Metagenomics applied to surveillance of pathogens and antimicrobial resistance
提供方
Metagenomics applied to surveillance of pathogens and antimicrobial resistance
Technical University of Denmark (DTU)
課程信息
4.7
18 個評分
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 !
教學大綱 - 您將從這門課程中學到什麼
Week
1From 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.
10 個視頻（共 112 分鐘）, 13 個閱讀材料, 2 個測驗
10 個視頻
Welcome14分鐘
Introduction to metagenomics10分鐘
Considerations and controls for metagenomic/microbiome projects10分鐘
Introduction to antimicrobial resistance11分鐘
Sampling for surveillance18分鐘
Sampling at farms and slaughterhouses14分鐘
Sample storage2分鐘
Isolation of DNA from complex samples10分鐘
Sample processing for viral metagenomics7分鐘
Sequencing platforms12分鐘
13 個閱讀材料
Glossary20分鐘
Get started !5分鐘
Introduction to metagenomics2分鐘
Considerations and controls for metagenomic/microbiome projects2分鐘
Introduction to antimicrobial resistance2分鐘
Sampling for surveillance5分鐘
Sampling at farms and slaughterhouses2分鐘
Sample storage2分鐘
Isolation of DNA from complex samples2分鐘
Notes on library preparation5分鐘
Sequencing platforms10分鐘
Assessment case-study - part 15分鐘
Assessment case study - part 22分鐘
2 個練習
Module 1 assessment - part 18分鐘
Module 1 assessment - part 212分鐘
Week
2FROM 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.
6 個視頻（共 64 分鐘）, 11 個閱讀材料, 1 個測驗
6 個視頻
Overview of available metagenomic analysis tools7分鐘
MGmapper13分鐘
ResFinder database5分鐘
Demo of metagenomic classification using KRAKEN16分鐘
Real example of metagenomic analysis - lessons learned14分鐘
11 個閱讀材料
General introduction to bioinformatics analysis of metagenomics data5分鐘
Overview of available metagenomic analysis tools10分鐘
MGmapper10分鐘
MGmapper - Best mode vs Full mode10分鐘
ResFinder database3分鐘
Assessment case-study - part 310分鐘
Samples sheet10分鐘
Report A - FastQC results10分鐘
Report B - MGmapper results10分鐘
Report C - KRAKEN results10分鐘
Report D10分鐘
1 個練習
Module 2 assessment24分鐘
Week
3Interpretation 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
6 個視頻（共 81 分鐘）, 15 個閱讀材料, 6 個測驗
6 個視頻
Metagenomic assembly and binning: reconstructing genomes from reads15分鐘
Application of metagenomics in surveillance - methods (part 1)10分鐘
Application of metagenomics in surveillance - methods (part 2)16分鐘
Application of metagenomics in surveillance - opportunities and challenges21分鐘
Farewell3分鐘
15 個閱讀材料
Virtual Machine setup分鐘
Analysis and visualization of read count data10分鐘
Metagenomic assembly and binning: reconstructing genomes from reads10分鐘
Application of metagenomics in surveillance - methods10分鐘
Potential of metagenomics for surveillance10分鐘
Challenges of metagenomics for surveillance10分鐘
Assessment case-study - part 45分鐘
Report D10分鐘
Epidemiology sheet and Report E10分鐘
Introduction5分鐘
Final quiz - section I - Sampling10分鐘
Final quiz - section II - Quality control30分鐘
Final quiz - section III - Bioinformatics analysis of metagenomics30分鐘
Final quiz - section IV - Interpretation of metagenomics results10分鐘
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10分鐘
6 個練習
Module 3 assessment10分鐘
Final quiz - section I - Sampling18分鐘
Final quiz - section II - Quality control30分鐘
Final quiz - section III - Bioinformatics analysis of metagenomics30分鐘
Final quiz - section IV - Interpretation of metagenomics results30分鐘
Final quiz - section V - Analysis of metagenomics results in a surveillance context30分鐘
講師
Ana Sofia Ribeiro Duarte
Assistant ProfessorNational Food Institute
Sünje Johanna Pamp
Associate ProfessorResearch Group for Genomic Epidemiology, Technical University of Denmark
Liese Van Gompel
PhD Candidate EpidemiologyUtrecht University, Institute for Risk Assessment Sciences (IRAS)
Pimlapas Leekitcharoenphon
PostDocResearch Group for Genomic Epidemiology, DTU Food
關於 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.
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