Metagenomics applied to surveillance of pathogens and antimicrobial resistance
от партнера
Metagenomics applied to surveillance of pathogens and antimicrobial resistance
Technical University of Denmark (DTU)
Об этом курсе
4.7
Оценки: 18
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 !
Программа курса: что вы изучите
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 видео (всего 112 мин.), 13 материалов для самостоятельного изучения, 2 тестов
10 видео
Welcome14мин
Introduction to metagenomics10мин
Considerations and controls for metagenomic/microbiome projects10мин
Introduction to antimicrobial resistance11мин
Sampling for surveillance18мин
Sampling at farms and slaughterhouses14мин
Sample storage2мин
Isolation of DNA from complex samples10мин
Sample processing for viral metagenomics7мин
Sequencing platforms12мин
13 материала для самостоятельного изучения
Glossary20мин
Get started !5мин
Introduction to metagenomics2мин
Considerations and controls for metagenomic/microbiome projects2мин
Introduction to antimicrobial resistance2мин
Sampling for surveillance5мин
Sampling at farms and slaughterhouses2мин
Sample storage2мин
Isolation of DNA from complex samples2мин
Notes on library preparation5мин
Sequencing platforms10мин
Assessment case-study - part 15мин
Assessment case study - part 22мин
2 практического упражнения
Module 1 assessment - part 18мин
Module 1 assessment - part 212мин
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 видео (всего 64 мин.), 11 материалов для самостоятельного изучения, 1 тест
6 видео
Overview of available metagenomic analysis tools7мин
MGmapper13мин
ResFinder database5мин
Demo of metagenomic classification using KRAKEN16мин
Real example of metagenomic analysis - lessons learned14мин
11 материала для самостоятельного изучения
General introduction to bioinformatics analysis of metagenomics data5мин
Overview of available metagenomic analysis tools10мин
MGmapper10мин
MGmapper - Best mode vs Full mode10мин
ResFinder database3мин
Assessment case-study - part 310мин
Samples sheet10мин
Report A - FastQC results10мин
Report B - MGmapper results10мин
Report C - KRAKEN results10мин
Report D10мин
1 практическое упражнение
Module 2 assessment24мин
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 видео (всего 81 мин.), 15 материалов для самостоятельного изучения, 6 тестов
6 видео
Metagenomic assembly and binning: reconstructing genomes from reads15мин
Application of metagenomics in surveillance - methods (part 1)10мин
Application of metagenomics in surveillance - methods (part 2)16мин
Application of metagenomics in surveillance - opportunities and challenges21мин
Farewell3мин
15 материала для самостоятельного изучения
Virtual Machine setupмин
Analysis and visualization of read count data10мин
Metagenomic assembly and binning: reconstructing genomes from reads10мин
Application of metagenomics in surveillance - methods10мин
Potential of metagenomics for surveillance10мин
Challenges of metagenomics for surveillance10мин
Assessment case-study - part 45мин
Report D10мин
Epidemiology sheet and Report E10мин
Introduction5мин
Final quiz - section I - Sampling10мин
Final quiz - section II - Quality control30мин
Final quiz - section III - Bioinformatics analysis of metagenomics30мин
Final quiz - section IV - Interpretation of metagenomics results10мин
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10мин
6 практического упражнения
Module 3 assessment10мин
Final quiz - section I - Sampling18мин
Final quiz - section II - Quality control30мин
Final quiz - section III - Bioinformatics analysis of metagenomics30мин
Final quiz - section IV - Interpretation of metagenomics results30мин
Final quiz - section V - Analysis of metagenomics results in a surveillance context30мин
Преподавателя
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
О 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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