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Exploring the Landscape of Antibiotic Resistance in Microbiomes

Explore the exciting microbial world and how this knowledge is revolutionising our understanding of antibiotic resistance.

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Microbial community: Humans in the team looking at the globe, all made from bacteria
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Find out why and how to perform large scale studies on antibiotic resistance

In the fight against antibiotic resistance, microbial communities and the resistomes they carry are increasingly important data sources. This field is rapidly advancing, but the big data generated is creating a gap between health sciences and bioinformatics.

On this three-week course from the University of Oslo, you’ll begin to close this gap. With the help of a team of experts, you’ll explore why and how to study resistomes, including hands-on resistome analysis.

Discover how antibiotic resistance has become one of the most urgent health threats

The misuse and overuse of antibiotics has accelerated the development and spread of antibiotic resistance, making antibiotics ineffective.

You’ll start by looking at how studies are contributing to the current understanding of drug resistance. Through this examination, you’ll discover the relation between antibiotic use, its lack of target specificity, the void in discovery of new antibiotics, and the current drug resistance crisis.

Examine how the study of antibiotic resistance genes helps us understand antimicrobial resistance

Microbes develop antibiotic resistance by using instructions from their genes, and there can often be a variety within a microbial community.

This course will guide you through the study of resistomes, exploring the different resistance mechanisms, how drug resistance genes are exchanged among bacteria, how studies are designed, how to handle samples, and how to analyse the data.

Embark on a journey of real exploration of resistome data using ResistoXplorer

Through hands-on exercises and analysis, you’ll be introduced to a real experience of resistome analysis. You’ll use ResistoXplorer, a web-based resource developed at the University of Oslo that doesn’t require advanced bioinformatics skills.

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Skip to 0 minutes and 2 seconds Invisible to the naked eye, microbes are everywhere. And so are the antimicrobial resistance genes they carry. These have increased in abundance and types due to overuse. Antibiotic resistance is now one of our largest health threats. To slow down the problem actions to reduce antibiotic use are being implemented worldwide. An important data source is microbial communities and the resistance genes they carry; the resistome. They help us to answer questions such as how drug resistance is acquired and how it is transmitted. This field is rapidly advancing thanks to new sequence technologies and analytical tools. It’s revolutionising the way we understand antimicrobial resistance. But there is a challenge.

Skip to 1 minute and 3 seconds The large data generated from such communities is creating a growing gap between health science disciplines and bioinformatics. This threatens the speed that research needs to address the current crisis. This course aims to help closing this gap. [- We often find ourselves wondering–] We bring together experienced clinicians. [- But first, I have to kill a myth.] Public health experts. [- And boy, is this a story to be shared.] Molecular microbiologists and bioinformatitions to explore with you why we want and how we can study resistomes in microbial communities. You will experience an exciting and demystifying course, including hands-on exploration of real resistome data. Join us in this fascinating journey.

Syllabus

  • Week 1

    Antibiotic resistance: a global crisis

    • Welcome

      Time to start: Meet your educators and your fellow learners! Learn also what is waiting for you in this exciting week.

    • The landscape of antibiotic resistance in humans

      Microbes are everywhere, and so are the antibiotic resistance genes that they carry. In this section you will learn how resistome studies are contributing to our understanding of antibiotic resistance.

    • Antibiotic resistance is a global crisis

      Antimicrobials are critical for fighting infections in humans, animals and plants, but they are stopping working. In this section, you will learn about the global crisis this represents to humanity.

    • Collateral effect of antibiotics

      Antibiotics lack specificity towards targeted infectious microbes. In this section you will learn about the off-target impact of antibiotics on the human microbiome, with particular focus on resistomes.

    • Summary of week 1

      We have arrived to the end of week 1. Time to recall the highlights and reflect upon what we have learned so far.

  • Week 2

    The study of resistomes

    • Antibiotic resistance mechanisms and exploration tools

      Resistomes are diverse and susceptible to many changes. In this section you will learn about mechanisms by which bacteria can acquire resistance genes and will be introduced to the tools for exploring human resistomes.

    • Designing a study

      Don't rush to collect samples! Designing a study is one of the most crucial aspects of a research project, and in this section you will learn important lessons about sample size, proper controls and possible biases.

    • Handling of samples

      After the study design is complete, it is time for sample collection, DNA extraction, library preparation and DNA sequencing. In this section you will explore each step with exciting reads and discussions.

    • Upstream data processing

      What happens to the data after it is back from sequencing? In this section you will learn what is needed for pre-processing of sequencing data. You will also hear an exciting talk by experienced bioinformatician Dr. George Chen.

    • Databases and Visual Exploration

      How are ARGs present in the samples annotated? Have they been characterized before? Get ready for exciting activities in this section! You will also hear Dr. Jonathon Baker talk about compositional data in microbiome studies.

    • Summary of week 2

      This week you learned important concepts regarding the emergence and spread of antimicrobial resistance. Also, now you know what happens from sample collection to sequencing and initial analysis. Let's go analyse real data?

  • Week 3

    Analyzing resistomes with ResistoXplorer: a hands-on exploration

    • Introduction to the tool

      How do we make sense of hundreds of resistance genes identified and quantified in resistome studies? Here, you will be introduced to a visual-analytics tool called ResistoXplorer that will help you to interpret such information.

    • Preprocessing of the resistome data

      To make the results more meaningful and comparable, several steps must be completed before analyzing resistome data. In this section, we will introduce and guide you through different preprocessing steps using ResistoXplorer.

    • Composition profiling

      In this section, you will learn how to visualise the composition of resistome data using different methods present in ResistoXplorer. You will perform a hands-on exercise on visualising the real resistome data in ResistoXplorer.

    • Comparative and Statistical analyses

      How similar are resistome samples in their composition? How do we detect differences in resistome composition between samples? Here you will learn and perform exercises to identify clusters and explore various statistical methods.

    • Integrative and Network analyses

      Are the microbiome and resistome associated? Can one microbe carry many resistance genes? With ResistoXplorer you will learn to perform integrative analysis of microbiome and resistome data, and explore such complex networks.

    • Summary of week 3

      We have arrived to the end of week 3. Let's take some time to recall the highlights of this week and reflect upon what we have learned.

    • Dear future, welcome!!!

      In this final section you are invited to reflect upon what you have learned in the course, and experiences that may have changed your views.

When would you like to start?

Start straight away and join a global classroom of learners. If the course hasn’t started yet you’ll see the future date listed below.

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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...

  • Reflect upon the urgency in addressing the antimicrobial resistance crisis
  • Demonstrate knowledge on why microbial communities and the antibiotic resistance genes they carry-the resistome-are relevant for the understanding of drug resistance
  • Discuss the consequences of the off-target impact of antibiotics on microbial communities
  • Demonstrate knowledge on how resistome studies are designed and conducted
  • Apply the acquired knowledge in a hands-on activity that uses ResistoXplorer for visual, statistical and functional analysis of resistome data

Who is the course for?

This course will be particularly useful for clinicians, basic research students, and scientists in health-science fields, as well as public health professionals. You may also find it appealing if you work in the field of bioinformatics, with a special interest in strengthening multi-disciplinary collaborations.

What software or tools do you need?

You will be invited for a hands-on experience using ResistoXplorer, a free web tool developed at the University of Oslo. The tool works with major modern browsers such as Google Chrome, Mozilla Firefox, Safari, and Microsoft Internet Explorer.

Who will you learn with?

I am Fernanda Petersen, a Professor at the University of Oslo in Norway. My group brings together scientists from various fields, to address challenges related to infections and antibiotic resistance.

I am an Associate Professor at the University of Oslo and my interests span from understanding the molecular interactions between microbes to exploring strategies to fight antibiotic resistance.

I am a bioinformatician pursuing my Ph.D. at the University of Oslo, Norway. My research interest involves analyzing and visualizing big Omics data such as metagenomics.

I am Gabriela Salvadori, a postdoc researcher at the University of Oslo.
My main interests are the study of human resistome and state-of-the-art methods to hunt for new antibiotic resistance genes.

Who developed the course?

University of Oslo

Founded in 1811, the University of Oslo (UiO) is the highest ranked institution of education and research in Norway.

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