Whole Genome Sequencing: How PulseNet Finds Foodborne Outbreaks

What it is

Every organism — bacterium, plant or animal — has a unique genetic code made of the nucleotide bases A, T, C and G. Whole genome sequencing (WGS) reads the complete sequence of those bases: the organism's DNA.

How it works

Scientists first extract the DNA from an organism, then prepare it for sequencing in a series of steps; once it's sequenced, they analyze it to find each organism's unique DNA fingerprint. PulseNet, CDC's network for tracking foodborne disease, sequences the DNA of bacteria to find foodborne outbreaks in the United States and abroad.

The steps PulseNet scientists follow to sequence bacteria. CDC.

1. Shearing — cutting DNA into pieces small enough for the sequencer to read.
2. Barcoding — adding unique tags to the pieces so each organism's code can be told apart.
3. Sequencing — pooling DNA from different bacteria in the sequencer, which reads the bases that make up each one's fingerprint.
4. Analysis — comparing the fingerprints with software to find the differences.

Detecting disease

PulseNet and other public health scientists use WGS to identify foodborne outbreaks and to learn why some bacteria make people sicker or resist antibiotics more than others. It is now PulseNet's standard method for outbreaks caused by bacteria such as Shiga toxin-producing E. coli (STEC), Salmonella, Vibrio and Listeria.

WGS in public health laboratories has improved outbreak surveillance and made it easier to spot trends in foodborne infections and antimicrobial resistance. Its precise fingerprints find outbreaks sooner: before PulseNet, identifying an outbreak could take up to 39 days; now it takes about 16.

Building the capacity

PulseNet helped public health laboratories adopt WGS by training scientists, buying equipment and supplies, and updating software and data systems. The network includes 83 U.S. laboratories and more than 100 abroad. The work was made possible with CDC's Advanced Molecular Detection office, Food Safety Office and Antimicrobial Resistance Solutions Initiative.

As WGS spreads, CDC's surveillance systems and labs must keep pace. WGS is a fast, affordable way to get detailed information about bacteria from a single test — helping to diagnose infections quickly and cheaply, and to solve and prevent foodborne outbreaks.

Sources

Based on "About Whole Genome Sequencing," PulseNet, Centers for Disease Control and Prevention (January 8, 2024); a work of the United States government in the public domain. Misspellings in the source ("preform" for "perform") are corrected.