Genomes to Action: AMR in Bacteria

This course is part of the "From Microbial Genomes to Reliable Predictions" series, organized by the Pathogen Data Network (PDN) project, which is supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under Award Number U24AI183840.

Attendance is free of charge; however, registration is mandatory.

Do you want to know more about how PDN resources can help you with your bacterial and fungal analysis? We have designed a series of half-day courses to introduce researchers, clinicians and public health professionals to the bacterial and fungal side of the PDN ecosystem, best practices and useful tools.

Overview

The first course will focus on antimicrobial resistance (AMR) in bacteria: how resistance develops, the importance of diagnosing resistance, and predicting it from genomic data. Learn how we are tacking it at PDN / SIB, and the online tools that you can use now to get started.

Using provided genomic data of bacteria, you will learn how to:

• Run quality control on your data

• Determine species and sequence type

• Find AMR determinants using web-based tools

• Interpret the results

Audience

This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who wish to deepen their knowledge and understanding of antimicrobial resistance prediction from genome data.

Learning outcomes

At the end of the course, the participants should be able to:

• Determine antimicrobial resistance gene content in bacterial genomes through browser-based and command-line tools.
• Explain the possibilities and challenges of genotypic resistance prediction.
• Identify best practices and respective tools for AMR prediction

Prerequisites

Knowledge / competencies

This course has no knowledge requirements.

Technical

You will need access to a computer installed with a web browser. Data to download will be available before the course. If you have Galaxy access, you can also test programs there.

Schedule – CE(S)T time zone

This course will take place from 13:00 to 17:30 CET and will be recorded.

Application

There is no registration fees for this course.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close on 04/12/2026 or as soon as the places will be filled up. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

This course will be streamed.

The course will start at 13:00 CET and end around 17:30 CET.

Precise information will be provided to the registered participants in due time.

Additional information

Coordination: Grégoire Rossier, SIB Training group.

A Certificate of Attendance will be sent provided you were present at the course.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.