Jaap A. Wagenaar

This paper analyzes STEC population structure and host-disease associations using whole genome sequencing of 3,418 isolates from 11 European countries, identifying distinct subpopulations linked to disease severity.

The paper identifies Lactococcus lactis strains that inhibit livestock-associated Staphylococcus aureus in pig nasal microbiomes through sequencing-guided isolation and in vitro testing.

This study uses cfDNA sequencing in newborn foals to detect sepsis-causing bacteria and identifies host-related biomarkers associated with sepsis.

The paper investigates whether flumequine selects for the same resistance mechanisms in E. coli as enrofloxacin, finding similar SNPs in gyrA and comparable resistance rates.

This study examines the longitudinal development of the piglet nasal microbiome and identifies microbial interactions that could help control respiratory pathogens.

The paper determines the minimal selective concentrations of three antibiotics in broiler cecal fermentations to identify thresholds for antimicrobial resistance selection.

This study shows that persistent antimicrobials in broilers lead to prolonged antimicrobial resistance, while non-persistent ones have shorter effects.

RFPlasmid predicts whether contigs from draft genomes are plasmid or chromosomal using machine learning, improving accuracy over single-feature methods.

The paper sequences whole genomes of Giardia duodenalis assemblages C and D from dog feces, revealing host-associated gene differences.