Aims: To equip ECRs, researchers and decision-makers with a foundational, end-to-end understanding of culture-based whole genome sequencing (WGS) and how it is applied in One Health AMR research.

Background: WGS enables high-resolution tracking of resistant organisms and mobile genetic elements across human, animal, food and environmental sectors. Yet it remains underused in environmental AMR research, where metagenomic approaches are widely applied. While metagenomics captures community-level diversity, it often cannot reliably resolve the host of a resistance gene, plasmid architecture, or transmission linkages. This workshop addresses that skills and knowledge gap with accessible, foundational training in how WGS data is generated, analysed and interpreted in a One Health context.

Workshop Participants and Activity: Open to ECRs, researchers, industry end-users and decision-makers working at the environmental interface of AMR; no prior WGS experience is required. Across five short modules, the session moves from why One Health WGS matters, through the bioinformatics workflow, to how WGS and metagenomics work as complementary tools — anchored by a step-by-step One Health E. coli surveillance case study spanning multiple sectors. The format combines accessible presentations with facilitated case-study discussion and Q&A throughout.

Participants will:

Understand the end-to-end WGS workflow — from project design, sampling and platform selection through to quality assurance, bioinformatics analysis and phylogenetics
Learn how WGS complements and contextualises metagenomics-based AMR studies, interpreting ARG detection in terms of host organism, gene mobility and clinical relevance
Explore a real-world One Health E. coli surveillance case study and leave with best-practice guidance, key databases and platforms

Workshop Overview