PARE-Seq: A Virtual Short Course on the Bioinformatics of Antibiotic Resistance


Video Lectures

Course Schedule

The video content of this course is divided into three components. Part 1 includes a background on antimicrobial resistance (AMR) and an overview of its public health significance. Part 2 covers various environmental surveillance methods for AMR, explains the benefits of long read sequencing, and involves an interactive activity, using the platform Galaxy, introducing students to the applications of bioinformatics for AMR surveillance. In Part 3 you will be complete a final project, challenging you to develop potential experiments and hypotheses for AMR research implementing the bioinformatics workflow you've learned to use.


Sample Learning Schedule:

Part One: For background on the structure of the course and to meet your co-teachers, watch the Introduction Video. Then, watch Videos 1-4 below. After Video 4, complete the Student Quiz before continuing.

Part Two: Watch Videos 5 and 6 to get an introduction to metagenomics, bioinformatics, and the Galaxy platform. Next you will conduct the bioinformatics activity, and analyze and interpret your output data. 

Part Three: We encourage instructors to host a student discussion (using this guide) to allow for collective student analysis of findings and exploration of hypothesis-driven inquiry and experimental design. Next, there are two options of final projects, for use at the discretion of the instructor, which can be found in Materials.


At the end of PARE-Seq, students will take a post-assessment to evaluate PARE-Seq learning gains and course quality.

Part One

Background on Antimicrobial Resistance

Antibiotics and Antimicrobial Resistance

Eve Abraha

9 min

Antimicrobial Resistant Bacteria Spread: Through the Environment and to Our Bodies

Eve Abraha

8 min

Why is Antimicrobial Resistance a Global Public Health Issue?

Eve Abraha & Maya Nadimpalli, Phd.

15 min

Spotlight on Antimicrobial Resistance Genes of Clinical Significance

Scarlet Bliss

12 min

Part Two

Introduction to ARG Detection Techniques, Bioinformatics, & Galaxy