1. Future Directions Unknowns:
What should we consider a cluster for other Salmonella serotypes and other pathogens or when using a different reference genome- i.e., how closely related do case-isolates have to be for us to investigate as a possible outbreak?
Flexibility!
How will lab and epi communicate?
What should we consider a cluster for other Salmonella serotypes and other pathogens or when using a different reference genome- i.e., how closely related do case-isolates have to be for us to investigate as a possible outbreak?
We need to get used to being flexible
How will lab and epi communicate? It’s important to meet with your lab early on and discuss a plan-who will be responsible for identifying clusters, and how will the data be communicated

2. Future Directions In the near future: PulseNet (BioNumerics)
More easily analyze our sequencing data at the state level
wgMLST
Nomenclature
Beyond cluster detection: Salmonella serotyping, STEC virulence factors, presence of antimicrobial resistance genes…
In the near future:
We should be able to more easily analyze our sequencing data at the state level using BioNumerics.
We’ll likely start using wgMLST for most pathogens, although SNP analysis will still be available.
Using wgMLST will allow us to have a naming system, which should make it easier to communicate results and across jurisdictional lines.
The use of WGS will go beyond cluster detection: WGS can be and will be used for Salmonella serotyping, for identifying STEC virulence factors, identify the presence of antimicrobial resistance genes…

3. As we move forward in implementing WGS, if you need help with training or discussion specifically for your state, if you have questions or if you want to discuss an outbreak you are working on, feel free to contact your regional Center of Excellence- we’ll be able to help you or refer you to a COE that can.

4. Questions?
Thank you!
Any questions or comments?