This recorded live learning series (LLS) introduces epidemiologists to the fundamentals of whole genome sequencing (WGS) for cluster detection and investigation. It covers WGS basics, allele codes, X codes, REP strains, NCBI Pathogen Detection, SEDRIC, data visualization, communication strategies, and PulseNet 2.0 access.
It consists of three sessions:
- WGS Fundamentals
- REP Strains, NCBI Pathogen Detection, and SEDRIC
- WGS Data Visualization & Communication and PulseNet 2.0 Access
Series Learning Objectives
By the end of this series, participants will be able to:
- Describe WGS concepts
- Utilize tools to access, visualize, track and analyze WGS data
- Interpret WGS data
- Communicate WGS findings to stakeholders in the context of foodborne/enteric cluster detection and investigation
Session 1 Learning Objectives
- Explain what a SNP is and describe how hqSNP analyses are performed
- Describe how cgMLST/wgMLST analyses are performed
- Explain the difference between cgMLST and wgMLST
- Determine relatedness of isolates using SNP and allele distance matrices
- Interpret phylogenetic trees
- Interpret allele codes
- Explain the limitations of using allele codes
- Explain what X codes are and how they have changed with the updated allele codes
- Understand that distance threshold guidelines for cluster detection are flexible, not fixed
Session 2 Learning Objectives
- Describe the concept of REP codes
- Explain the purpose and benefits of tracking and investigating REP codes
- Identify and document local REP codes
- Utilize the NCBI Pathogen Detection Portal for cluster investigation
- Set up e-mail notifications for when a new isolate gets added to a SNP tree/cluster in NCBI Pathogen Detection
- Utilize SEDRIC for cluster detection and investigation
- Utilize SEDRIC to obtain historical context for rare serotypes
- Choose the appropriate cluster detection/identification tool (e.g., NCBI Pathogen Detection, SEDRIC) and use them different contexts
Session 3 Learning Objectives
- Recognize how data visualization can support cluster/outbreak investigations
- Evaluate impact vs. investment of routine use of data visualization tools
- Apply standard phrasing for communicating WGS results
- Summarize complex laboratory testing and genetic comparisons during outbreak investigations for a general public audience
- List the requirements to obtain access to PulseNet 2.0
Time Commitment
Session 1: 1.5 hrs
Session 2: 1.5 hrs
Session 3: 1.0 hrs
Estimated time to complete all sessions: 4 hours
Recommended Audience
This series was developed for foodborne/enteric epidemiologists and other public health professionals involved in investigating local and multistate clusters, identifying clusters and sub-clusters, and interpreting WGS data.
Additional Resources
Studies evaluating thresholds for cluster detection:
- Multi-county and intersectoral assessment of cluster congruence between pipeline for genomics surveillance of foodborne pathogens
- Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations
- Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA
- Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA
- Challenges Associated with Investigating Salmonella Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data
- Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection
- Genetic Diversity in Salmonella enterica in Outbreaks of Foodborne and Zoonotic Origin in the USA in 2006–2017
- Retrospective Analysis of Historical Listeria monocytogenes Clinical Isolates, New York, USA, 2000–2021