AMR Genomic Surveillance: Whole-Genome Sequencing, Resistome Analysis & Genomic Epidemiology

Aim

Workshop Objectives

Workshop Structure

📅 Day 1: Whole-Genome Sequencing for AMR Surveillance

Focus: Understand antimicrobial resistance mechanisms, bacterial whole-genome sequencing, sequencing data quality, and genome assembly for genomic AMR surveillance.

• Introduction to antimicrobial resistance and its global significance
• Major mechanisms of bacterial antimicrobial resistance
• Intrinsic and acquired resistance mechanisms
• Horizontal gene transfer and the spread of resistance determinants
• Introduction to bacterial whole-genome sequencing (WGS)
• Short-read and long-read sequencing technologies
• Understanding FASTQ files, sequencing quality, coverage, and depth
• Quality control and preprocessing of bacterial sequencing data
• Fundamentals of bacterial genome assembly
• Overview of WGS-based AMR surveillance workflows

🛠️ Hands-on:

Analyze a public bacterial whole-genome sequencing dataset, assess sequencing read quality, perform quality control, and explore bacterial genome assembly using bioinformatics tools.

🧰 Tools Covered:

NCBI SRA, FastQC, Galaxy

📅 Day 2: Resistome Analysis & AMR Gene Detection

Focus: Identify antimicrobial resistance genes and resistance-associated mutations, characterize bacterial resistomes, and interpret genomic predictions of antimicrobial resistance.

• Understanding the bacterial resistome and its significance in AMR surveillance
• Acquired resistance genes and resistance-associated mutations
• Major molecular mechanisms of antimicrobial resistance
• Resistance genes associated with different antibiotic classes
• Genotype-to-phenotype interpretation in antimicrobial resistance
• Introduction to CARD, ResFinder, NCBI AMRFinderPlus, and MEGARes
• Identification and annotation of antimicrobial resistance determinants
• Comparative resistome analysis across bacterial isolates
• Multidrug-resistance profiling and resistance gene distribution
• Interpretation of AMR prediction reports and limitations of genomic resistance prediction

🛠️ Hands-on:

Analyze bacterial genome sequences using AMR bioinformatics resources, identify resistance genes and associated determinants, compare resistome profiles across multiple isolates, and interpret predicted resistance patterns.

🧰 Tools Covered:

CARD, ResFinder, NCBI AMRFinderPlus, MEGARes, Galaxy

📅 Day 3: Pathogen Tracking & Genomic Epidemiology

Focus: Apply bacterial strain typing, genomic comparison, and phylogenetic analysis to investigate pathogen relatedness and potential transmission patterns in AMR surveillance.

• Introduction to genomic epidemiology and its applications in infectious disease surveillance
• Bacterial strain typing and pathogen characterization
• Multilocus sequence typing (MLST) and sequence type identification
• SNP-based genomic comparison of bacterial isolates
• Principles of phylogenetic analysis and evolutionary relationships
• Interpretation of genomic relatedness among pathogenic isolates
• Identification of potential transmission clusters and outbreak investigation
• Integration of genomic findings with epidemiological metadata
• Hospital-associated antimicrobial resistance surveillance
• Public-health applications of genomic pathogen tracking

🛠️ Hands-on:

Compare bacterial isolates using sequence typing and genomic relationships, explore phylogenetic patterns, and investigate potential transmission links using genomic surveillance tools and available epidemiological information.

🧰 Tools Covered:

PubMLST, PathogenWatch, Galaxy

Who Should Enrol?

Important Dates

Workshop Outcomes