Add Module 4: Wet Lab Analytical Methods

wastewater_surveillance/module_4_wet_lab_analytical_methods/README.md

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+# WWBT4: Wet Lab Analytical Methods
+
+## Contributors
+- Farzaana Diedericks (Research Trainer | PHA4GE)  
+- Barbara Ghiglione (Assistant Researcher at the National Research Council | CONICET)  
+- Alan Elena (Postdoctoral Scientist | Technische Universität Dresden)
+
+## Module Details
+- **Number of Sessions**: 1  
+- **Total Learning Time**: 40–50 min  
+- **Target Audience**: Bioinformaticians, Environmental Scientists, Biotechnologists, Biodiversity and Conservation Biologists, Health Officials  
+- **Format**: Lectures, Q&A and Interactive Discussions  
+- **Module Level**: Beginner  
+- **Required Topics**: None  
+
+---
+
+## Learning Objectives
+
+- Introduce participants to wet lab techniques in wastewater surveillance  
+- Understand the role of molecular biology in pathogen and contaminant detection  
+- Gain knowledge of SOPs and molecular data from WWS  
+- Understand chemical parameters and their effects on microbial growth
+
+---
+
+## Module Videos
+
+1. [Introduction to Wet Lab Analysis](https://drive.google.com/file/d/17eFc1Auy0fGe7rZePQYwuf-MzLE0JrNT/view?usp=drivesdk)  
+2. [Pollutants in Raw Wastewater](https://drive.google.com/file/d/1NRytOU03pzMEtPhAkSk1XZrdClueq2Wz/view?usp=drivesdk)  
+3. [Wastewater Surveillance Definition](https://drive.google.com/file/d/12Li0M2ri8Lcl4x0T-8qZ-uZffl7_nq5Z/view?usp=drivesdk)  
+4. [Wet Lab for Public Health](https://drive.google.com/file/d/1yanqkH4bTQMLt469VdYS8eowh_cIz7L0/view?usp=drivesdk)  
+5. [Molecular Techniques Overview](https://drive.google.com/file/d/1TETpsxc3P8omxG44urS_exEQmmRhmXmh/view?usp=drivesdk)  
+6. [Molecular vs Traditional Methods](https://drive.google.com/file/d/1Q5rLkHI3h7yjQtLgr3AhU3OtgfsMkin8/view?usp=drivesdk)  
+7. [NGS and Public Health Labs](https://drive.google.com/file/d/191WtLIJrE-l12ikYrV8kfsuw5N0mgZMw/view?usp=drivesdk)  
+8. [Sequencing Techniques](https://drive.google.com/file/d/15PGbKetuILxUpLiNwGfjFIogvsfYdSo1/view?usp=drivesdk)  
+9. [Chemical, Biological & Physical Analysis](https://drive.google.com/file/d/1BgAmC4ckYHuW1G9leBpHdiUUlmoCX9ll/view?usp=drivesdk)  
+10. [Biosafety & Biosecurity](https://drive.google.com/file/d/1zNHG2cZvo22evBmWDBV-6tXSPV_37ecm/view?usp=drivesdk)  
+
+---
+
+## Module Topics Overview
+
+### 🧪 Introduction to Wet Lab Analysis
+- Composition of wastewater
+- Key pollutants and pathogens
+- What is WWS?
+- Importance for public health
+
+### 🔬 Molecular and Sequencing Techniques
+- PCR, qPCR, HT-PCR
+- NGS: marker-based and shotgun metagenomics
+- Public health relevance
+- Infrastructure, collaboration and challenges
+
+### 🧫 Microbiological Methods
+- Culture-based methods (e.g. ESBL-producing *E. coli*)
+- Limitations and integration with NGS
+- WHO Tricycle Protocol
+
+### ⚗️ Chemical, Physical and Biological Analyses
+- Physical: pH, temperature, turbidity, etc.
+- Chemical: BOD, COD, TOC, metals, drugs
+- Microbiological: indicators, ARGs
+- Ecotoxicological: bioassays, endocrine disruptors
+
+### ✅ Quality Management
+- ISO/IEC 17025, SOPs
+- Equipment and reagents
+- QA/QC measures
+- LIMS and data integrity
+
+### 🧷 Biosafety and Biosecurity
+- Risk assessment
+- PPE requirements
+- Sample handling
+- Facility requirements
+
+---
+
+## 💬 Discussion Points
+
+- What are your lab's capabilities and challenges?
+- What platforms and techniques do you use?
+- Why is qPCR still widely used over metagenomics?
+- In what cases would metagenomics be preferred?
+
+**Question:** How can we balance feasibility and scientific value in LMIC settings?
+
+**Question:** How do method choices (culture vs molecular) affect target selection?
+
+---
+
+## 📖 Recommended Reading
+
+- WHO Tricycle Protocol
+[https://www.who.int/publications/i/item/9789240021402]  
+- Liguori et al. (2022). *Antimicrobial resistance monitoring of water environments: A framework for standardized methods and quality control*. Environmental Science & Technology, 56(13).  
+  [https://pubs.acs.org/doi/10.1021/acs.est.1c08918]