What PulseNet and whole genome sequencing do
PulseNet is a laboratory network that compares the DNA fingerprints of bacteria from ill people so that scattered cases can be linked into outbreaks. Whole genome sequencing has replaced older fingerprinting methods because it is more precise.
- CDC describes PulseNet as a national network of 83 public health and food regulatory laboratories that uses DNA fingerprinting to find clusters of illness.1
- The network gathers DNA fingerprints of bacteria from ill people in a national database so that cases in different places can be linked. CDC says the network began in 1996.1
- CDC says PulseNet was created after a 1993 E. coli O157:H7 outbreak that caused more than 700 illnesses and four deaths.1
- CDC scientists wrote in 2016 that whole genome sequencing was replacing pulsed-field gel electrophoresis, the main subtyping method for more than 20 years, and that routine sequencing for listeriosis began in 2013.2
- Sequencing compares isolates at the level of single nucleotide differences or individual genes, rather than the 15 to 30 bands used by the older method, and can also predict serotype, virulence and antimicrobial resistance from one data set.2
- Sequencing also links human cases to food and environmental samples across borders. In 2022 ECDC and EFSA said that sequencing data and molecular typing linked human Salmonella cases in several countries to a chocolate factory in Belgium.3
Sources
- US Centers for Disease Control and Prevention, About PulseNet (9 September 2026)
- US Centers for Disease Control and Prevention, Whole-Genome Sequencing Is Taking Over Foodborne Disease Surveillance (Carleton and Gerner-Smidt, Microbe 11(7)) (2016)
- European Centre for Disease Prevention and Control and European Food Safety Authority, Rapid outbreak assessment, first update: Multi-country Salmonella outbreak linked to chocolate products (18 May 2022)