This recorded three-part live learning series (LLS) provides practical training for foodborne and enteric disease epidemiologists and other public health professionals involved in cluster detection, cluster investigation, and interpretation of whole genome sequencing (WGS) data.
The series covers foundational and applied topics including SNP and allele-based analyses, interpretation of phylogenetic trees and allele codes, REP strains, cluster detection thresholds, NCBI Pathogen Detection, SEDRIC, PulseNet 2.0 access, alternative cluster detection tools, and communication of WGS findings to stakeholders.
Session 1 WGS Fundamentals
Presenter: Dr. Lauren K. Hudson, University of Tennessee
Topics covered:
- hqSNP and cg/wgMSLT refresher
- Interpret phylogenetic trees, matrices, allele codes, and X codes
- Cluster detection thresholds
- REP codes and REP strains
By the end of this session learners will be able to:
- Determine relatedness of isolates using SNP and allele distance matrices
- Interpret phylogenetic trees and allele codes
- Explain what X codes are and how they have changed with allele code updates
- Explain REP codes and their function
Session 2 NCBI Pathogen Detection, SEDRIC, & Recent Case Study
Presenters: Jack Marr, MPH and Kelly Orejuela, MPH, Tennessee Department of Health
Topics covered:
- Using NCBI Pathogen Detection for cluster investigation
- Using SEDRIC for cluster detection and investigation
- Case studies
- PulseNet 2.0 Access
By the end of this session learners will be able to:
- Utilize the NCBI Pathogen Detection Portal for cluster investigation (e.g., to find other cases)
- 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) to use in different contexts
- List the requirements to obtain access to PulseNet 2.0
Session 3 Alternative Cluster Detection Methods and Communications
Presenters: Sharon K. Greene, PhD, MPH, New Your City Department of Health and Mental Hygiene and Kelly Orejuela, MPH, Tennessee Department of Health
Topics covered:
- SaTScan, TreeScan, and ESSENCE
- Communicating WGS findings to stakeholders
- Standard terminology and communication strategies
By the end of this session learners will be able to:
- Describe how SaTScan and related spatiotemporal scan statistic tools are used for prospective disease cluster detection and monitoring
- Identify situations where non-WGS surveillance tools are particularly useful
- Summarize complex laboratory testing and genetic comparisons during outbreak investigations for a general public audience
Time Commitment
Session 1: 1.5 hrs
Session 2: 1.5 hrs
Session 3: 1.5 hrs
Estimated time to complete all sessions: 4.5 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
PulseNet 2.0 Resources
Allele Databases Genotyping Tools
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