Whole Genome Sequencing

CDC is tracking and classifying illness in a new way, using advanced technology to find and stop outbreaks and combat drug-resistant germs.


PulseNet scientist

Microbiologist evaluating a whole genome sequencing run for quality control purposes.

Whole genome sequencing (WGS) provides detailed genetic information about germs that make people sick. CDC’s Division of Foodborne, Waterborne, and Environmental Diseases uses this information to improve efforts to find, investigate, and prevent illnesses caused by bacteria, fungi, and parasites. This is especially important when looking for the source of an outbreak or predicting drug resistance in bacteria and fungi. WGS provides highly detailed and timely information that helps CDC and other government agencies protect the public’s health.

What It Does

EDLB Microbiologists setting up a bacterial DNA whole genome sequencing run

Microbiologists setting up a bacterial DNA whole genome sequencing run on a whole genome sequencing machine.

Like people, germs have DNA. WGS allows scientists to study these germs by looking at their DNA fingerprints with extreme precision. How precise? Imagine someone giving you two books to compare, and you could use a tool that showed whether virtually every letter of every word in both books is the same. That’s how precise WGS is. By comparing the whole genome sequences of germs, scientists can determine if they are closely related to one another (very similar), which indicates those germs likely came from the same source.

WGS provides a nearly complete reading of the millions of units that make up a germ’s DNA. By knowing what order these units are in, scientists can identify the type of germ and learn more about its genes, including the genes that cause antimicrobial resistance. This detailed information also allows outbreak investigators to link cases of illness and find sources of infection with greater confidence than with other DNA fingerprinting methods. Information from whole genome sequencing can identify where a germ originated, whether from another country or a nearby healthcare facility.

Foodborne Outbreak Investigations

Success Stories

Learn how CDC is using WGS to transform illness detection, investigation, and prevention.

Caramel apple involved in Listeria outbreak

Beginning with Listeria in 2013, WGS has helped scientists detect more outbreaks, solve them while they are still small, and identify new food sources for germs that make people sick.

Read more about how WGS helped make the match in a Listeria outbreak.


Girl drinking out of water fountain

The information from WGS helped CDC scientists update CryptoNet, a DNA fingerprinting system for Cryptosporidium, a waterborne parasite that can get into our drinking water and swimming pools.

Romaine lettuce involved in E. coli outbreak.

In 2018, WGS allowed CDC and FDA scientists to link two different outbreaks of E. coli O157 illnesses to contaminated water, in California’s Central Coastal growing region and in the Yuma, Ariz., growing region. Lessons learned from these romaine lettuce outbreak investigations will help guide industry and government efforts to protect the public’s health and prevent future outbreaks.

The results from WGS help investigators determine which ill people are part of an outbreak by precisely comparing the DNA of the foodborne bacteria making people sick.

CDC began using WGS to investigate foodborne disease outbreaks in 2013 with Listeria — bacteria that cause a severe illness that is fatal in 1 of every 5 cases. CDC uses WGS for almost all of its investigations of outbreaks caused by foodborne bacteria. CDC and its partners in all 50 states use the same WGS methods and technology to detect, investigate, and stop foodborne outbreaks.

Outbreak investigators combine WGS data with information from interviews with sick people, such as what they ate before becoming ill and what animals were in their environment, to do the following:

  • Link cases: By comparing the DNA fingerprints of bacteria taken from sick people, scientists can determine if the bacteria are closely related to one another. If so, this close genetic relationship provides evidence that people got sick from the same source.
  • Find the source: Scientists from state health departments, CDC, the U.S. Food and Drug Administration, and the U.S. Department of Agriculture’s Food Safety and Inspection Service analyze bacterial DNA taken from possible outbreak sources. If bacteria found in a food product, a food production environment, or an animal environment have DNA sequences similar to bacteria from sick people, investigators are more confident that people got sick from that exposure.

WGS data also help shape government food safety policies and food industry practices that help to make food safer and save lives. Federal agencies use whole genome sequencing to detect and investigate foodborne disease outbreaks through two networks:

  • PulseNet, a laboratory network managed by CDC; focuses on bacteria from sick people.
  • GenomeTrakrexternal icon, a database of foodborne bacteria managed by FDA; focuses on germs from food products and the environment.

Beyond Foodborne Outbreaks

Scientists regularly analyze samples of germs collected from sick people to better understand how diseases are spread around the world, to discover trends in disease transmission, and to uncover new or unknown sources of infections. Information gathered through whole genome sequencing can help us combat those diseases more effectively. Some sequencing activities are:

Antibiotic Resistance

Whole genome sequencing can tell us if bacteria and fungi have genes that make them resistant to antibiotics. When germs are resistant to certain antibiotics, those drugs can no longer be used to fight infections. Using WGS, scientists can better understand how germs become resistant and how resistance spreads. This information helps find ways to combat the spread of antibiotic-resistant infections. Learn more about how CDC’s National Antimicrobial Resistance Monitoring System is using WGS to study antibiotic resistance in bacteria.