Metagenomics applied to surveillance of pathogens and antimicrobial resistance (Coursera)

In this course, we teach about the potential of metagenomics for surveillance and give the learners an overview of the steps and considerations in a metagenomics study. After this course, the learners will know:

• the difference between the concepts of metagenomics and other microbial genomics
• the need to use controls in different steps of a metagenomics study
• the advantages of metagenomics for the surveillance of antimicrobial resistance
• how sampling design, sample size, sample material and sample handling influence the outcome of a metagenomics study
• sample processing for bacterial and viral metagenomics
• different sequencing platforms and their possibilities regarding metagenomics
• the steps involved in a general metagenomics study, including quality control, mapping to different databases, and read count analysis
• the principles behind various tools available for analysis of metagenomics data
• how to interpret read classification results
• the need for epidemiology in surveillance
• the concept of global and integrated surveillance
• the challenges for the use of metagenomics in surveillance
• the potential of metagenomics for surveillance

Syllabus

WEEK 1
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; 3) Sequencing - from library preparation to the basics of different sequencing technologies.

WEEK 2
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.

WEEK 3
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 vizualize read counts and to analyze 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