Updates on PulseNet’s Transition to Whole Genome Sequencing for Foodborne Surveillance in 2019

The Association of Public Health Laboratories (APHL) received a letter from CDC’s Enteric Diseases Laboratory Branch (EDLB) regarding the following updates and modifications to the timeline for implementation of whole genome sequencing (WGS) for PulseNet.


  • As of January 3, 2019, up to 24 laboratories have either started the process or have finished the BioNumerics 7.6 conversion of their databases;
  • It is anticipated that the remaining PulseNet laboratories will finish BioNumerics 7.6 conversions by March 2019;
  • CDC EDLB have experienced some delays with updating and testing WGS databases and migrating these to a production system at CDC; however, it is anticipated that the databases will be functional by March 15, 2019 for PulseNet participants to access.

Revised Timelines for WGS Implementation:

  • The primary subtyping method for E. coli/STEC/Shigella and Salmonella will be March 15, 2019.

The PulseNet team at CDC asks that all participating PulseNet laboratories ensure that their databases are cleaned prior to starting the conversion process. Cleaning databases will help with a smooth conversion process. PulseNet instructions and PulseNet QuickTips to prepare for upgrading databases to BioNumerics v7.6 are available and have been posted onto the PulseNet SharePoint site under Library of PulseNet documents/Database Cleaning Guidelines.

The PulseNet Steering Committee continues to actively monitor the transition at the local and state levels and will be providing further guidance to all PulseNet laboratories to assist with this transition.

For further questions, please contact the CDC Enteric Diseases Laboratory Branch:

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