Willem van Schaik

This study identifies IS1216 as a key driver in the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium through comparative genomic analysis of 152 plasmid sequences.

This study analyzes the population genomics of Staphylococcus haemolyticus to understand its transition from commensal to pathogenic states.

This paper introduces plaque-2-sequence, a low-cost, high-throughput method for sequencing phage genomes directly from plaques, enabling rapid and scalable genomic analysis of phages.

The paper characterizes a laboratory contaminant, Noodlococcus, as a new species within the Kocuria genus, revealing two phylogenetically distinct clades with significant ANI differences.

This study examines how early antibiotic and probiotic treatments affect the gut microbiome and resistome in preterm infants, finding that probiotics reduce antibiotic resistance genes and MDR pathogens but do not eliminate them.

This study identifies Staphylococcus haemolyticus as a common gut colonizer in preterm infants and reveals its role as a reservoir of antibiotic resistance genes through genomic analysis.

The paper develops a TraDIS platform for Enterococcus faecium using nanopore sequencing and a WebAssembly tool to study vancomycin resistance and persistence.

This study uses genomic sequencing to show low levels of multi-drug resistant E. coli in a UK ICU during strict COVID-19 measures, with only one carbapenemase-producing strain identified.

The paper analyzes the potential transfer of antimicrobial resistance genes by strain VE202-06 and concludes there is no risk of vancomycin resistance transfer.

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.

The paper compares ARGs and microbiota in hospital sewage, WWTP influent, effluent, and surface water to assess hospital contributions to ARG spread in sewer systems.

The paper develops a 3D-based method to predict antibiotic resistance determinants in the human intestinal microbiota and identifies resistotypes in a cohort.

The paper models how host metapopulation structure affects bacterial genetic diversity, showing migration can increase or decrease strain relatedness depending on microepidemic rates.