Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

Records 1 - 20 / 148

  • help
  • print

    Print search results

  • export

    Export search results

  • alert
    We will mail you new results for this query: q=Hordijk
Check title to add to marked list
Successful Host Adaptation of IncK2 Plasmids
Rozwandowicz, Marta ; Brouwer, Michael S.M. ; Mughini-Gras, Lapo ; Wagenaar, Jaap A. ; Gonzalez-Zorn, Bruno ; Mevius, Dik J. ; Hordijk, Joost - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
chicken - conjugation - IncK2 - plasmid - sigma-32

The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ–32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates.

Phylogenomic investigation of IncI1-I plasmids harboring blaCMY-2 and blaSHV-12 in salmonella enterica and Escherichia coli in multiple countries
Castellanos, Luis Ricardo ; Graaf-Van Bloois, Linda van der; Donado-Godoy, Pilar ; Mevius, Dik J. ; Wagenaar, Jaap A. ; Hordijk, Joost ; Zomer, Aldert L. - \ 2019
Antimicrobial Agents and Chemotherapy 63 (2019)7. - ISSN 0066-4804
Blc - Broiler - Chicken - DeoR - IS1294 - IS26 - ISEcp1 - S. Heidelberg - Salmonella Paratyphi B var. Java - SugE - Tn1721

The objective of this study was to elucidate the genetic and evolutionary relatedness of blaCMY-2- and blaSHV-12-carrying IncI1-I plasmids. Phylogenomic analysis based on core genome alignments and gene presence/absence was performed for different IncI1-I sequence types (STs). Most IncI1-I/ST12 and IncI1-I/ ST231 plasmids had near-identical core genomes. The data suggest that widely occurring blaCMY-2-carrying IncI1-I/ST12 plasmids originate from a common ancestor. In contrast, blaSHV-12 was inserted independently into different IncI1-I/ST231-related plasmids.

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.

Diversity of plasmids and genes encoding resistance to extended spectrum cephalosporins in commensal Escherichia coli From Dutch livestock in 2007-2017
Ceccarelli, Daniela ; Kant, Arie ; Essen-Zandbergen, Alieda Van; Dierikx, Cindy ; Hordijk, Joost ; Wit, Ben ; Mevius, Dik J. ; Veldman, Kees T. - \ 2019
Frontiers in Microbiology 10 (2019)FEB. - ISSN 1664-302X
ESBL - Escherichia coli - Livestock - PAmpC - Plasmid

Extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) genes confer resistance to extended spectrum cephalosporin's. The spread of these genes is mostly facilitated by plasmid-mediated horizontal transfer. National surveillance activities to detect ESBL/pAmpC-producers in commensal bacteria from livestock are in place in the Netherlands since several years. This study aimed at reporting gene and plasmid diversity of commensal ESBL/pAmpC-producing Escherichia coli isolated from healthy animals during surveillance activities between 2007 and 2017. A collection of 2304 extended-spectrum cephalosporin-resistant (ESC-R) E. coli isolated from feces of broilers, dairy cattle, slaughter pigs, turkeys, ducks, and veal calves was investigated and ESBL/pAmpC genes were determined. Gene location of a selection of 473 E. coli isolates was determined and typing of plasmids linked to the ESBL/pAmpC genes was performed. Twenty-two different ESBL/pAmpC genes were identified with bla CTX-M-1 being the most prevalent gene in livestock (43.7%), followed by bla CMY -2 and bla SHV -12 , independent of the animal source. Prevalence of typically human associated bla CTX-M-15 was highest in cattle. Less than 10% E. coli isolates owed their ESC-R phenotype to promoter mutations of the chromosomal ampC gene. Majority (92%) of ESBL/pAmpC genes analyzed were plasmid located, with IncI1α being the most represented plasmid family in isolates from all animals, followed by IncF (veal calves, dairy cattle and slaughter pigs), IncK (broilers and laying hens), IncX1 in broilers, and emerging IncX3 in broilers and dairy cattle. Prevalence and molecular diversity of ESC-R E. coli isolated from livestock over an 11-year period revealed a composite scenario of gene-plasmid combinations.

Cattle affect regeneration of the palm species Attalea princeps in a Bolivian forest–savanna mosaic
Hordijk, Iris ; Meijer, Fabian ; Nissen, Esther ; Boorsma, Tjalle ; Poorter, Lourens - \ 2019
Biotropica 51 (2019)1. - ISSN 0006-3606 - p. 28 - 38.
Beni savanna - Bolivia - landscape mosaic - Llanos de Moxos - Motacú palm

Attalea princeps is an important palm species that shapes the forest–savanna mosaic in Beni, Bolivia, as it dominates the two principal forest landscape elements (forest islands and gallery forest), and provides a vital microhabitat, food, and nesting source for numerous plant and animal species. The forest–savanna mosaic is used for extensive grazing, and the palm population is declining on the forest islands due to a low regeneration rate, which threatens the maintenance of this landscape. We therefore examined the (a)biotic factors that influence the population structure of Attalea in the centers and edges of forest islands and gallery forests. Ninety-one 0.1-ha plots were established, and 500 palm adults and 3,700 juveniles were measured for their size, health condition, and fire damage. For each plot, habitat characteristics, such as landscape position, grazing pressure, and soil conditions, were measured. Attalea population density was significantly lower on the forest islands than in the gallery forests, especially in the juvenile life stage. A structural equation model showed that juvenile density is positively related to the health condition of juveniles and amount of fruits present, where the amount of fruits is positively affected by the condition of adults. Juvenile density is negatively influenced by grazing, affecting the health condition of the juvenile, as well as organic matter and phosphate availability in the soil. Therefore, it is recommended to decrease the grazing pressure by decreasing livestock densities, fencing off vulnerable forest islands, or by rotating cattle.Abstract in Spanish is available with online material.

Data from: Cattle affect regeneration of the palm species Attalea princeps in a Bolivian forest-savanna mosaic
Hordijk, Iris ; Meijer, Fabian ; Nissen, Esther ; Boorsma, Tjalle ; Poorter, L. - \ 2018
Wageningen University & Research
landscape mosaic - Motacú palm - Attalea princeps
Attalea princeps is an important palm species that shapes the forest-savanna mosaic in Beni, Bolivia, because it dominates and shapes the two principal forest landscape elements (forest islands and gallery forest), and it provides a vital microhabitat, food and nesting source for numerous plant and animal species. The forest-savanna mosaic is used for extensive grazing, and the palm population is declining on the forest islands due to a low regeneration rate, which threatens the maintenance of this landscape. We therefore examined the (a)biotic factors that influence the population structure of Attalea in the centers and edges of forest islands and gallery forests. Ninety-one 0.1 ha plots were established and 500 palm adults and 3700 juveniles were measured for their size, health condition and fire damage. For each plot habitat characteristics, such as landscape position, grazing pressure, and soil conditions were measured. Attalea population density was significantly lower on the forest islands than in the gallery forests, especially in the juvenile life stage. A structural equation model showed that juvenile density is positively related to the health condition of the juveniles and amount of fruits present, where the amount of fruits is positively affected by the condition of the adults. Juvenile density is negatively influenced by grazing, affecting the health condition of the juvenile, as well as organic matter and phosphate availability in the soil. Therefore, it is recommended to decrease the grazing pressure by decreasing livestock densities, fencing off vulnerable forest islands, or by rotating cattle.
Genomic characterization of extended-spectrum cephalosporin-resistant Salmonella enterica in the Colombian poultry chain
Castellanos, Luis Ricardo ; Graaf-van Bloois, Linda van der; Donado-Godoy, Pilar ; León, Maribel ; Clavijo, Viviana ; Arévalo, Alejandra ; Bernal, Johan F. ; Mevius, Dik J. ; Wagenaar, Jaap A. ; Zomer, Aldert ; Hordijk, Joost - \ 2018
Frontiers in Microbiology 9 (2018)OCT. - ISSN 1664-302X
Chicken - Latin America - MLST - pMLST - S. Heidelberg - S. Java - S. paratyphi B d-tartrate positive

Salmonella enterica serovars have been isolated from Colombian broilers and broiler meat. The aim of this study was to investigate the diversity of ESBL/pAmpC genes in extended-spectrum cephalosporin resistant Salmonella enterica and the phylogeny of ESBL/pAmpC-carrying Salmonella using Whole Genome Sequencing (WGS). A total of 260 cefotaxime resistant Salmonella isolates, obtained between 2008 and 2013 from broiler farms, slaughterhouses and retail, were included. Isolates were screened by PCR for ESBL/pAmpC genes. Gene and plasmid subtyping and strain Multi Locus Sequence Typing was performed in silico for a selection of fully sequenced isolates. Coregenome-based analyses were performed per ST encountered. blaCMY-2-like was carried in 168 isolates, 52 carried blaCTX-M-2 group, 7 blaSHV, 5 a combination of blaCMY-2-like-blaSHV and 3 a combination of blaCMY-2-likeblaCTX-M-2 group. In 25 isolates no ESBL/pAmpC genes that were screened for were found. WGS characterization of 36 selected strains showed plasmid-encoded blaCMY-2 in 21, blaCTX-M-165 in 11 and blaSHV-12 in 7 strains. These genes were mostly carried on IncI1/ST12, IncQ1, and IncI1/ST231 plasmids, respectively. Finally, 17 strains belonged to S. Heidelberg ST15, 16 to S. Paratyphi B variant Java ST28, 1 to S. Enteritidis ST11, 1 to S. Kentucky ST152 and 1 to S. Albany ST292. Phylogenetic comparisons with publicly available genomes showed separate clustering of Colombian S. Heidelberg and S. Paratyphi B var. Java. In conclusion, resistance to extended-spectrum cephalosporins in Salmonella from Colombian poultry is mainly encoded by blaCMY-2 and blaCTX-M-165 genes. These genes are mostly associated with IncI1/ST12 and IncQ1 plasmids, respectively. Evolutionary divergence is observed between Colombian S. Heidelberg and S. Paratyphi B var. Java and those from other countries..

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae
Rozwandowicz, M. ; Brouwer, M.S.M. ; Fischer, J. ; Wagenaar, J.A. ; Gonzalez-Zorn, B. ; Guerra, B. ; Mevius, D.J. ; Hordijk, J. - \ 2018
Journal of Antimicrobial Chemotherapy 73 (2018)5. - ISSN 0305-7453 - p. 1121 - 1137.
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
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.
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
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.
High heterogeneity of Escherichia coli sequence types harbouring ESBL/AmpC genes on IncI1 plasmids in the Colombian poultry chain
Castellanos, Luis Ricardo ; Donado-Godoy, Pilar ; León, Maribel ; Clavijo, Viviana ; Arevalo, Alejandra ; Bernal, Johan F. ; Timmerman, Arjen J. ; Mevius, Dik J. ; Wagenaar, Jaap A. ; Hordijk, Joost - \ 2017
PLoS ONE 12 (2017)1. - ISSN 1932-6203

Background: Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread. Objectives: To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars). Methods: A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC ≥ 4 mg/L) were screened for ESBL/AmpC genes including blaCTX-M, blaSHV, blaTEM, blaCMY and blaOXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization. Results: In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured blaCMY-2 (75%), fourteen blaSHV-12 (11%), three blaSHV-5 (2%), five blaCTX-M-2 (4%), one blaCTX-M-15 (1%), one blaCTX-M-8 (1%), four a combination of blaCMY-2 and blaSHV-12 (4%) and two a combination of blaCMY-2 and blaSHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly blaCMY-2 (16/22), and to a lesser extend blaSHV-12 (5/22) and blaCTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), IncB/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with blaCMY-2 (12/16) and IncHI2/ST7 with blaCTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates. Conclusions: Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by blaCMY-2 and blaSHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.

Plasmids of distinct IncK lineages show compatible phenotypes
Rozwandowicz, Marta ; Brouwer, Michael S.M. ; Zomer, Aldert L. ; Bossers, Alex ; Harders, Frank ; Mevius, Dik J. ; Wagenaar, Jaap A. ; Hordijk, Joost - \ 2017
Antimicrobial Agents and Chemotherapy 61 (2017)3. - ISSN 0066-4804
IncK - Incompatibility - Plasmid

IncK plasmids are some of the main carriers of blaCTX-M-14 and blaCMY-2genes and show high similarity to other plasmids belonging to the I complex, including IncB/O plasmids. Here, we studied the phylogenetic relationship of 37 newly sequenced IncK and IncB/O plasmids. We show that IncK plasmids can be divided into two compatible lineages named IncK1 and IncK2.

ESBL prevalentie op vleeskuikenbedrijven 2016
Graveland, H. ; Hordijk, Joost ; Dierikx, C.M. ; Goot, J.A. van der; Heederik, Dick ; Garcia, Alejandro Dorado ; Mevius, D.J. ; Wagenaar, J.A. - \ 2016
Universiteit Utrecht
Tom als inspiratiebron : Aflevering Afscheid Tom Ottervanger
Meulen, B.M.J. van der; Damme, E. van; Dekker, C. ; Drijber, B.J. ; Pijnacker Hordijk, E. ; Lugard, P. ; Niels, G. ; Wesseling, R. - \ 2016
Markt & Mededinging 2016 (2016). - ISSN 1387-6236 - p. 1 - 6.
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.

Non-random species loss in bacterial communities reduces antifungal volatile production
Hol, G. ; Garbeva, P. ; Hordijk, C. ; Hundscheid, M.P.J. ; Klein Gunnewiek, P.J.A. ; Agtmaal, M. van; Boer, W. de - \ 2015
Ecology 96 (2015)8. - ISSN 0012-9658 - p. 2042 - 2048.
The contribution of low-abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil-borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution-to-extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon-limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil-borne pathogens.
Longitudinal study of extended-spectrum-β-lactamase- and AmpC-Producing Enterobacteriaceae in household dogs
Baede, V.O. ; Wagenaar, J.A. ; Broens, E.M. ; Duim, Birgitta ; Dohmen, Wietske ; Nijsse, Rolf ; Timmerman, Arjen J. ; Hordijk, Joost - \ 2015
Antimicrobial Agents and Chemotherapy 59 (2015)6. - ISSN 0066-4804 - p. 3117 - 3124.

A longitudinal study was performed to (i) investigate the continuity of shedding of extended-spectrum-beta-lactamase (ESBL)-producing Enterobacteriaceae in dogs without clinical signs, (ii) identify dominant plasmid-mediated ESBL genes, and (iii) quantify ESBL-producing Enterobacteriaceae in feces. Fecal samples from 38 dogs were collected monthly for 6 months. Additional samples were collected from 7 included dogs on a weekly basis for 6 weeks. Numbers of CFU per gram of feces for non-wild-type Enterobacteriaceae were determined by using MacConkey agar supplemented with 1 mg/liter cefotaxime (MCC), and those for total Enterobacteriaceae were determined by using MacConkey agar. Cefotaxime-resistant isolates were screened by PCR and sequence analysis for the presence of blaCTX-M, blaCMY, blaSHV, blaOXA, and blaTEM gene families. Bacterial species were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. PCR-negative isolates were tested by a double-disk synergy test for enhanced AmpC expression. A total of 259 samples were screened, and 126 samples were culture positive on MCC, resulting in 352 isolates, 327 of which were Escherichia coli. Nine dogs were continuously positive during this study, and 6 dogs were continuously negative. Monthly or weekly shifts in fecal shedding were observed for 23 dogs. Genotyping showed a large variety of ESBL genes and gene combinations at single and multiple consecutive sampling moments. The ESBL genes blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaSHV-12, and blaCMY-2 were most frequently found. The mean number of CFU of non-wild-type Enterobacteriaceae was 6.11 × 108 CFU/g feces. This study showed an abundance of ESBL-producing Enterobacteriaceae in dogs in the Netherlands, mostly in high concentrations. Fecal shedding was shown to be highly dynamic over time, which is important to consider when studying ESBL epidemiology.

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles
Os, G.J. van; Agtmaal, M. van; Hol, G. ; Hundscheid, M.P.J. ; Runia, W.T. ; Hordijk, C. ; Boer, W. de - \ 2015
Frontiers in Microbiology 6 (2015). - ISSN 1664-302X
pythium root-rot - soilborne plant-diseases - microbial-populations - organic amendments - biological-control - bulbous iris - fungistasis - growth - biocontrol - diversity
There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.
Check title to add to marked list
<< previous | next >>

Show 20 50 100 records per page

 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.