Training on Genomic Surveillance for Pathogens (Antimicrobial Resistance and Pandemic Preparedness)

Genomic surveillance has transformed infectious disease monitoring by enabling precise identification, tracking, and analysis of pathogens. By sequencing and analyzing pathogen genomes, public health systems can detect outbreaks early, trace transmission pathways, monitor antimicrobial resistance (AMR), and identify emerging variants; critical components of pandemic preparedness.

This 10-day course provides participants with both the technical foundations and practical skills needed to implement genomic surveillance programs. The training covers sequencing technologies, genomic data analysis and interpretation, bioinformatics workflows, data integration with routine surveillance, and application of genomic insights for public health decision-making.

Participants will also explore operational considerations, including laboratory capacity, workforce skill requirements, data governance, quality assurance, and coordination between laboratories, epidemiologists, and health authorities. Through case studies and hands-on exercises, learners will gain practical experience in designing, operating, and strengthening genomic surveillance initiatives for infectious diseases and AMR.

By the end of the course, participants will be able to leverage genomic data to improve outbreak detection, guide interventions, and enhance the resilience and preparedness of public health systems.

Duration

10 Days

Who Should Attend

• Public health officials and epidemiologists

• Laboratory scientists and technicians

• Disease surveillance managers

• Health information system professionals

• Policymakers and regulators

• Researchers in infectious diseases

Individual Impact

• Understand genomic surveillance principles
• Gain practical knowledge of sequencing workflows
• Improve data interpretation skills
• Strengthen outbreak detection capabilities
• Enhance collaboration between labs and public health teams

Organizational Impact

• Improve early detection of outbreaks
• Strengthen antimicrobial resistance monitoring
• Enhance pandemic preparedness
• Support evidence-based public health decisions
• Build sustainable surveillance capacity

By the end of this course, participants will be able to:

• Explain the role of genomics in disease surveillance
• Understand sequencing technologies and workflows
• Interpret genomic data for public health action
• Integrate genomic surveillance into routine systems
• Develop genomic surveillance implementation plans

Module 1: Introduction to Genomic Surveillance

• Basics of genomics and pathogen biology
• Role of genomics in public health
• Applications in outbreak detection and AMR monitoring
• Global genomic surveillance initiatives
• Practical Exercise: Identify surveillance needs for genomics

Module 2: Pathogen Sampling and Laboratory Workflows

• Sample collection and transport
• Laboratory biosafety and quality control
• DNA/RNA extraction techniques
• Sequencing preparation processes
• Case Study: Setting up a sequencing workflow in public health labs

Module 3: Sequencing Technologies

• Next-generation sequencing platforms
• Portable sequencing tools
• Strengths and limitations of different technologies
• Cost and infrastructure considerations
• Practical Exercise: Compare sequencing options for surveillance programs

Module 4: Bioinformatics and Data Analysis

• Genome assembly and alignment
• Variant detection
• Phylogenetic analysis
• Basic bioinformatics pipelines
• Case Study: Tracing an outbreak using genomic data

Module 5: Genomic Surveillance for Antimicrobial Resistance

• Genetic markers of resistance
• Tracking AMR trends
• Integrating genomics with laboratory testing
• Public health implications
• Practical Exercise: Interpret AMR genomic data

Module 6: Genomic Surveillance for Emerging Diseases and Pandemics

• Variant monitoring
• Transmission mapping
• Early warning systems
• International data sharing
• Case Study: Genomics in pandemic response

Module 7: Data Integration and Interoperability

• Linking genomic data with epidemiological data
• Health information systems integration
• Data visualization tools
• Real-time reporting
• Practical Exercise: Design an integrated surveillance dashboard

Module 8: Governance, Ethics, and Data Sharing

• Data ownership and access
• Privacy concerns
• Ethical use of genomic data
• International collaboration frameworks
• Case Study: Cross-border genomic data sharing challenges

Module 9: Building Capacity and Sustainability

• Workforce training strategies
• Infrastructure planning
• Funding models
• Partnership development
• Practical Exercise: Develop a capacity-building plan

Module 10: Future Trends in Genomic Surveillance

• AI and automation in genomics
• Rapid field sequencing
• Global surveillance networks
• Preparing for future health threats
• Practical Exercise: Create a future genomic surveillance roadmap