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Module 13: Antimicrobial-resistant gene analysis

2024-01-27

Overview

Module 13 is dedicated to the analysis of antimicrobial-resistant (AMR) genes, a growing concern in global health due to the increasing prevalence of drug-resistant bacterial strains. This module will cover the principles of AMR, the mechanisms by which bacteria acquire resistance, and the methods used to predict and analyze AMR genes in bacterial genomes. Students will learn about the tools and databases that are essential for identifying and characterizing AMR genes, as well as the implications of AMR in clinical and environmental settings. Practical labs will provide hands-on experience in AMR prediction and analysis, reinforcing the theoretical knowledge gained.

Introduction

  • The significance of AMR gene analysis in the context of public health and medicine
  • An overview of the types of antimicrobial resistance and the genetic basis of AMR
  • The challenges and importance of accurate AMR prediction in combating antibiotic resistance

Topics

Fundamentals of Antimicrobial Resistance

  • Understanding the different mechanisms of antimicrobial resistance, including target modification, efflux pumps, enzymatic degradation, and others
  • The role of horizontal gene transfer and mutations in the spread of AMR genes

AMR Prediction Tools and Databases

  • Introduction to bioinformatics tools for AMR gene prediction, such as ResFinder, TBprofiler, CARD, and ARG-ANNOT Utilizing databases like NCBI’s AMRFinderPlus and the Comprehensive Antibiotic Resistance Database (CARD) for AMR gene characterization
  • Evaluating the performance and specificity of different AMR prediction tools

Analyzing AMR Genes in Genomic Data

  • Methods for detecting AMR genes in whole-genome sequencing data
  • The use of metagenomics for the surveillance of AMR genes in environmental samples
  • Strategies for interpreting the clinical relevance of identified AMR genes

Addressing the Challenges in AMR Analysis

  • Overcoming the difficulties in distinguishing between AMR genes and closely related non-resistant genes
  • The importance of contextualizing AMR gene analysis within the bacterial genome and its environment

Labs

  • Lab 1: Predicting AMR Genes Using TBprofiler, ResFinder and CARD
  • Lab 2: Characterizing AMR Genes with AMRFinderPlus and Analyzing Results
  • Lab 3: Case Studies in AMR Gene Analysis from Clinical and Environmental Samples

Learning Outcomes

By the end of this module, students will be able to:

  • Describe the mechanisms by which bacteria acquire and confer antimicrobial resistance.
  • Use bioinformatics tools and databases to predict the presence of AMR genes in bacterial genomes.
  • Analyze and interpret the results of AMR gene predictions in the context of genomic data.
  • Understand the clinical and environmental implications of AMR gene analysis.
  • Address the challenges associated with the accurate prediction and analysis of AMR genes.
  • Communicate the outcomes of AMR gene analysis effectively in scientific and healthcare settings.