Roger Stephan

The paper uses whole genome sequencing to analyze Vibrio cholerae O1 isolates from 2023-2024 European cholera cases, confirming their lineage and identifying drug-resistant clones.

This paper develops a method to link plasmid-encoded AMR genes to their bacterial hosts using nanopore sequencing methylation data, achieving high accuracy in clinical samples.

This paper evaluates standalone Oxford Nanopore sequencing for foodborne pathogen surveillance, showing it can achieve high accuracy with quality control tools like alpaqa.

This paper develops a metagenomic framework for detecting Listeria monocytogenes in food environments, showing that direct metagenomics captures more strain diversity than culture-based methods.

This study evaluates Oxford Nanopore Technologies for Listeria monocytogenes outbreak detection, finding most assemblies suitable for high-resolution genotyping but with challenges from methylation motifs.

This study isolates and characterizes reuterin-producing Lactobacillus reuteri strains from poultry, showing their phylogenetic grouping and antimicrobial resistance profiles.