E. J. Kuijper

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.

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.

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

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.

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.

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.

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.

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.

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