observations between different studies concerning the identification of signature microbes for obesity, irritable bowel syndrome and other diseases.

    Besides the biological drivers for cohort specific inconsistencies in identified microbial biomarkers, there are also technological factors. Although high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes, evidence is increasing that methodology rather than the biological variation is responsible for observed sample composition and distribution. Large meta-analyses would aid in elucidating whether the basis for these observed inconsistencies is biological, technical or maybe a combination of both. To facilitate these meta-analyses of microbiota studies we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different Mock Communities (MC). NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies. The analysis of α- and β-diversity of these MC confirmed conclusions guided by biology rather than the methodological aspects. This pipeline was applied to biological samples to monitor the developing communities an in vitro gut model (TIM-2) fed either with a normal diet, or modified versions from which the carbohydrate (MPLC) or protein fraction was diluted (LPMC) for 72h. In combination with global metatranscriptomics and metabolomics this revealed that each diet produced distinct microbial communities and temporal patterns and ratios of metabolites. The microbiota in reactors fed diets containing normal carbohydrate levels were enriched in members of the genera Prevotella, Subdoligranulum, Blautia and Bifidobacterium, all associated with carbohydrate fermentation. In turn, the microbiota in the reactors fed the MPLC diet, containing ten-fold less carbohydrates, was enriched in the genus Bacteroides, which is associated with diets rich in protein and animal fat. This setup allows researchers to study the (trophic) interactions and task division within a community and how they are impacted by diet-related factors under controlled conditions, which may assist in defining causal links between specific diet-derived parameters microbial groups and their activities.

    In conclusion, currently it seems that GI microbiota based biomarkers associated with metabolic impairments and anthropometric variables associated with the metabolic syndrome are cohort specific or possibly individual, which could partly be due to the use of incompatible analytical approaches. Nevertheless, there is growing evidence that human health is a collective property of the human body and its associated microbiome and thus requires to study the interface of two very complex systems, i.e. on one side the extraordinary coding capacity, high inter-individuality and complex dynamics of the microbiome and on the other side the multifactorial individual nature of human disease. In light of these observations the manifestation of individual dynamics of the microbiota with the host when homeostasis is lost seems plausible and likely.

    Interplay between gut microbiota and antibiotics
    Jesus Bello Gonzalez, Teresita de - \ 2016
    Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): M.W.J. van Passel. - Wageningen : Wageningen University - ISBN 9789463430043 - 293
    antibiotics - intestinal microorganisms - aminoglycoside antibiotics - enterococcus - interactions - zoo animals - man - patients - dna sequencing - polymerase chain reaction - antibiotica - darmmicro-organismen - aminoglycoside antibiotica - enterococcus - interacties - dierentuindieren - mens - patiënten - dna-sequencing - polymerase-kettingreactie

    The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria.

    Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them.

    The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence.

    Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype. In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated.

    Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosyl-hydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of non-human primates, the applicability of Human Intestinal Tract Chip (HITChip) to study the gut microbiota composition of these animals was assessed, including a comparison with healthy human volunteers (Chapter 3). It was concluded that the HITChip can be successfully applied to the gut microbiota of closely related hominids, and the microbiota dynamics can therefore be quickly assessed by the HITChip.

    In Chapter 4, a combination of 16S rRNA phylogenetic profiling using the HITChip and metagenomics sequencing was implemented on samples from a single ICU hospitalized patient that received antibiotic prophylactic therapy (Selective Digestive Decontamination - SDD). The different approaches showed a highly dynamic microbiota composition over time and the prevalence of aminoglycoside resistance genes harbored by a member of the commensal anaerobic microbiota, highlighting the role of the commensal microbiota as a reservoir of antibiotic resistance genes. As an extension of this study (Chapter 5), 11 ICU patients receiving SDD were followed using 10 healthy individuals as a control group to compare the diversity and dynamics of the gut microbiota and resistome by HITChip and nanolitre-scale quantitative PCRs, respectively. The microbial diversity of the healthy individuals was higher compared to ICU patients, and it was less dynamic compared to ICU patients under antibiotic treatment. Likewise, the levels of antibiotic resistance genes increased in ICU patients compared to healthy individuals, indicating that during ICU hospitalization and the SDD, gut microbiota diversity and dynamics are profoundly affected, including the selection of antibiotic resistance in anaerobic commensal bacteria.

    This was further expanded in an extensive study focusing on colonization dynamics with antibiotic resistant bacteria as described in Chapter 6. This was performed in the same group of ICU-hospitalized patients receiving SDD therapy and showed that by using a range of culture media and selective conditions a variety of taxonomic groups could be isolated, including aerobic and anaerobic antibiotic resistant bacteria. The overall composition of the faecal microbiota detected by HITChip indicated mainly a decrease of Enterobacteriaceae and an increase of the enterococcal population. Since critically ill patients are susceptible to hospital-acquired infections and the control of the emergence of antibiotic resistance is crucial to improve therapeutic outcomes, an extended analysis of the Enterococcus colonization dynamics in this group of patients by cultivation and phenotypic and genotypic characterization of the isolates provided new information about carriage of antibiotic resistance and virulence factor encoding genes (Chapter 7). It also highlighted the opportunity for the exchange of resistance and virulence genes, which could increase the risk of acquiring nosocomial infections.

    Next, chapter 8 described the implementation of high-throughput cultivation-based screening using the Microdish platform combined with high-throughput sequencing (MiSeq) using faecal samples from ICU patients receiving SDD. This allowed for the recovery of previously uncultivable bacteria, including a pure culture of a close relative of Sellimonas intestinalis BR72T that was isolated from media containing tobramycin, cefotaxime and polymyxin E. This strain could therefore represent a potential antibiotic resistance reservoir.

    In conclusion, this thesis provides broad insight into the diversity and dynamics of the gut microbiota and resistome in ICU hospitalized patients receiving SDD therapy as well as the dynamics of colonization with antibiotic resistant bacteria. Especially our extensive study of the colonization dynamics of Enterococcus spp. during ICU stay reinforced the notion that SDD therapy does not cover this group of bacteria and highlights the importance of a critical control of the emergence of antibiotic resistance in enterococci and their spread and dissemination as known potential pathogens.

    Furthermore, the extensive use of antibiotics could select for an increase in the rate of antibiotic resistance against aminoglycosides and beta-lactams, indicating that a control in the use of broad spectrum antibiotics needs to be considered. In addition, this thesis provides evidence regarding the possible genetic background involved in the subsistence phenotype, however, future studies on metabolic pathways could provide novel insight into the underlying mechanisms.

    Gezonde vleeskuikens - Een goede start: belang van voer en water : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - pluimvee - vleeskuikens - animal welfare - animal production - animal health - antibiotics - poultry - broilers
    Een gezond kuiken kan onder optimale omstandigheden zijn voordeel doen van directe beschikking over voer en water. Het kuiken kan de dooierrest dan beter benutten voor ontwikkeling, immuniteit en groei. De juiste temperatuur van de omgeving is hierbij een zeer belangrijke factor, want als kuikens het koud of te warm hebben eten ze niet en zal van een goede start geen sprake zijn.

    In de kuikenbroederij komen kuikens niet allemaal tegelijk uit. De kuikens die het eerst uit komen, moeten wachten totdat alle kuikens uit zijn, en dat kan nog wel een dag duren. Daarna worden de kuikens verwerkt en geteld, en worden ze naar de boerderij gebracht. Zo kan het wel 36 uur duren voordat de eerst uitgekomen kuikens voer en water krijgen.

    Innovaties in de pluimveehouderij richten zich op vroege voeding als pluspunt onder optimale omstandigheden: direct verstrekken van water en voer in de uitkomstkast, en het laten uitkomen van broedeieren in de stal.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskuikens - hygiëne troef: een beetje preventie is geen preventie : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - pluimvee - vleeskuikens - animal welfare - animal production - animal health - antibiotics - poultry - broilers
    Ziekteverwekkers bij vleeskuikens kun je indelen in virussen, bacteriën en parasieten. Antibiotica werken alleen tegen bacteriën. De voornaamste bacteriën bij vleeskuikens zijn E-coli en enterococcen. De meest voorkomende virussen zijn ademhalingsvirussen. Van de parasieten komt de darmparasiet Eimera veelvuldig voor, veroorzaker van coccidiose.

    Ziekteverwekkers kunnen op een bedrijf en in de stal worden binnengebracht door personen, voertuigen, het pluimvee zelf, voer, water, ongedierte, materialen en de lucht. Ze kunnen ook al aanwezig zijn in de stal. Er moet dus aandacht besteed worden aan zowel bedrijfshygiëne (externe biosecurity) als stalhygiëne (interne biosecurity).

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskuikens - Schoon en smakelijk: belang van goede kwaliteit drinkwater : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - pluimvee - vleeskuikens - animal welfare - animal production - animal health - antibiotics - poultry - broilers
    Goede kwaliteit drinkwater is essentieel voor een gezond vleeskuiken. Niet alleen aan de bron, maar ook daar waar de dieren het water opnemen: bij de nippel dus. Goed drinkwater is niet alleen belangrijk voor optimale bedrijfsresultaten, maar ook voor voedselveiligheid en diergezondheid.

    Van onderzochte watermonsters uit de drinknippel bleek bijna 8 procent ongeschikt en bijna 20 procent minder geschikt als drinkwater voor pluimvee! De kwaliteit van drinkwater wordt vooral beïnvloed door de mogelijke aanwezigheid van biofilm aan de binnenzijde van de drinkleiding. Deze bestaat uit micro-organismen die groeien op afzettingen van vuil en mineralen.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskuikens : goed ter been: belang van een goede strooiselkwaliteit : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - pluimvee - vleeskuikens - animal welfare - animal production - animal health - antibiotics - poultry - broilers
    Voetzoollaesies zijn aantastingen van de voetzolen van vleeskuikens. Bij een milde laesie is er sprake van een oppervlakkige aantasting (verkleuring, verdikking) van de huid van de voetzool. Bij een ernstige laesie is de opperhuid aangetast tot in de diepere huidlagen en is er sprake van onderhuidse ontstekingen. Deze ernstige voetzoollaesies zijn pijnlijk, en zijn een risico voor diergezondheid.

    Voetzoollaesies bij vleeskuikens worden veroorzaakt door een slechte strooiselkwaliteit: nat en plakkerig strooisel. De strooiselkwaliteit wordt door veel factoren beïnvloed, zoals het klimaat, de voersamenstelling en ziekten. De aanpak ervan verschilt van bedrijf tot bedrijf. In de Nederlandse regelgeving is een norm voor voetzoollaesies opgenomen die van toepassing is voor de hoogste bezettingsgraad (39-42 kg/m2).

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskuikens - Campylobacter de baas – belang van het weren van vliegen : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - antibiotica - pluimvee - vleeskuikens - animal welfare - animal production - antibiotics - poultry - broilers
    Campylobacter is de meest voorkomende bacteriële veroorzaker van voedselinfecties in Nederland. 20-30% van de Campylobacter-besmettingen van de mens wordt veroorzaakt door consumptie van ongaar of onhygiënisch bereid pluimveevlees. De dieren zelf worden er na besmetting niet ziek van.

    Vliegen zijn een belangrijke besmettingsbron op pluimveebedrijven. Het weren van vliegen is daarom een belangrijk aandachtspunt, maar moet gecombineerd worden met een goede biosecurity. Momenteel wordt onderzocht wat het effect is van het plaatsen van vliegennetten, zodat pluimveestallen vliegenvrij zijn.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskalveren - Een sterk kalf: belang van een goede opfok op het melkveebedrijf : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - vleeskalveren - rundvee - animal welfare - animal production - animal health - antibiotics - veal calves - cattle
    Stierkalveren die op het melkveebedrijf al goed groeien en op gewicht komen presteren ook in de mestperiode beter en hebben minder medicijnen en antibiotica nodig. Bij opzet van minder vitale nuchtere kalveren op het vleeskalverbedrijf is de uitval circa 2 procent hoger, en het kost €20 tot €30 per kalf extra aan arbeid en medicijnen.

    Factoren in de kalveropfok die bijdragen aan de weerstand en gezondheid van vleeskalveren zijn: een hygiënische, tochtvrije huisvesting, voldoende biest van goede kwaliteit, goede kwaliteit melk en het vrij zijn van ziektes. Deze factoren geven een sterker vleeskalf, waardoor de kans op problemen in de mestfase vermindert.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskalveren : een warm welkom: belang van een goede opvang : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - vleeskalveren - rundvee - animal welfare - animal production - animal health - antibiotics - veal calves - cattle
    Vleeskalveren komen van melkveebedrijven, vanaf een leeftijd van twee weken. Ze komen vaak eerst bij elkaar op een verzamelplaats en gaan van daar naar het vleeskalverbedrijf. Ongeveer de helft van de kalveren komt van Nederlandse melkveebedrijven, de rest komt uit het buitenland, vooral Duitsland en Oost-Europa.

    Een optimale opvang bevordert een goede start op het vleeskalverbedrijf. Hiervoor is het van belang de kalveren rustig op te vangen in een verwarmde stal, individuele aandacht en zorg te bieden, en lauw water met elektrolytenmix te verstrekken om een tekort aan vocht en lichaamszouten aan te vullen.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO- 20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskalveren - Goede opstart: infectiedruk en weerstand in balans : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - vleeskalveren - rundvee - animal welfare - animal production - animal health - antibiotics - veal calves - cattle
    In de vleeskalverhouderij komen gezondheidsproblemen - met name luchtwegproblemen - vooral in de eerste 3 weken voor. In deze periode zijn de dieren individueel gehuisvest om ze goed te kunnen controleren. Er is regelmatig contact met de dierenarts.

    De gezondheid van vleeskalveren wordt bepaald door de balans tussen infectiedruk en weerstand tegen ziektes. Infectiedruk in de vleeskalverhouderij wordt voor een groot deel bepaald door ziekteverwekkers die de kalveren meenemen van het melkveebedrijf. Verminderen van stress en optimaliseren van voeding en klimaat hebben een positieve invloed op de weerstand van de dieren.

    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO 20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Gezonde vleeskalveren : optimale groei: verbeteringen in voer : Kennisclip
    Ruis, M.A.W. - \ 2016
    dierenwelzijn - dierlijke productie - diergezondheid - antibiotica - vleeskalveren - rundvee - animal welfare - animal production - animal health - antibiotics - veal calves - cattle
    Traditioneel werd aan vleeskalveren alleen kalvermelk gevoerd. Nu wordt vanaf opzet op het vleeskalverbedrijf naast kalvermelk ook ruw- en krachtvoer verstrekt. Rosé kalveren gaan na een week of 6-7 melkvoeding volledig over op ruw- en krachtvoer.

    Voldoende ruwvoer komt tegemoet aan de natuurlijke kauwbehoefte van kalveren. Hoe vezelrijker het rantsoen, hoe meer ‘pensprik’, en hoe beter de vertering. Een blankvleeskalf van 6 maanden beschikt bij voorkeur dagelijks over 2 kg krachtvoer, 1 kg ruwvoer en 2 kg droge stof kalvermelk. Nieuw onderzoek richt zich op het verbeteren van weerstand en vitaliteit van kalveren via de voeding.
    In opdracht van Wageningen UR Livestock Research en het Ontwikkelcentrum, project 'Naar gezonde kalveren en kippen' (BO-20-011-032). Meer informatie over diergezondheid en dierenwelzijn:
    Mining into interspecific bacterial interactions
    Tyc, Olaf - \ 2016
    Wageningen University. Promotor(en): Wietse de Boer, co-promotor(en): Paolina Garbeva. - Wageningen : Wageningen University - ISBN 9789462578340 - 234
    soil bacteria - secondary metabolites - microbial interactions - antibiotics - nutrients - bodembacteriën - secundaire metabolieten - microbiële interacties - antibiotica - voedingsstoffen

    In terrestrial ecosystems bacteria live in close proximity with many different microbial species and form complex multi-species networks. Within those networks bacteria are constantly interacting with each other and produce a plethora of secondary metabolites like antibiotics, enzymes, volatiles and other compounds from diverse chemical classes. Several independent studies revealed that the production of secondary metabolites by soil bacteria can be influenced by the interaction with other microorganisms in their vicinity.

    In this thesis we show how interspecific interactions between soil bacteria influence the production of soluble and volatile secondary metabolites, gene expression and fitness. To elucidate the effect of interspecific interactions on antimicrobial activity in soil bacteria a high-through-put screening method was developed and applied on a collection of 146 rhizobacterial isolates obtained from similar habitats. In addition we examined if the production of volatile organic compounds is influenced by interspecific interactions. Thus, the identity and antimicrobial activity of volatiles produced by bacteria cultivated in monoculture as well in interaction were examined. Furthermore a sand microcosm approach was applied to investigate how Pseudomonas fluorescens strain Pf0-1 responded to the presence of monocultures and mixtures of a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) bacterial strain under two nutritional conditions.

    The interaction between a gram-negative Burkholderia and a gram-positive Paenibacillus isolate was subjected to detailed metabolome, volatolome and transcriptome analysis. One distinct volatile and one non-volatile compound produced only during interspecific interaction but not in the monoculture were identified. The activity of the interacting bacteria and the compounds produced during interaction were tested against a range of human and plant pathogens.

    In summary, this thesis extends the knowledge about the effect of interspecific bacterial interactions on secondary metabolites production (soluble and volatiles), gene expression and fitness in bacteria. The exploitation of such bacterial interspecific interactions can be an important “tool” for the discovery of novel antimicrobial and agro-chemical compounds. The obtained knowledge can help in selecting the right players in synthetic communities that fulfil important ecosystem services like disease suppression in agricultural crop systems.

    Effects of early life conditions on immunity in broilers and layers
    Simon, K. - \ 2016
    Wageningen University. Promotor(en): Bas Kemp, co-promotor(en): Aart Lammers. - Wageningen : Wageningen University - ISBN 9789462576711 - 188
    broilers - hens - ontogeny - poultry feeding - chicken housing - immune response - antibiotics - gastrointestinal microbiota - immunology - immunity - vleeskuikens - hennen - ontogenie - pluimveevoeding - huisvesting van kippen - immuniteitsreactie - antibiotica - microbiota van het spijsverteringskanaal - immunologie - immuniteit


    The course for later life immune responses is set early in life during the developmental phase of the immune system and accordingly disturbances of immune development may have long-term consequences for host health. In terms of immune activation and immune development the gut microbiota play an important role and consequently disturbances of early life microbial colonization may affect host immunity later in life. In chickens, disturbances of microbial colonization may be caused by various early life conditions which in turn may affect robustness of the chick in the long term. The aim of this thesis was to assess the effects of several early life factors including time of access to feed post hatch (immediately or 72 hours delayed), housing conditions, antibiotic treatment, and intestinal pathology on the intestinal microbiota composition, immune development, and specific antibody response later in life in chickens. Additionally, possible differences between broilers and layers were taken into account as unintentional co-selection of immunological traits may have taken place during the selection process for different production traits. Delayed access to feed and administration of antibiotics early in life led to a shift in early life microbiota composition, which seemed to be restored quite quickly in both cases. Microbiota composition in response to DSS was not investigated, but based on rodent studies was expected to be influenced. Ileal immune development, which was assessed in terms of relative cytokine and immunoglobulin mRNA expression levels was not affected by feeding strategy post hatch (early vs. delayed), but a downregulation of ileal immunoglobulin expression levels could be observed during DSS treatment. All early life factors investigated affected the specific antibody response towards an immunological challenge later in life. Interestingly, there seemed to be an interaction between immediate access to feed post hatch and immune responsiveness towards the environment, thus early feeding may influence the adaptive capacity of chickens in different environments. Regarding the differences between breeds it is interesting to note that broilers seem to have developed a more humoral oriented immune strategy, while layers seem to react in a more pro-inflammatory way. Taken together, results suggested that early life conditions may influence priming of the immune system during its developmental phase, leading to altered antibody responses later in life. Furthermore, broilers and layers seem to have developed different immune strategies. Early life conditions as well as possible differences between breeds should therefore be taken into account in future immunological studies.

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