Antimicrobial Resistance Surveillance: Whole-Genome Sequencing, Resistome Analysis & Pathogen Tracking
Decode Resistance. Track Pathogens. Strengthen Surveillance.
About This Course
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.
Aim
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.
Workshop Objectives
- 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.
Workshop Structure
Day 1 — Whole-Genome Sequencing for 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 spread of resistance determinants.
- Introduction to bacterial whole-genome sequencing.
- 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
Bacterial WGS Quality Control & Genome Assembly
Analyze a public bacterial sequencing dataset, assess read quality, and explore genome assembly using bioinformatics tools.
Day 2 — Resistome Analysis & AMR Gene Detection
- Understanding the bacterial resistome.
- Acquired resistance genes and resistance-associated mutations.
- Major mechanisms of antimicrobial resistance.
- Resistance genes associated with different antibiotic classes.
- Genotype-to-phenotype interpretation in AMR.
- Introduction to CARD, ResFinder, AMRFinderPlus, and MEGARes.
- Comparative resistome analysis across bacterial isolates.
- Multidrug-resistance profiling.
- Interpretation of AMR prediction reports.
- Limitations of genomic resistance prediction.
Hands-On
AMR Gene Detection & Resistome Profiling
Identify resistance genes from bacterial genomes and compare AMR profiles across multiple isolates.
Day 3 — Pathogen Tracking & Genomic Epidemiology
- Introduction to genomic epidemiology.
- Bacterial strain typing and pathogen characterization.
- Multilocus sequence typing and sequence types.
- SNP-based genomic comparison.
- Principles of phylogenetic analysis.
- Interpretation of pathogen relatedness.
- Transmission clusters and outbreak investigation.
- Integration of genomic and epidemiological metadata.
- Hospital-associated AMR surveillance.
- Public-health applications of genomic pathogen tracking.
Hands-On
Genomic Pathogen Tracking
Compare bacterial isolates using strain typing and genomic relationships to identify potential transmission patterns.
Tools & Resources Covered
- NCBI SRA
- FastQC
- Galaxy
- CARD
- ResFinder
- NCBI AMRFinderPlus
- MEGARes
- PubMLST
- PathogenWatch
Who Should Enrol?
- 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
Important Dates
Registration Ends
October 15, 2026
IST 5:00 PM IST
Workshop Dates
October 15, 2026 – October 17, 2026
IST 5:30 pm IST
Workshop Outcomes
- 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.
Fee Structure
Student Fee
₹1999 | $60
Ph.D. Scholar / Researcher Fee
₹2999 | $70
Academician / Faculty Fee
₹3999 | $80
Industry Professional Fee
₹4999 | $90
What You’ll Gain
- Live & recorded sessions
- e-Certificate upon completion
- Post-workshop query support
- Hands-on learning experience
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