Nienke L. Plantinga

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 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.

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.