Wastewater & Environmental AMR Surveillance Using Metagenomics
Tracking antimicrobial resistance beyond hospitals — from wastewater to actionable insights.
About This Course
This 3-day intensive workshop introduces participants to antimicrobial resistance (AMR) surveillance using wastewater metagenomics. With 1.5 hours of expert-led lecture each day followed by guided discussions and demonstrations, the program integrates theory with practical bioinformatics workflows. Participants will learn how to retrieve, process, analyze, and interpret environmental metagenomic datasets to identify antimicrobial resistance genes (ARGs), compare resistomes across sites, and generate research-grade visualizations and reports relevant to public health and environmental monitoring.
Aim
To equip participants with conceptual understanding and practical bioinformatics skills required for environmental AMR surveillance using wastewater metagenomics data.
Workshop Objectives
- To introduce the concept of environmental resistome and its global health significance
- To understand wastewater-based epidemiology (WBE) as an early AMR surveillance tool
- To train participants in retrieving and preprocessing metagenomic datasets
- To perform ARG profiling using established databases (CARD, MEGARes)
- To conduct comparative resistome analysis across environmental and clinical samples
- To develop skills in visualization, diversity analysis, and reproducible reporting
Workshop Structure
Day 1: Introduction to Environmental AMR and Wastewater Metagenomics
- Environmental resistome and its global significance
- Wastewater-based epidemiology (WBE) as an early indicator of AMR outbreaks
- Clinical vs environmental resistomes
- Overview of ARG databases: CARD, MEGARes
- Tools: SRA Toolkit, FastQC, Trimmomatic, Python (optional for preprocessing)
- Outcome: Participants can retrieve and prepare wastewater metagenomic datasets for analysis
Day 2: ARG Profiling and Comparative Analysis
- Taxonomic profiling of metagenomic samples (Kraken2 / MetaPhlAn)
- Mapping reads to ARG databases (CARD / MEGARes)
ARG abundance normalization and comparative analysis across site - Tools: Kraken2, MetaPhlAn, CARD / MEGARes, Python (pandas, matplotlib), R (optional)
- Outcome: Participants can identify and quantify ARGs and compare resistomes across environmental samples
Day 3: Visualization, Trend Analysis, and Research-Grade Reporting
- Visualizing ARG abundance and diversity using heatmaps and plots
- Alpha & beta diversity metrics for resistome analysis
- Comparing environmental vs clinical resistomes
- Reproducible reporting and interpretation of AMR surveillance data
- Tools: R (phyloseq, ggplot2), Python (matplotlib, seaborn), CARD / MEGARes
- Outcome: Participants can perform environmental AMR surveillance, visualize trends, and generate reproducible reports for research or policy applications
Who Should Enrol?
- Doctoral Scholars & Researchers: PhD candidates seeking to integrate computational workflows into their molecular research.
- Postdoctoral Fellows: Early-career scientists aiming to enhance their data-driven publication profile.
- University Faculty: Professors and HODs interested in modern bioinformatics pedagogy and tool mastery.
- Industry Scientists: R&D professionals from the Biotechnology and Pharmaceutical sectors transitioning to genomic-driven discovery.
- Postgraduate Students: Final-year PG students looking for specialized research-grade exposure beyond standard curricula.
Important Dates
Registration Ends
02/17/2026
IST 07:00 PM
Workshop Dates
02/17/2026 – 02/19/2026
IST 08:00 PM
Workshop Outcomes
By the end of the workshop, participants will be able to:
- Retrieve wastewater metagenomic datasets from public repositories
- Perform quality control and preprocessing of sequencing data
- Identify and quantify antimicrobial resistance genes (ARGs)
- Compare resistome profiles across environmental sites
- Conduct alpha and beta diversity analysis
- Visualize ARG abundance and trends using R and Python
- Generate research-grade reports suitable for publications, policy briefs, or surveillance documentation
Fee Structure
Student Fee
₹1699 | $65
Ph.D. Scholar / Researcher Fee
₹2699 | $75
Academician / Faculty Fee
₹3699 | $85
Industry Professional Fee
₹4699 | $95
What You’ll Gain
- Live & recorded sessions
- e-Certificate upon completion
- Post-workshop query support
- Hands-on learning experience
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