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Metagenomics applied to surveillance of pathogens and antimicrobial resistance

Technical University of Denmark (DTU) via Coursera

This course may be unavailable.


Hello learners enrolled in the course,

We are reaching out to let you know that the “Metagenomics applied to surveillance of pathogens and antimicrobial resistance” course will close for new learner enrollment on 7th February 2024. Since you have already enrolled, you will continue to see it on your Coursera Dashboard as long as you remain enrolled in the course.

The reason for ending the course is that we don’t have the sufficient resources for keeping the course content updated any longer.

If you are interested in earning a Course Certificate for this course, please upgrade or apply for Financial Aid by 6th February 2024, if you have not already done so. If you are a Coursera for Business learner, you can continue to use your sponsored credit. In order to earn a Course Certificate, you will need to complete all graded assignments, including peer reviews, by 7th August 2024. After that point, no new assignment submissions will be accepted for Certificate credit.

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Happy learning,

The Course Team

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, 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

We look forward to welcoming you !


  • 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.
    • 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 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

Taught by

Patrick Munk, Liese Van Gompel, Valeria Bortolaia, Ana Sofia Ribeiro Duarte , Pimlapas Leekitcharoenphon, Tine Hald and Sünje Johanna Pamp


4.7 rating at Coursera based on 295 ratings

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