Metagenomics applied to surveillance

The field of metagenomics and whole community sequencing is a promising area to unravel the content of microbial communities and their relationship to disease and antimicrobial resistance in the human population. Bioinformatic tools are extremely important for making sense out of metagenomics data, by estimating the presence of pathogens and antimicrobial resistance determinants in complex samples. Combined with relevant explanatory data, metagenomics is a powerful tool for surveillance.

In this course, Metagenomics applied to surveillance of pathogens and antimicrobial resistance, we teach about the potential of metagenomics for surveillance and give the learners an overview of the steps and considerations in a metagenomics study.

This course is for those who have a general interest in surveillance, epidemiology of antimicrobial resistance, genomics, DNA sequencing, bioinformatics. Here you will learn basic theoretical background on surveillance, metagenomics, DNA sequencing and interpretation of sequencing results.

Course modules:

From sampling to sequencing

In this module, you will be introduced to metagenomics, some of the considerations and controls that need to be in place in a metagenomics study, and to the topic of antimicrobial resistance. You will also learn about: 1) Sampling and sample handling - the considerations behind a sampling plan, how to perform sampling in practice, and how sample storage can affect metagenomics results; 2) DNA and RNA extraction methods - both for bacterial and viral microorganisms; and 3) Sequencing - from library preparation to the basics of different sequencing technologies.

From reads to results

In this module, you will be introduced to the basics of bioinformatics analysis of metagenomics data, including the different types of analysis possible and the different algorithms available. You will then learn about quality control, MGmapper and KRAKEN (two freely available bioinformatics pipelines), and ResFinder (a database of antimicrobial resistance genes). An example from a real study will demonstrate some of the challenges of a bioinformatics analysis.

Interpretation of results and potential of metagenomics for surveillance

In this module you will learn about two different approaches to analyse and interpret sequence reads - classification and assembly. You will see examples of methods to visualize read counts and to analyse metagenomics together with explanatory data. Last, you will learn the potential of metagenomics for the development of a future global and integrated surveillance, and the challenges you may encounter during that process.
19 MAY 2024