Workshop Registration End Date :15 Oct 2026

Virtual Workshop

Antimicrobial Resistance Surveillance: Whole-Genome Sequencing, Resistome Analysis & Pathogen Tracking

Decode Resistance. Track Pathogens. Strengthen Surveillance.

Skills you will gain:

About Workshop:

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.

What you will learn?

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

Mentor Profile

Fee Plan

StudentINR 1999/- OR USD 60
Ph.D. Scholar / ResearcherINR 2999/- OR USD 70
Academician / FacultyINR 3999/- OR USD 80
Industry ProfessionalINR 4999/- OR USD 90

Important Dates

Registration Ends
15 Oct 2026 Indian Standard Timing 5:00 PM IST
Workshop Dates
15 Oct 2026 to
17 Oct 2026  Indian Standard Timing 5:30 pm IST

Get an e-Certificate of Participation!

Intended For :

  • 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

Career Supporting Skills

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.

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