Molecular Epidemiology and Sequencing Approaches in Public Health - Modules

Module title After completion of the module, attendees will know… Presenter(s)
(1) Genetics & evolution 101 
(15.6 MB file)
  • How different organisms (viruses, bacteria etc.) differ in their genetic material and how this effects interpretation of “genetic subtyping” data
  • Different mechanisms of how genetic material changes (substitutions, horizontal gene transfer and recombination, indels) and how this effects interpretation of “genetic subtyping” data
 Emilio DeBess (Oregon)
and CDC
(2) Intro to next gen sequencing methodologies (NGS) 
(41.5 MB file)
  • How NGS differs from traditional Sanger sequencing
  • Different sequencing methodologies
  • Different quantitative measures used to assess the quality of sequencing data
 Matthew Schimenti (Florida); Paul Cieslak (Oregon) and CDC
(3) Introduction to sequence analyses 
(17.8 MB file)
  • How NGS data are assembled into contigs
  • The difference between de novo and reference-based assemblies
  • How two sequences are compared to determine the level of similarity
 Madhu Anand and Martin Wiedmann (NY) and CDC
(4) Tree building 101- how to visualize genetic relatedness between large sets of individuals
(63.6 MB file)
  • How DNA sequence data can be used to build trees
  • Different types of methods to build tress (kSNP)
 Madhu Anand and Martin Wiedmann (NY) and CDC

Pathogen Specific Modules

Module title After completion of the module, attendees will know… Presenter(s)
(1) Introduction to HIV Evolution
  • How evolution leads to HIV genetic sequence divergence.
  • Basic concepts of genetic sequence alignment and genetic distance.  
  • How HIV-TRACE uses pairwise genetic distance calculation to define potential transmission clusters.
 Joel Wertheim (California, UCSD)
and Cheryl Ocfemia
(CDC)

Whole-genome sequencing for investigation of recent TB transmission in the United States: Current uses and future plans

Part 1  |  Part 2  |  Part 3
  • Key Differences between conventional genotyping and WGS
  • What is being represented on a phylogenetic tree 
  • How WGS is used to assess whether patients are potentially linked by recent transmission.
  • Why WGS alone cannot be used to infer direction of transmission
  • How TB control programs can use WGS analysis in an investigation
 Sarah Talarico
and Benjamin Silk (CDC), Tambi Shaw and Martin Cilnis (California DPH)
Use of Routine Whole Genome Sequencing to Improve Investigation of Listeriosis Outbreaks
  • How WGS is used to detect Listeriosis clusters
  • Ways WGS has affected outbreak investigations
  • Future directions of WGS relating to Listeria monocytogenes
 Matthew Wise (CDC) and Amanda Conrad (CDC)