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

Antimicrobial resistance (AMR) is a major global challenge affecting clinical treatment, infectious disease control, food safety, and public health. Whole-genome sequencing enables researchers to identify resistance genes, characterize pathogenic strains, compare microbial isolates, and investigate transmission patterns with high genomic resolution. This 3-day workshop introduces participants to the complete genomic workflow for AMR surveillance, from bacterial whole-genome sequencing and resistome analysis to strain typing and pathogen tracking.

To provide participants with practical knowledge of whole-genome sequencing, antimicrobial resistance gene detection, resistome profiling, and genomic pathogen surveillance using modern bioinformatics tools and databases.

• Understand the biological and clinical foundations of antimicrobial resistance.
• Explore the role of whole-genome sequencing in AMR surveillance.
• Learn the complete workflow from sequencing reads to bacterial genome analysis.
• Perform quality assessment and preprocessing of microbial sequencing data.
• Understand genome assembly, annotation, and bacterial strain characterization.
• Identify antimicrobial resistance genes and resistance-associated mutations.
• Compare resistome profiles between pathogenic bacterial isolates.
• Explore multilocus sequence typing and genomic strain classification.
• Understand phylogenetic analysis for pathogen surveillance.
• Interpret genomic relationships during transmission and outbreak investigations.
• Explore internationally used AMR genomic databases and surveillance resources.
• Develop an integrated workflow for genomic AMR monitoring.

📅 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

• Understand major mechanisms of antimicrobial resistance.
• Explain the role of whole-genome sequencing in AMR surveillance.
• Assess bacterial sequencing data and genome quality.
• Identify antimicrobial resistance genes from microbial genomes.
• Interpret resistome profiles across bacterial isolates.
• Understand bacterial strain typing and genomic epidemiology.
• Interpret phylogenetic relationships between pathogen isolates.
• Identify potential transmission patterns using genomic information.
• Integrate genomic and epidemiological information for AMR surveillance.
• Understand a complete WGS-based pathogen surveillance workflow.

Biotechnology students Microbiology students Bioinformatics students Biomedical science students PhD scholars Research scholars Clinical microbiologists Molecular biologists Infectious-disease researchers Public-health professionals Epidemiologists Faculty members Researchers working on antimicrobial resistance