Aims: Evaluate how the choice of antibiotic resistance gene (ARG) annotation pipelines influences resistome characterization. Explore the methodological sources of variation among commonly used pipelines and assess their implications. Discuss best practices for analysing, reporting, and communicating results, promoting broader community dialogue.

Background: Sequencing-based detection of ARGs is foundational to global antimicrobial resistance surveillance. However, current computational pipelines produce strikingly inconsistent results. These discrepancies severely distort our understanding of the resistome and can lead to unsuitable public health risk assessments and policy decisions, as well as flawed evolutionary and ecological interpretations of bacterial adaptation. This workshop addresses the urgent need to critically evaluate current pipelines and clearly communicate inferences of the resistome.

Workshop Participants and Activity: The workshop will bring together a cohort of 60–80 researchers specialising in metagenomics, bioinformatics, or AMR surveillance. Moving beyond passive listening, the session is structured around interactive small-group problem solving and collective framework building.

Participants will:

Critically evaluate resistome outputs: Use a provided interactive Shiny web application to actively dissect and compare conflicting results generated by different ARG annotation pipelines.
Troubleshoot habitat-specific challenges: Engage in hands-on group work to identify sources of uncertainty when detecting both well-characterized and latent ARGs across diverse environments.
Shape the future of the field: Directly contribute to developing a community-driven guideline framework for resistome reporting.

Workshop Overview