CDC’s PulseNet tracks sources of bad lettuce, eggs, other foodborne illnesses

Eggs and romaine lettuce are just the latest culprits in food poisoning outbreaks in the United States. With the first reports of E. coli infections from bad lettuce, the Centers for Disease Control and Prevention’s PulseNet system was on the case tracking the bacteria’s DNA fingerprints from individual patients to find the common source of the bad greens.

So far, the CDC has narrowed the search for the E. coli-contaminated romaine lettuce to the Yuma, Arizona area, but not to a specific farm or farms.

When people in the U.S. get sick, the CDC wants to know. It plays many roles in the U.S. health system, just one of which is detecting outbreaks of food or waterborne illness.

A foodborne disease outbreak is the occurrence of two or more cases of illness from eating a common food. Viral outbreaks from viruses can also be spread by food as well as by surface contact, among people, and in the water and air. The CDC draws on a variety of disease surveillance systems. PulseNet’s role is limited to bacteria sleuthing.

The PulseNet network of 83 labs throughout the states and U.S. territories is the CDC’s primary detection system for outbreaks from bacteria. The network also includes food regulatory labs run by the Food and Drug Administration (FDA) and the U.S. Department of Agriculture (USDA). If an outbreak goes beyond our borders, PulseNet is a member of PulseNet International, with 88 member countries.

PulseNet International member map

PulseNet’s official name is two mouthfuls but explains the network’s role: The National Molecular Subtyping Network for Foodborne Disease Surveillance.

PulseNet detection methods — mugshots, twins, and books

PulseNet currently tracks eight bacteria based on growing DNA fingerprint databases for each. Not unlike the FBI’s Integrated Automated Fingerprint Identification System (IAFIS) and Combined DNA Index System (CODIS), PulseNet’s value as a detection tool depends on the number of samples, in this case, samples of E. coli DNA. The more DNA fingerprints in the respective bacteria’s database, the greater the chance of finding a genetic match.

The three main DNA subtyping tools in PulseNet’s arsenal are pulsed-field gel electrophoresis (PFGE), multiple locus variable number tandem repeat analysis (MLVA), and whole genome sequencing (WGS). Take a look at the graphics and brief descriptions of each method below.

Pulsed-field gel electrophoresis (PFGE
Pulsed-field gel electrophoresis (PFGE) CDC

PFGE is today’s gold-standard DNA fingerprinting method. With PFGE, CDC scientists crack open the DNA fragments, separate them, and take their mugshots. The images are then stored in the database.

Multiple Locus Variable-number Tandem Repeat Analysis (MLVA)

MLVA is typically used following PFGE to learn more details about a bacteria causing an outbreak. Particularly helpful with fast-evolving bacteria, MLVA is helpful to differentiate when bacteria have similar PFGE patterns.

So, if you were trying to solve a crime and discovered the members were from the same family, including twins, MLVA would help. Good luck with that if they’re identical twins, but it may be OK with bacteria.

Whole Genome Sequencing (WGS)

Whole genome sequencing is the new kid on the block, destined to take over. According to the CDC, “Whole genome sequencing provides more detailed and precise data for identifying outbreaks than the current standard technique that PulseNet uses, pulsed-field gel electrophoresis (PFGE). Instead of only having the ability to compare bacterial genomes using 15-30 bands that appear in a PFGE pattern, we now have millions of bases to compare.”

In further describing what is obviously the agency’s best bet for faster disease detection, the CDC likens WGS to comparing all the words in a book instead of counting the number of chapters, as with PFGE.

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