Author

E. J. Kuijper

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 9

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Organism:C. elegans· 5 Approach:experimental assay· 5 Assay:whole-genome sequencing· 5 Approach:statistical model· 4 Research Focus:gene regulatory network inference· 3 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2

Frequent Co-Authors

W. K. Smits· 7 shared C. Harmanus· 4 shared Q. R. Ducarmon· 4 shared B. V. H. Hornung· 3 shared I. M. J. G. Bos-Sanders· 3 shared R. D. Zwittink· 3 shared I. M. Boekhoud· 2 shared M. J. T. Crobach· 2 shared

Activity by Year

2018-2023 · peak 3/yr

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10 top collaborators · 30 mutual co-author links

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7 shared papersMicrobiology

W. K. Smits

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9 papers

Recent·Most cited

Fungal-bacterial gut microbiota interactions in patients with Clostridioides difficile colonisation and infection

J. G. E. Henderickx, M. J. T. Crobach, E. M. Terveer, W. K. Smits, E. J. Kuijper, R. D. Zwittink

This study examines fungal-bacterial gut microbiota interactions in patients with C. difficile colonisation and infection, finding differences in fungal abundance and indirect interactions with bacteria.

bioRxiv · Jul 12, 2023 · PreprintMicrobiology

Clostridioides difficile PCR ribotype 151 is polyphyletic and includes pathogenic isolates from cryptic clade C-II with mono-toxin pathogenicity loci that can escape routine diagnostics

Q. R. Ducarmon, T. van der Bruggen, C. Harmanus, I. M. J. G. Sanders, L. G. M. Daenen, A. C. Fluit, R. H. A. M. Vossen, S. L. Kloet, E. J. Kuijper, W. K. Smits

The paper identifies that PCR ribotype 151 of Clostridioides difficile is polyphyletic, includes both non-toxigenic and toxigenic isolates, and contains pathogenic variants that evade routine diagnostics.

bioRxiv · Aug 17, 2022 · PreprintMicrobiology

Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile

A. M. Roseboom, Q. R. Ducarmon, B. V. H. Hornung, C. Harmanus, M. J. T. Crobach, E. J. Kuijper, R. H. A. M. Vossen, S. L. Kloet, W. K. Smits

The paper describes a C. difficile clinical isolate carrying three compatible plasmids and identifies functional replicons in two of them.

bioRxiv · Jul 10, 2022Microbiology

Asymptomatic gut colonization by extended-spectrum beta-lactamase-producing Escherichia coli is not associated with an altered gut microbiome or metabolome in Dutch adults

Q. R. Ducarmon, R. D. Zwittink, R. P. J. Willems, A. Verhoeven, S. Nooij, F. R. M. van der Klis, E. Franz, J. Kool, M. Giera, C. M. J. E. Vandenbroucke-Grauls, S. Fuentes, E. J. Kuijper

This study finds that asymptomatic gut colonization by ESBL-producing E. coli in Dutch adults is not linked to changes in microbiome or metabolome composition.

bioRxiv · May 18, 2021 · PreprintMicrobiology

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile

I. M. Boekhoud, I. Sidorov, S. Nooij, C. Harmanus, I. M. J. G. Bos-Sanders, V. Viprey, B. Spittal, E. Clark, K. Davies, J. Freeman, E. J. Kuijper, W. K. Smits, COMBACTE-CDI Consortium, European Study Group for Clostridioides difficile

The paper shows heme dependence in metronidazole resistance in C. difficile clinical isolates, linked to a SNP in hsmA and associated with a resistant lineage.

bioRxiv · Nov 18, 2020Microbiology

Toward standards in clinical microbiome studies: comparison of three DNA extraction methods and two bioinformatic pipelines

Q. R. Ducarmon, B. B. V. H. Hornung, A. R. Geelen, E. J. Kuijper, R. D. Zwittink

This study compares three DNA extraction methods and two bioinformatic pipelines for microbiome analysis, finding that methods vary in accuracy and that negative controls are critical for low-biomass samples.

bioRxiv · Aug 30, 2019 · PreprintMicrobiology

An in silico survey of Clostridioides difficile extrachromosomal elements

B. V. H. Hornung, E. J. Kuijper, W. K. Smits

This study identifies extrachromosomal elements in C. difficile strains using in silico analysis, finding 13% of strains contain 1-6 elements, including 6 novel plasmid families.

bioRxiv · May 29, 2019Microbiology

Plasmid-mediated metronidazole resistance in Clostridioides difficile

I. Boekhoud, B. V. H. Hornung, A. E. Sevilla Romeo, C. Harmanus, I. M. J. G. Bos-Sanders, E. Terveer, R. Bolea, J. Corver, E. J. Kuijper, W. K. Smits

This paper identifies a plasmid, pCD-METRO, as the first reported cause of plasmid-mediated metronidazole resistance in Clostridioides difficile, showing its global dissemination and horizontal transfer potential.

bioRxiv · May 29, 2019Microbiology

Genome location dictates the transcriptional response to PolC-inhibition in Clostridium difficile

E. van Eijk, I. M. Boekhoud, E. J. Kuijper, I. M. J. G. Bos-Sanders, G. Wright, W. K. Smits

This study shows that genome location influences the transcriptional response to PolC-inhibition in C. difficile, with origin-proximal genes being more upregulated.

bioRxiv · Sep 21, 2018Microbiology