Whole Genome Sequencing
CDC is tracking and classifying illness in a new way, using advanced technology to find and stop outbreaks and combat antimicrobial-resistant germs.
Microbiologist evaluating a whole genome sequencing run for quality control purposes.
Whole genome sequencing (WGS) provides detailed genetic information about bacteria and other 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 antimicrobial 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
Microbiologists setting up a bacterial DNA whole genome sequencing run on a whole genome sequencing machine.
Like people, bacteria and other 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 used a tool that showed whether 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 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 and mutations that cause antimicrobial resistance. This detailed information also allows outbreak investigators to link cases of illness and of infection with greater confidence than with previous DNA fingerprinting methods. Information from WGS can help identify where a germ originated—for example, from a food processing facility or a restaurant.
Foodborne Outbreak Investigations
Learn how CDC is using WGS to transform illness detection, investigation, and prevention.
WGS was first used to investigate foodborne disease outbreaks in 2013 to study Listeria illnesses. Since then, WGS has helped scientists detect more outbreaks, solve them while they are smaller, and identify new food sources for bacteria that make people sick.
Read more about how WGS helped find the source of a Listeria outbreak.
The information from WGS helped CDC scientists update CryptoNet, a DNA fingerprinting system for Cryptosporidium, a parasite that can be found in soil, food, drinking or recreational water, or surfaces.
In 2018, two different outbreaks of E. coli O157 illnesses were linked to romaine lettuce. WGS allowed CDC and FDA scientists to link the outbreaks to contaminated irrigation water in California’s Central Coastal growing region and in the . As a result, FDA released the , which provides guidance on inspections, sampling, data sharing, and root cause investigations to help protect the public’s health and prevent future outbreaks.
CDC scientists have used WGS to help prevent the spread of fungal diseases. In 2021, CDC launched FungiNet—a new network using WGS data for tracking illness caused by fungi. One of its goals is to use WGS data to detect fungal disease outbreaks faster, track the spread of illness, and confirm possible sources for 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—a bacterium that can cause a severe illness that is fatal in 1 of every 6 cases. CDC now uses WGS to investigate outbreaks caused by all major foodborne bacteria. CDC and its partners in all 50 states use the same WGS methods and technology to detect, investigate, solve, 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. Investigators use this information to:
- 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 likely got sick from the same source, such as a contaminated food.
- 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 the DNA of bacteria taken from possible outbreak sources. If bacteria found in a food, a food production environment, or an animal environment have DNA fingerprints that are similar to bacteria from sick people, investigators are more confident that people got sick from that source.
WGS data also help shape government food safety policies and food industry practices that help make food safer and save lives. For example, WGS data helped identify an outbreak of salmonella infections linked to ground beef in 2018. Federal agencies use WGS to detect and investigate foodborne disease outbreaks through two networks:
- PulseNet, a laboratory network managed by CDC; focuses on bacteria from sick people.
- GenomeTrakr, a database of foodborne bacteria managed by FDA; focuses on germs from food products and the environment.
DNA fingerprints generated by laboratories participating in PulseNet and GenomeTrakr are publicly available through the National Center for Biotechnology Information.
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 antimicrobial resistance, 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:
- Tracking U.S. Candida auris cases, which helps investigators determine how this multidrug-resistant fungus is being introduced and spread in U.S. healthcare facilities and around the world.
- Investigating the expanding geographic range of Valley fever [PDF – 2 pages], which helped researchers detect where the soil-dwelling fungus was present in a new part of the country.
- Showing that Cryptococcus gattii was present in the Southeastern United States in addition to the Pacific Northwest. This finding alerted doctors to the need to consider infection with this fungus when treating patients.
- Identifying and comparing profiles of the parasite Cryptosporidium (“Crypto”) in the CryptoNet tracking system, to support outbreak investigations and improve prevention strategies.
- Comparing strains of the “brain-eating ameba,” Naegleria fowleri, from patients and the environment. This work helps develop new methods to diagnose these rare but usually fatal infections and identify where someone was exposed to the ameba.
Antibiotic Resistance
Whole genome sequencing can tell us if bacteria and fungi have genes that make them antimicrobial resistant. Antimicrobial resistance happens when germs like bacteria and fungi develop the ability to defeat the drugs designed to kill them. That means the germs are not killed and continue to grow.
Using WGS, scientists can better understand how germs become resistant and how resistance spreads. This information helps find ways to prevent the spread of antimicrobial-resistant infections. Learn more about how CDC’s National Resistance Monitoring System is using WGS to study antimicrobial resistance in bacteria.