Metagenomics applied to surveillance of pathogens and antimicrobial resistance from Coursera

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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Examines various sequencing platforms, providing learners with knowledge on different possibilities for metagenomics

Lays a solid foundation for beginners by explaining fundamental concepts in metagenomics

Provides practical guidance on sample processing and analysis methods for both bacterial and viral metagenomics

Discusses the significance of epidemiology in surveillance, emphasizing its role in disease control

Emphasizes the need for controls throughout a metagenomics study, ensuring reliable and accurate results

Taught by reputable instructors with expertise in metagenomics, providing valuable insights and industry knowledge

Reviews summary

Metagenomics for pathogens and antimicrobial resistance

This in-depth course teaches the fundamentals of metagenomics applied to surveillance of pathogens and antimicrobial resistance. It is highly informative, with practical and up-to-date resources. The well-structured lectures cover all aspects of a metagenomics project, from study design to data analysis and result interpretation. Despite some minor issues with the virtual machine, the course is highly recommended for those interested in the field.

Excellent instructors and topics.

"Excellent instructors and topics. "

Emphasizes practical applications.

"The problem chosen as an example is relevant to the real-world situation..."

Demonstrates data analysis and interpretation.

"Excellent course. It requieres to have a little previous knowledge on statistics..."

Occasional issues with the virtual machine.

"Despite the difficulty with the VM, this course was very interesting!..."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Metagenomics applied to surveillance of pathogens and antimicrobial resistance with these activities:

Review basic microbiology

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Strengthen your knowledge of microbiology to enhance your understanding of metagenomics.

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Identify key concepts and terminology in microbiology.
Review textbooks, articles, or online resources to refresh your knowledge.
Consider taking practice quizzes or exercises to test your understanding.

Review statistical inference

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Review the basics of statistical inference, including hypothesis testing, confidence intervals, and regression analysis. This will help you understand the statistical methods used in metagenomics studies.

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Identify key concepts
Practice solving problems

Use R for metagenomics data analysis

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Learn how to use R for metagenomics data analysis. This will allow you to analyze your own data and interpret the results.

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Install R and RStudio
Load and clean data
Perform basic data analysis

Five other activities

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Practice read classification

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Solidify your understanding of read classification techniques through targeted practice.

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Find practice datasets or online exercises for read classification.
Attempt the practice exercises and review your results.
Seek feedback on your results to identify areas for improvement.

Practice identifying pathogens and antimicrobial resistance genes

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Practice identifying pathogens and antimicrobial resistance genes in metagenomics data. This will help you develop the skills needed to interpret metagenomics data in a clinical setting.

Browse courses on Pathogen Identification

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Use online resources
Complete practice exercises

Bioinformatics software tutorials

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Enhance your practical skills in bioinformatics by following tutorials on relevant software.

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Identify useful software for metagenomics analysis.
Locate tutorials for the identified software.
Work through the tutorials and practice using the software.

Develop a metagenomics data analysis pipeline

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Develop a metagenomics data analysis pipeline that can be used to analyze data from your own research projects or from public databases. This will allow you to automate the data analysis process and make it more efficient.

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Design the pipeline
Implement the pipeline
Test the pipeline

Participate in a metagenomics challenge

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Participate in a metagenomics challenge to test your skills and learn from others. This will help you stay up-to-date on the latest advances in metagenomics and data analysis.

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Find a challenge
Prepare your submission
Submit your work

Career center

Learners who complete Metagenomics applied to surveillance of pathogens and antimicrobial resistance will develop knowledge and skills that may be useful to these careers:

Microbiologist

Metagenomics applied to surveillance of pathogens and antimicrobial resistance is an essential course for Microbiologists who want to stay up-to-date on the latest techniques for detecting and tracking pathogens. This course provides a comprehensive overview of the field of metagenomics, including the different sequencing platforms and their possibilities regarding metagenomics, the steps involved in a general metagenomics study, and the principles behind various tools available for analysis of metagenomics data.

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Biostatistician

This course would be extremely useful for Biostatisticians who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Epidemiologist

This course is highly recommended for Epidemiologists who want to learn more about metagenomics and its applications in public health. The course introduces the basic concepts of metagenomics and its potential for surveillance of pathogens and antimicrobial resistance. It also provides an overview of the different steps involved in a metagenomics study, from sample collection to data analysis.

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Public Health Scientist

This course would be beneficial for Public Health Scientists who want to learn more about metagenomics and its applications in public health. The course provides an overview of the field of metagenomics, including the different sequencing platforms and their possibilities regarding metagenomics, the steps involved in a general metagenomics study, and the principles behind various tools available for analysis of metagenomics data.

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Research Scientist

This course could be useful for Research Scientists who are interested in learning more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Laboratory Technician

This course may be helpful for Laboratory Technicians who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Healthcare Data Scientist

This course would be helpful for Healthcare Data Scientists who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Computational Biologist

This course would be helpful for Computational Biologists who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Bioinformatician

This course would be helpful for Bioinformaticians who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Data Analyst

This course would be helpful for Data Analysts who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Clinical Research Associate

This course may be helpful for Clinical Research Associates who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Science Writer

This course may be helpful for Science Writers who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Technical Writer

This course may be helpful for Technical Writers who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Health Communicator

This course may be helpful for Health Communicators who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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Medical Writer

This course may be helpful for Medical Writers who want to learn more about metagenomics and its applications in public health. The course covers a wide range of topics, including the use of metagenomics for surveillance of pathogens and antimicrobial resistance, the design and analysis of metagenomics studies, and the interpretation of metagenomics data.

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