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

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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.

Video Lectures

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

Tools of Bioinformatics: how do you find a needle in a haystack?

Scarlet Bliss & Amy Pickering, PhD.

19 min

Analyzing a Metagenomic Sample in Galaxy

Scarlet Bliss 

19 min

Galaxy Tutorial Video

Scarlet Bliss

5 min

Part Three

Class Discussion & Final Project

Your instructor will determine the format of your final project. For assignment details, see the Materials page here:

 

About PARE-Seq

Welcome to the Prevalence of Antibiotic Resistance in the Environment (PARE) short course, a bioinformatics-based approach to studying the emerging public health issue of antibiotic, or antimicrobial, resistance (AMR). We are offering PARE-Seq as an alternative laboratory experience for high school and undergraduate students in the wake of COVID-19 and through the transition to virtual education. When participating in this course, please complete the pre- and post- evaluation surveys in the menu bar above, helping us to improve the quality of remote STEM learning for future participants. We hope you enjoy the course.

PARE-Seq is a program created by Tufts University undergraduate students Scarlet Bliss (Laidlaw Scholar) and Eve Abraha in collaboration with Dr. Bascom Slack (director of the PARE program), Dr. Amy Pickering (Assistant Professor, UC Berkeley), and Dr. Erica Fuhrmeister (postdoctoral fellow, Tufts University).