Anita C. Schürch

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.

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.

This study evaluates the effectiveness of Oxford Nanopore adaptive sampling in metagenomic profiling of clinical sputum samples, finding limited enrichment and significant pore loss issues.

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

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.

The paper introduces a computational pipeline for consistent plasmid typing using long-read sequencing data, enabling classification of novel and known plasmid types.

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.

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.

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

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

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.