About this Course
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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 !...
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Approx. 13 hours to complete

Suggested: 3 weeks of study, 1-3 hours/week...
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English

Subtitles: English...
Globe

100% online courses

Start instantly and learn at your own schedule.
Calendar

Flexible deadlines

Reset deadlines in accordance to your schedule.
Clock

Approx. 13 hours to complete

Suggested: 3 weeks of study, 1-3 hours/week...
Comment Dots

English

Subtitles: English...

Syllabus - What you will learn from this course

Week
1
Clock
3 hours to complete

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....
Reading
10 videos (Total 112 min), 13 readings, 2 quizzes
Video10 videos
Introduction to metagenomics10m
Considerations and controls for metagenomic/microbiome projects10m
Introduction to antimicrobial resistance11m
Sampling for surveillance18m
Sampling at farms and slaughterhouses14m
Sample storage2m
Isolation of DNA from complex samples10m
Sample processing for viral metagenomics7m
Sequencing platforms12m
Reading13 readings
Glossary20m
Get started !5m
Introduction to metagenomics2m
Considerations and controls for metagenomic/microbiome projects2m
Introduction to antimicrobial resistance2m
Sampling for surveillance5m
Sampling at farms and slaughterhouses2m
Sample storage2m
Isolation of DNA from complex samples2m
Notes on library preparation5m
Sequencing platforms10m
Assessment case-study - part 15m
Assessment case study - part 22m
Quiz2 practice exercises
Module 1 assessment - part 18m
Module 1 assessment - part 212m
Week
2
Clock
3 hours to complete

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. ...
Reading
6 videos (Total 64 min), 11 readings, 1 quiz
Video6 videos
Overview of available metagenomic analysis tools7m
MGmapper13m
ResFinder database5m
Demo of metagenomic classification using KRAKEN16m
Real example of metagenomic analysis - lessons learned14m
Reading11 readings
General introduction to bioinformatics analysis of metagenomics data5m
Overview of available metagenomic analysis tools10m
MGmapper10m
MGmapper - Best mode vs Full mode10m
ResFinder database3m
Assessment case-study - part 310m
Samples sheet10m
Report A - FastQC results10m
Report B - MGmapper results10m
Report C - KRAKEN results10m
Report D10m
Quiz1 practice exercise
Module 2 assessment24m
Week
3
Clock
8 hours to complete

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 ...
Reading
6 videos (Total 81 min), 15 readings, 6 quizzes
Video6 videos
Metagenomic assembly and binning: reconstructing genomes from reads15m
Application of metagenomics in surveillance - methods (part 1)10m
Application of metagenomics in surveillance - methods (part 2)16m
Application of metagenomics in surveillance - opportunities and challenges21m
Farewell3m
Reading15 readings
Virtual Machine setupm
Analysis and visualization of read count data10m
Metagenomic assembly and binning: reconstructing genomes from reads10m
Application of metagenomics in surveillance - methods10m
Potential of metagenomics for surveillance10m
Challenges of metagenomics for surveillance10m
Assessment case-study - part 45m
Report D10m
Epidemiology sheet and Report E10m
Introduction5m
Final quiz - section I - Sampling10m
Final quiz - section II - Quality control30m
Final quiz - section III - Bioinformatics analysis of metagenomics30m
Final quiz - section IV - Interpretation of metagenomics results10m
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10m
Quiz6 practice exercises
Module 3 assessment10m
Final quiz - section I - Sampling18m
Final quiz - section II - Quality control30m
Final quiz - section III - Bioinformatics analysis of metagenomics30m
Final quiz - section IV - Interpretation of metagenomics results30m
Final quiz - section V - Analysis of metagenomics results in a surveillance context30m

Instructors

Ana Sofia Ribeiro Duarte

Assistant Professor
National Food Institute

Sünje Johanna Pamp

Associate Professor
Research Group for Genomic Epidemiology, Technical University of Denmark

Liese Van Gompel

PhD Candidate Epidemiology
Utrecht University, Institute for Risk Assessment Sciences (IRAS)

Pimlapas Leekitcharoenphon

PostDoc
Research Group for Genomic Epidemiology, DTU Food

About Technical University of Denmark (DTU)

DTU focuses on research in technical and natural sciences that contributes to the development of society. As an industrially orientated university, our goal is to supply high-level international research based on combining theory with constructing models and empirical methods....

Frequently Asked Questions

  • Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.

  • When you purchase a Certificate you get access to all course materials, including graded assignments. Upon completing the course, your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.

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