Rob J. L. Willems

Post-transfer instability, not initial transfer, limits dissemination of IncI1-blaCTX-M-1 plasmids between chicken and human Escherichia coli.

This study shows that IncI1-blaCTX-M-1 plasmids transfer efficiently between chicken and human E. coli but are less stable in human hosts, limiting their spread.

Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli

This study compares the pangenome composition of ESBL-E. coli isolates from patients receiving selective digestive decontamination (SDD) and those receiving standard care, finding no major differences in overall pangenome but some antibiotic resistance gene associations.

gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species

gplasCC classifies and reconstructs plasmids from short-read sequencing data across multiple bacterial species using simplified plasmidEC and species-specific databases.

PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

PlasmidEC and gplas2: An optimised short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli

This paper introduces plasmidEC and gplas2 to accurately predict and reconstruct antibiotic resistance plasmids in E. coli using short-read sequencing data, outperforming existing methods.

Recovering Escherichia coli plasmids in the absence of long-read sequencing data

This study benchmarks six plasmid prediction tools for E. coli short-read data, finding that none reliably reconstruct all plasmids, especially those carrying antibiotic resistance genes.

Mode and dynamics of vanA-type vancomycin-resistancedissemination in Dutch hospitals

This study quantifies the modes of vanA-type vancomycin resistance dissemination in Dutch hospitals, finding clonal spread as the dominant mechanism with significant contributions from horizontal gene transfer.

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen Enterococcus faecium

This paper uses genome-wide co-evolution analysis to identify genomic rearrangements in Enterococcus faecium, linking them to adaptation to hospital environments.

gplas: a comprehensive tool for plasmid analysis using short-read graphs

gplas separates plasmid contigs from bacterial genomes using short-read data to enable plasmid epidemiology analysis.

Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

This study analyzes the genomes of Enterococcus faecium strains to understand their adaptive evolution, identifying plasmids as key indicators of host specificity through population-wide genomic analysis.