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DTU - Metagenomics applied to surveillance of pathogens and antimicrobial resistance 

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Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Overview

Duration

15 hours

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Total fee

Free

Mode of learning

Online

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Credential

Certificate

Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Highlights

  • 67% started a new career after completing these courses.
  • Earn a shareable certificate upon completion.
  • Flexible deadlines according to your schedule.
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Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Course details

More about this course
  • 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
Read more

Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Curriculum

From sampling to sequencing

Welcome

Introduction to metagenomics

Considerations and controls for metagenomic/microbiome projects

Introduction to antimicrobial resistance

Sampling for surveillance

Sampling at farms and slaughterhouses

Sample storage

Isolation of DNA from complex samples

Sample processing for viral metagenomics

Sequencing platforms

Glossary

Get started !

Introduction to metagenomics

Considerations and controls for metagenomic/microbiome projects

Introduction to antimicrobial resistance

Sampling for surveillance

Sampling at farms and slaughterhouses

Sample storage

Isolation of DNA from complex samples

Notes on library preparation

Sequencing platforms

Assessment case-study - part 1

Assessment case study - part 2

Module 1 assessment - part 1

Module 1 assessment - part 2

FROM READS TO RESULTS

General introduction to bioinformatics analysis of metagenomics data

Overview of available metagenomic analysis tools

MGmapper

ResFinder database

Demo of metagenomic classification using KRAKEN

Real example of metagenomic analysis - lessons learned

General introduction to bioinformatics analysis of metagenomics data

Overview of available metagenomic analysis tools

MGmapper

MGmapper - Best mode vs Full mode

ResFinder database

Assessment case-study - part 3

Samples sheet

Report A - FastQC results

Report B - MGmapper results

Report C - KRAKEN results

Report D

Module 2 assessment

Interpretation of results and potential of metagenomics for surveillance

Analysis and visualization of read count data

Metagenomic assembly and binning: reconstructing genomes from reads

Application of metagenomics in surveillance - methods (part 1)

Application of metagenomics in surveillance - methods (part 2)

Application of metagenomics in surveillance - opportunities and challenges

Farewell

Virtual Machine setup

Analysis and visualization of read count data

Metagenomic assembly and binning: reconstructing genomes from reads

Application of metagenomics in surveillance - methods

Potential of metagenomics for surveillance

Challenges of metagenomics for surveillance

Assessment case-study - part 4

Report D

Epidemiology sheet and Report E

Introduction

Final quiz - section I - Sampling

Final quiz - section II - Quality control

Final quiz - section III - Bioinformatics analysis of metagenomics

Final quiz - section IV - Interpretation of metagenomics results

Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context

Extra material for final assessment

Module 3 assessment

Final quiz - section I - Sampling

Final quiz - section II - Quality control

Final quiz - section III - Bioinformatics analysis of metagenomics

Final quiz - section IV - Interpretation of metagenomics results

Final quiz - section V - Analysis of metagenomics results in a surveillance context

Faculty Icon

Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Faculty details

Ana Sofia Ribeiro Duarte
University : Technical University of Denmark (DTU)

Metagenomics applied to surveillance of pathogens and antimicrobial resistance
 at 
Coursera 
Admission Process

    Important Dates

    May 25, 2024
    Course Commencement Date

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