Genomic Epidemiology

The Research Group for Genomic Epidemiology enables global detection, prediction and prevention of infectious diseases from gene level to global scale, with a specific focus on AMR and bacterial pathogens. Integrating microbiology, bioinformatics and epidemiology, it ranks among the global leaders in sequence-based surveillance, with emphasis on the application of sequencing technologies for diagnostics, antimicrobial susceptibility prediction, and surveillance of pathogens and microbiomes.

Approaches and methods

• Sequence-based surveillance: whole-genome sequencing (WGS) and metagenomic sequencing for diagnostics, antimicrobial susceptibility testing, outbreak investigation and population-level surveillance.
• Pathogen and AMR genomics: genomic analyses of bacterial pathogens and resistomes; genotype–phenotype linking; and evidence-based tools for AMR detection and interpretation.
• Bioinformatic pipelines and enabling technologies: development and maintenance of user-friendly online tools and scalable workflows for frontline laboratories.
• Phylogenomics and phylodynamics: investigation of relatedness and spread by comparing pathogen genomes and linking them to incidence data and environmental factors (e.g. climate); model development to predict likely outbreak trajectories.
• Microbiome and transmission dynamics: surveillance across hosts, foods and environments to trace emergence, transmission routes and hotspots.
• Sampling strategy from gene level to global scale: targeted hotspot sampling and integration of global datasets to understand selection, transmission and spread.

Collaborations and impact

The group applies whole-genome and metagenomic sequencing in diagnostics, surveillance, antimicrobial susceptibility testing and surveillance, and translates its research into regulatory advice and training in collaboration with national and international authorities and programmes.

Increasingly, the group focuses on enabling technologies – robust, shareable bioinformatic pipelines and laboratory methods – while strengthening foundational laboratory research that explains global observations. This approach supports rapid, reproducible analyses and improves the evidence base for decision-making in the global community.