Metagenomics applied to surveillance of pathogens and antimicrobial resistance

Go to Course: https://www.coursera.org/learn/metagenomics

Introduction

# Course Review: Metagenomics Applied to Surveillance of Pathogens and Antimicrobial Resistance ## Overview In an age where infectious diseases and antimicrobial resistance are significant global health threats, understanding microbial communities and their interactions with human health is paramount. The "Metagenomics Applied to Surveillance of Pathogens and Antimicrobial Resistance" course on Coursera is an exceptional resource that delves into this nascent yet critical field. This course provides the theoretical background and practical skills needed to harness the power of metagenomics for public health applications, primarily focusing on pathogen surveillance and understanding antimicrobial resistance. ## Course Structure & Content The course is divided into three comprehensive modules, each addressing unique aspects of metagenomics: ### 1. From Sampling to Sequencing This foundational module lays the groundwork for metagenomic studies. Participants are introduced to the myriad considerations and controls essential for effective metagenomic research. Key topics include: - **Sampling Techniques:** The module outlines how to strategize a sampling plan, execute effective sampling, and understand the influence of sample storage on results. - **Extraction Methods:** Both DNA and RNA extraction techniques for bacterial and viral microorganisms are covered, providing a solid understanding of sample preparation. - **Sequencing Technologies:** Dive into the essentials of library preparation and familiarize yourself with various sequencing technologies. ### 2. From Reads to Results After building a solid foundation, the second module pivots towards bioinformatics, the backbone of metagenomics data analysis. Participants will gain insights into: - **Bioinformatics Analysis:** Learn different types of analyses available and explore the various algorithms utilized in the field. - **Quality Control:** Understand the importance of maintaining data integrity and how to apply tools such as MGmapper and KRAKEN for effective data analysis. - **Resistance Gene Databases:** Explore ResFinder and its role in identifying antimicrobial resistance genes, along with case studies demonstrating the complexities involved in bioinformatics analysis. ### 3. Interpretation of Results and Potential of Metagenomics for Surveillance The final module focuses on how to analyze and interpret metagenomic data effectively. Students will learn: - **Analysis Approaches:** Discover the nuances of classification versus assembly analyses. - **Data Visualization:** Techniques to visualize read counts and integrate metagenomic data with explanatory data. - **Surveillance Potential:** Knowledge on how to harness metagenomics for integrated global surveillance and the challenges that accompany this process. ## Recommendation The "Metagenomics Applied to Surveillance of Pathogens and Antimicrobial Resistance" course is highly recommended for professionals in the fields of microbiology, public health, epidemiology, and bioinformatics. Here's why: 1. **Comprehensive Learning Experience:** The course offers a well-rounded perspective on metagenomics, breaking down complex concepts into manageable lessons. 2. **Practical Skills Development:** Participants acquire valuable skills in both laboratory techniques and bioinformatics that are directly applicable in real-world settings. 3. **Expert Instruction:** Taught by industry-leading experts, students will benefit from both theoretical insights and practical applications. 4. **Real-World Applications:** The course emphasizes the impact of metagenomics on public health surveillance, making it relevant not only for academic purposes but also for those working in healthcare and research. 5. **Flexible Learning:** As an online course, it provides the flexibility to learn at your own pace while still allowing for an interactive and engaging educational experience. In conclusion, this course stands out as an essential stepping stone for those looking to contribute to advancements in microbiology and public health. By understanding and applying the concepts explored in this course, participants will be well-equipped to address the increasingly complex challenges presented by pathogens and antimicrobial resistance in today's world.

Syllabus

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.

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