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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Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms
Hordijk, Joost ; Fischer, Egil A.J. ; Werven, Tine van; Sietsma, Steven ; Gompel, Liese Van; Timmerman, Arjen J. ; Spaninks, Mirlin P. ; Heederik, Dick J.J. ; Nielen, Mirjam ; Wagenaar, Jaap A. ; Stegeman, Arjan - \ 2019
Journal of Antimicrobial Chemotherapy 74 (2019)6. - ISSN 0305-7453 - p. 1531 - 1538.

OBJECTIVES: To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding. METHODS: The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently. RESULTS: In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0-80.0)] and the PAF of AMU was 0.36 (95% CI 0.08-0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7-4.9, P = 0.28)]. CONCLUSIONS: The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction.

Comparative genomics of phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius of canine origin
Wegener, Alice ; Broens, Els M. ; Zomer, Aldert ; Spaninks, Mirlin ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2018
Veterinary Microbiology 225 (2018). - ISSN 0378-1135 - p. 125 - 131.
Comparative genomics - MIC - Multidrug resistance - Phenotype - Staphylococcus pseudintermedius

Staphylococcus pseudintermedius is an important pathogen in dogs. Since 2004, methicillin- resistant S. pseudintermedius (MRSP) isolates, often multidrug resistant, have been observed in dogs in the Netherlands. This study aims to link the observed resistance phenotypes in canine MRSP to genotypic antimicrobial resistance markers, and to study the phylogeny of MRSP by genomic comparisons. The genomes of fifty clinical isolates of MRSP from dogs from the Netherlands were sequenced. The resistance genes were identified, and for twenty one different antimicrobials their presence and sequence were associated with the resistance phenotypes. In case of observed discrepancies, the genes were aligned with reference genes. Of the phenotypic resistances, 98.3% could be explained by the presence of an associated resistance gene or point mutation. Discrepancies were mainly resistance genes present in susceptible isolates; 43.8% (7/16) were explained by an insertion, deletion or mutation in the gene. In relation with the resistance gene presence or absence, a single-nucleotide polymorphism (SNP) based phylogeny was constructed to define the population dynamics. The resistance gene content differed according to clonal complex, from very conserved (CC45), to partly conserved (CC71) to highly diverse (CC258) resistance gene patterns. In conclusion, this study shows that the antimicrobial genotype from whole genome sequencing is highly predictive of the resistance phenotype in MRSP. Interestingly, the observed clonal complexes of MRSP isolates were linked with resistance gene patterns

Campylobacter blaseri sp. Nov., isolated from common seals (Phoca vitulina)
Gilbert, Maarten J. ; Zomer, Aldert L. ; Timmerman, Arjen J. ; Spaninks, Mirlin P. ; Rubio-García, Ana ; Rossen, John W. ; Duim, Birgitta ; Wagenaar, Jaap A. - \ 2018
International Journal of Systematic and Evolutionary Microbiology 68 (2018)5. - ISSN 1466-5026 - p. 1787 - 1794.
Average nucleotide identity - Campylobacter - Common seal - Core genome phylogeny - Microbiome - Novel species
During a study to assess the faecal microbiome of common seals (Phoca vitulina) in a Dutch seal rehabilitation centre, 16S rRNA gene sequences of an unknown Campylobacter taxon were identified. Campylobacter isolates, which differed from the established Campylobacter taxa, were cultured and their taxonomic position was determined by a polyphasic study based on ten isolates. The isolates were characterized by 16S rRNA and atpA gene sequence analyses and by conventional phenotypic testing. Based on the whole genome sequences, the average nucleotide identity and core genome phylogeny were determined. The isolates formed a separate phylogenetic clade, divergent from all other Campylobacter taxa and most closely related to Campylobacter corcagiensis, Campylobacter geochelonis and Campylobacter ureolyticus. The isolates can be distinguished phenotypically from all other Campylobacter taxa based on their lack of motility, growth at 25 °C and growth on MacConkey agar. This study shows that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter blaseri sp. nov. is proposed. The type strain for this novel species is 17S00004-5T (=LMG 30333T=CCUG 71276T).
Raw pet food as a risk factor for shedding of extended-spectrum beta-lactamase-producing Enterobacteriaceae in household cats
Baede, Valérie O. ; Broens, Els M. ; Spaninks, Mirlin P. ; Timmerman, Arjen J. ; Graveland, Haitske ; Wagenaar, Jaap A. ; Duim, Birgitta ; Hordijk, Joost - \ 2017
PLoS ONE 12 (2017)11. - ISSN 1932-6203
Background: Close contact between pets and owners provides the opportunity for transmission of antimicrobial resistant organisms like extended-spectrum beta-lactamase (ESBL)/AmpC beta-lactamase (AmpC)-producing Enterobacteriaceae, posing a risk to public health. Objectives: To investigate whether raw feed is a risk factor for household cats to shed ESBL-producing Enterobacteriaceae, a cohort study was designed. Additionally, raw and non-raw commercial pet food products were screened for the presence of ESBL-producing Enterobacteriaceae. Methods: Weekly fecal samples of 17 cats in the control group and 19 cats in the exposed group were collected for three weeks and analyzed for the presence of ESBL-producing Enterobacteriaceae. Questionnaires were obtained to determine additional risk factors. Fecal samples were cultured on MacConkey agar supplemented with 1 mg/L cefotaxime. PCR and sequence analysis was used for screening for ESBL genes in suspected isolates. Pet food samples were cultured in LB broth supplemented with 1 mg/L cefotaxime and processed as described above. Results: In the cohort study, ESBL-producing bacteria were isolated from 3 of 51 (5.9%) samples in the control group compared to 37 of 57 (89.5%) samples in the exposed group. A significant association was found between ESBL shedding and feeding raw pet food products (OR = 31.5). No other risk factors were identified in this study. ESBL-producing Enterobacteriaceae were isolated from 14 of 18 (77.8%) raw pet food products and 0 of 35 non-raw pet food products. Conclusions: This study shows a strong association between shedding of ESBL-producing bacteria in household cats and feeding raw pet food. Raw pet food was often contaminated with ESBL-producing Enterobacteriaceae.
Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences
Verstappen, Koen M. ; Huijbregts, Loes ; Spaninks, Mirlin ; Wagenaar, Jaap A. ; Fluit, Ad C. ; Duim, Birgitta - \ 2017
PLoS ONE 12 (2017)8. - ISSN 1932-6203 - 10 p.

Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74) and non-pseudintermedius genomes (n = 138). Six sequences specific for S. pseudintermedius were identified (sequence length between 300–500 nt). One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54), and eight other staphylococcal species (n = 43). In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

Changes in the population of methicillin-resistant Staphylococcus pseudintermedius and dissemination of antimicrobial-resistant phenotypes in the Netherlands
Duim, Birgitta ; Verstappen, Koen M. ; Broens, E.M. ; Laarhoven, Laura M. ; Duijkeren, Engeline Van; Hordijk, Joost ; Heus, Phebe De; Spaninks, Mirlin ; Timmerman, Arjen J. ; Wagenaar, J.A. - \ 2016
Journal of Clinical Microbiology 54 (2016)2. - ISSN 0095-1137 - p. 283 - 288.

Methicillin-resistant Staphylococcus pseudintermedius (MRSP), which is often multidrug resistant (MDR), has recently emerged as a threat to canine health worldwide. Knowledge of the temporal distribution of specific MRSP lineages, their antimicrobial resistance phenotypes, and their association with clinical conditions may help us to understand the emergence and spread of MRSP in dogs. The aim of this study was to determine the yearly proportions of MRSP lineages and their antimicrobial-resistant phenotypes in the Netherlands and to examine possible associations with clinical conditions. MRSP was first isolated from a canine specimen submitted for diagnostics to the Faculty of Veterinary Medicine of Utrecht University in 2004. The annual cumulative incidence of MRSP among S. pseudintermedius increased from 0.9% in 2004 to 7% in 2013. MRSP was significantly associated with pyoderma and, to a lesser extent, with wound infections and otitis externa. Multilocus sequence typing (MLST) of 478 MRSP isolates yielded 39 sequence types (ST) belonging to 4 clonal complexes (CC) and 15 singletons. CC71 was the dominant lineage that emerged since 2004, and CC258, CC45, and several unlinked isolates became more frequent during the following years. All but two strains conferred an MDR phenotype, but strains belonging to CC258 or singletons were less resistant. In conclusion, our study showed that MDR CC71 emerged as the dominant lineage from 2004 and onward and that less-resistant lineages were partly replacing CC71.

The economic benefits to agriculture of a reduction of low-level ozone pollution in the Netherlands
Kuik, O.J. ; Helming, J.F.M. ; Dorland, C. ; Spaninks, F.A. - \ 2000
European Review of Agricultural Economics 27 (2000)1. - ISSN 0165-1587 - p. 75 - 90.
Low-level ozone pollution affects crop yields adversely. Reduction of ozone pollution would therefore increase crop yields and provide economic benefits to producers and consumers of farm products. This paper assesses the potential magnitude of these benefits for the Netherlands. Exposure-response functions were used to estimate initial yield responses when ozone pollution is reduced to natural background levels. These yield responses were fed into a spatial economic model of the Dutch farm sector, thereby allowing for demand and supply adjustments in all interrelated markets. A novelty in this analysis is the explicit attention to crop-livestock interactions. The annual economic benefits of ozone reduction for producers and consumers of farm products are estimated to be £310 million, of which £91 million goes to producers and £219 million to consumers.
Boekbespreking. P. Spaninks (ed.). Onderwijskundige ondersteuning van het HBO
Segeren, W.A.G. - \ 1985
Pedagogisch tijdschrift 10 (1985). - ISSN 0169-2127 - p. 167 - 167.
Design procedures for solid-liquid extractors and the effect of hydrodynamic instabilities on extractor performance
Spaninks, J.A.M. - \ 1979
Landbouwhogeschool Wageningen. Promotor(en): S. Bruin, co-promotor(en): H.A.C. Thijssen. - Wageningen : Pudoc - ISBN 9789022006931 - 100
oplossen - extractie - oplosmiddelen - dissolving - extraction - solvents

A design method is proposed for countercurrent mass transfer cascades with crossflow stages, and unsteady operated fixed beds in a countercurrent arrangement. The separation performance of these cascades is calculated from mathematical models and compared with a purely countercurrent extractor. The models are based on simple equations describing mass transfer in a single stage fixed bed. The results are presented as concise correlations between the number of true and exterior apparent transfer units.

Asymptotic values of the mass transfer coefficient for transient diffusion processes in cocurrent and countercurrent extractors are calculated for particles with simple geometry. Comparing the extraction efficiency calculated from the exact solutions of the diffusion equations and the values obtained from the asymptotic mass transfer coefficient shows that differences are small under normal operating conditions for countercurrent extraction. The use of the asymptotic values in design calculations is discussed.

Due to the commonly observed viscosity and density gradients in the solvent phase, non-uniform flow of liquid through the layer of solids subjected to extraction can occur. Then some fraction of the solids is not efficiently contacted with the solvent. Experiments show that a concentration gradient rather than a concentration jump in the liquid flowing through an inert packing material reduces the effect of channelling. The effect of mass transfer between the packing and the surrounding liquid on flow stability is studied. The results indicate that channelling can reduce the extraction efficiency in solid-liquid extractors.

Mathematical Simulation of the Performance of Solid-Liquid Extractors. II. Belt Type Extractors
Spaninks, J.A.M. ; Bruin, S. - \ 1979
Chemical Engineering Science 34 (1979). - ISSN 0009-2509 - p. 207 - 215.
Mathematical Simulation of the Performance of Solid-Liquid Extractors. I. Diffusion Batteries
Spaninks, J.A.M. ; Bruin, S. - \ 1979
Chemical Engineering Science 34 (1979). - ISSN 0009-2509 - p. 199 - 205.
Mathematical Simulation of the Performance of Belt Type Solid-Liquid Extractors and Diffusion Batteries
Spaninks, J.A.M. ; Bruin, S. - \ 1977
In: EFCE Mini Symposium-Mathematical Modelling in Food Processing. Lund Institute of Technology, Orenas, 1977
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