Day 4: Metagenomics

Day 4 introduces metagenomic sequencing as a practical tool for surveillance, diagnosis, and clinical decision-making. The lessons use compact teaching re-analyses so that you can focus on the workflow, interpretation, and limitations without needing to reproduce full published studies during the workshop.

In Clinical Foundations & AMR Surveillance, you will work with a six-sample demonstration re-analysis adapted from Pereira-Dias et al. The exercise uses a subset of a Vietnamese healthy gut microbiome and antimicrobial resistance surveillance dataset to show how shotgun metagenomic reads can be processed into taxonomic and AMR summaries. This is a teaching demonstration, not a full reproduction of the original paper.

In Actionable Diagnostics & Clinical Reasoning, you will move from surveillance to a clinical metagenomics case. The lesson focuses on when unbiased sequencing is useful, how infection results should be interpreted, and how metagenomic evidence supports clinical reasoning rather than replacing it.

Technical note

The Day 4 practical exercises use R 4.5.0 and Python 3.13. The Python examples also require numpy and pandas.

Lessons

1. Clinical Foundations & AMR Surveillance: Workflow Setup
2. Clinical Foundations & AMR Surveillance: Taxonomy Analysis
3. Clinical Foundations & AMR Surveillance: AMR Analysis & Summary
4. Actionable Diagnostics & Clinical Reasoning: Case Simulation
5. Actionable Diagnostics & Clinical Reasoning: Signal Analysis