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Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis

Predict antimicrobial resistance, master data-sharing, and enhance your expertise in AMR genomics using cutting-edge databases.

8,383 enrolled on this course

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  • Duration

    3 weeks
  • Weekly study

    5 hours
  • Digital upgrade

    Free
  • Accreditation

    AvailableMore info

Discover how to harness AMR genotype-phenotype databases to advance your career

Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with this online course from the Wellcome Sanger Institute.

Dive into the world of AMR genotype-phenotype databases and gain practical skills that will set you apart in your field.

Unlock the power of AMR data

On this course, you’ll learn how to effectively utilise antimicrobial resistance (AMR) genotype-phenotype databases to advance your research, clinical practice, and public health efforts. You’ll begin by understanding how AMR data is created and how these insights can enhance your work. This foundational knowledge will empower you to interpret AMR data with confidence and clarity.

Detect and analyse AMR in your data

After grasping data creation, you’ll discover how to effectively detect AMR in your own data using various tools and algorithms. You’ll learn to navigate AMR databases, understand their strengths and limitations, and harmonise outputs from different sources.

Share and leverage AMR data for impact

Next, you’ll learn how to share AMR data and understand how to do it in a FAIR (Findable, Accessible, Interoperable, Reusable) manner. At this point, you’ll also discuss the principles of open access data and explore databases for storing public data, as well as delving into future trends, including AI and machine learning, and how they are furthering AMR research and application.

Enhance your career prospects in the scientific arena

By the end of the course, you’ll be able to confidently contribute to AMR genotype-phenotype databases, improving your career mobility and making a tangible impact in your field.

You’ll join a global network of scientists and professionals dedicated to advancing AMR research and practice.

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Skip to 0 minutes and 14 seconds Welcome to the Antimicrobial Databases and Genotype Prediction Data Sharing and Analysis course. In this course, you’ll learn from a team of experts in the fields of bacterial genomics and data analysis about the different databases and approaches used for predicting anti referable resistance from genetic information. We will start with the fundamentals of a MR, how we link genotype and phenotype data together and discuss the scenarios where this is easy and where this is complex. Next, we will deep dive into the various online databases, which house a MR data and discuss how to use them. You will learn how to interpret and compare their outputs, as well as explore the pros and cons of each database and associated tools.

Skip to 0 minutes and 56 seconds But finally, we’ll come full circle and teach you how to contribute your own data to these databases using open research principles, and use your A MR predictions for future studies such as epidemiology and correlations, Using interactive exercises, peer and educator discussions, and various other tools. We will ensure that you come away from this course with an understanding of how you can better explore a MR patterns and insights from your own pathogen data sets.

Syllabus

  • Week 1

    AMR foundations: from mechanisms to data

    • Introduction to Week 1

      You'll be welcomed to the learning community, introduced to the course structure, content, and educators, and provided with a glossary to familiarize yourself with key terms. The week's learning will officially start!

    • Biological mechanisms of AMR

      You'll explore the importance of genotypic data in understanding the AMR, followed by basics on intrinsic and acquired resistance mechanisms. You'll engage in a discussion on how bacteria acquire AMR mechanisms.

    • AMR data generation

      This section covers key topics in AMR testing, including phenotypic methods (qualitative and quantitative). It advocates the importance of incorporating genotypic data, complemented by an article on downloading genotypic data.

    • Methods for linking genotypic with phenotypic evidence

      This section explores the association between genotypic and phenotypic data through exercises and case studies, including the WHO TB catalogue, and provides practical examples of linking genotype to phenotype for AMR.

    • Introduction to case studies

      Case studies that have successfully linked AMR genotype and phenotype data together.

    • Your learning progress

      This section includes a quiz to check your learning progress and a summary of the key points covered in Week 1.

  • Week 2

    Using databases and tools to detect AMR

    • Databases

      You'll be introduced to key databases through videos, audio, and a poll, followed by a case study on ResFinder. You'll also learn how to access databases and conclude with a quiz to assess your knowledge.

    • Tools for detecting AMR

      This section focuses on how AMR genes are detected, exploring different tools and understanding database input/output. You'll engage in hands-on activities connecting to databases to download specific gene and plasmid.

    • Data interpretation

      This section covers the constraints in working with AMR data through an exercise, followed by a discussion on identifying patterns in your work.

    • Harmonisation of AMR outputs/databases

      This section introduces the hAMRonization tool and discusses the harmonization of AMR outputs and databases.

    • Your learning progress

      This section includes a discussion to reflect on your learning progress, a quiz to check your understanding, and a summary of the key points covered in Week 2.

  • Week 3

    AMR genomic data: Analysis, integration, and sharing

    • AMR genomic epidemiology

      You'll be introduced to comparative analysis and some related case studies, including data integration. The week ends with a discussion on which further AMR analyses you plan to pursue.

    • AMR data sharing

      This section covers the principles of FAIR and open access data, followed by a discussion on whether you have shared or plan to share data in your work.

    • How to contribute data to global AMR resources

      This section explores public data storage, covering the International Nucleotide Sequence Database, metadata, and phenotypic depositing. You'll also learn about how to upload data.

    • Where do we go next?

      This section outlines the next steps for working with AMR databases and provides information on further training courses to enhance your knowledge.

    • Your learning outcomes

      In the final section, you'll review Week 3 with a summary, take a final test to assess your overall learning and explore what's next from WCS.

Who is this accredited by?

Royal College of Pathologists
Royal College of Pathologists:

The Royal College of Pathologists is a professional membership organisation with charitable status, concerned with all matters relating to the science and practice of pathology.

When would you like to start?

  • Date to be announced

Add to Wishlist to be emailed when new dates are announced

Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Explain the genotypic basis of AMR
  • Contrast and critique the various ways to predict AMR from linked genotype/phenotype data
  • Discuss the main AMR databases and their related pros and cons
  • Explain how different AMR prediction tools can be operated and their outputs interpreted and implemented, understanding the current pitfalls of those tools
  • Describe the process required to create and share FAIR and open AMR data
  • Explain metadata associated with AMR and how it can be used in genomic epidemiology

Who is the course for?

This course is designed for early career researchers, healthcare professionals at any stage, and public health experts who are familiar with AMR but have limited experience with genotypic data.

No advanced prior knowledge is required, just a basic understanding of AMR concepts and a desire to enhance your expertise. Links to background reading and revision materials are included.

Who will you learn with?

Associate Prof at Nottingham Trent University, UK. I work on evolution, epidemiology and genomics of pathogens such as Mycobacterium tuberculosis and anything else of interest.

Jane is currently a research fellow at Monash University in the Infectious Disease Genomics @ Alfred group, where she focuses on developing our understanding of AMR in the hospital setting.

Lead Bioinformatician AusTrakka platform. I have a keen interest translational AMR genomics and developing tools to deliver results that are actionable in a public and clinical health setting.

Who developed the course?

Wellcome Sanger Institute

Wellcome Sanger Institute Scientific Training and Events develops and delivers conferences, courses, and networking events aligned with the distinctive science led by the Institute’s core programmes, focusing on disease, planetary, and engineering genomics. 

What's included?

Wellcome Sanger Institute are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible
  • Learning on FutureLearn

    Your learning, your rules

    • Courses are split into weeks, activities, and steps to help you keep track of your learning
    • Learn through a mix of bite-sized videos, long- and short-form articles, audio, and practical activities
    • Stay motivated by using the Progress page to keep track of your step completion and assessment scores

    Join a global classroom

    • Experience the power of social learning, and get inspired by an international network of learners
    • Share ideas with your peers and course educators on every step of the course
    • Join the conversation by reading, @ing, liking, bookmarking, and replying to comments from others

    Map your progress

    • As you work through the course, use notifications and the Progress page to guide your learning
    • Whenever you’re ready, mark each step as complete, you’re in control
    • Complete 90% of course steps and all of the assessments to earn your certificate

    Want to know more about learning on FutureLearn? Using FutureLearn

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