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PulseNet Explained

What is PulseNet?

PulseNet connects cases of foodborne illness to potential outbreaks. PulseNet is a national laboratory network  made up of 87 laboratories−at least one in each state. PulseNet  connects foodborne illness cases together to detect and define outbreaks using DNA "fingerprinting" of the bacteria making people sick  using a standardized process called pulsed-field gel electrophoresis (PFGE). Every state has at least one public health laboratory that can match up bacteria from sick people in many different locations using PulseNet's DNA fingerprinting technique and database. PulseNet tracks what is being reported to CDC today compared to what was reported in the past to look for changes. This means that PulseNet keeps a cumulative database representing nearly half a million isolates of bacteria from food, the environment, and human foodborne illness.

Since its beginning in 1996, PulseNet has revolutionized the detection and investigation of foodborne disease outbreaks, especially in multiple sites across the country which, before PulseNet, often went undetected or were detected only after they grew very large.

What is PulseNet’s role?

PulseNet scientist reviews DNA fingerprints

PulseNet scientist reviews DNA fingerprints

PulseNet identifies outbreaks by connecting the dots. In this case, the "dots" are the DNA fingerprints of bacteria making people sick. Once PulseNet makes these connections and an outbreak is identified, PulseNet can work with teams at the CDC and state and local health departments to figure out what is causing people to get sick. Each year PulseNet identifies:

  • About 1,500 clusters of foodborne disease at local or state levels
  • About 250 clusters that span multiple states
  • 10-15 multistate outbreaks of foodborne disease that are widely dispersed

Detecting outbreaks makes it possible to remove contaminated food from the marketplace before more people become ill. Since the creation of PulseNet in 1996, more than one-half billion pounds of contaminated food have been recalled due, in part, to PulseNet activities.

More importantly, many products and services are safer today because of investigations PulseNet triggered. These have stimulated production changes by the food industry and helped federal agencies create new or improved recommendations and regulations to make our food supply safer.

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Why was PulseNet developed?

In 1993, more than 700 people fell ill and 4 died in the western U.S. after eating at a large, regional fast food restaurant chain. More than a month after the first person fell ill, investigators found the cause—a bacterium called Escherichia coli O157:H7—and 2 weeks after that, figured out that the burger patties were the culprit. During this outbreak, scientists at CDC performed laboratory tests to determine that the very specific strain of E. coli O157:H7 found in patients was the same as the strain found in the hamburgers.

But CDC wanted to be able to recognize foodborne outbreaks more quickly—so they could be stopped sooner. CDC worked with the Association of Public Health Laboratories (APHL) to develop PulseNet. This ensured that all participating laboratories would use the exact same methods for testing bacteria so the different strains could be compared in a single, shared database. If, upon searching the database, several ill people have bacteria with the same DNA fingerprint, an outbreak is possible.

How does PulseNet work?

CDC microbiologists and epidemiologists review laboratory reports

CDC microbiologists and epidemiologists review laboratory reports

  • A person falls ill and visits his or her doctor.
  • The doctor suspects a foodborne illness and asks for a sample (often a stool sample), which he or she sends to a laboratory at a clinic.
  • The clinic laboratory determines what type of bacteria is in the patient’s sample—for example, Salmonella.
  • The lab notifies the doctor, who will tell the patient and discuss treatment options, and also sends the sample to a public health lab, usually in the state.
  • The public health lab determines what kind of Salmonella it is—for example, Salmonella Enteritidis. . Public health labs are a first line of defense to protect the public against foodborne illnesses and other health hazards.
  • They then take a DNA “fingerprint” of the bacteria, using a process called pulsed-field gel electrophoresis (PFGE), to get its unique fingerprint, or pattern.
  • The public health lab uploads the pattern into an electronic database at their laboratory and also to a national database located at CDC.
  • Microbiologists and epidemiologists together review the laboratory reports to decide whether something unusual or unexpected is occurring that warrants further investigation.
  • Epidemiologists interview the patients.  These interviews may gather simple facts of their illness, or they may ask about everything they’ve eaten, where they’ve been, and other questions which might provide a clue as to what caused their illnesses.
  • They search the databases for patterns that are the same as one another. For example, if they find five patterns—which come from five different samples, from five different ill people—that appear to be the same, it is a clue that these five people may be part of a single outbreak, caused by a single food (or other source).
  • These groups of the same patterns, called clusters, spur investigations by local, state, and national agencies into the source of the outbreak.  By comparing answers to interview questions among members of a cluster, connecting PFGE patterns in patients to patterns found in food monitoring programs, and conducting epidemiological studies, specific causes of the outbreak may be identified, such as a particular type of food or activity.  When this happens, the agencies collaborate to control further spread of the outbreak, and to develop strategies to prevent the outbreak from happening again.  

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Why is PulseNet effective?

PulseNet is effective because all of the laboratories in its network follow the same procedures and standards—making it possible to compare fingerprints uploaded by labs in different places. In PulseNet, the quality and uniformity of the data is ensured by a quality assurance and quality control (QA/QC) program.

Why is PulseNet important to public health?

PulseNet helps scientists determine whether an outbreak is occurring, even if only a few people are ill or even if they are geographically far apart. It can also allow outbreaks and their causes to be identified in a matter of hours rather than days or weeks because PulseNet effectively allows investigators to focus their efforts on specific bacteria, people, and foods or other sources.
Epidemiologists at the local, state, and national levels use information gathered by PulseNet to help determine what specifically is making people sick. They also work with regulatory agencies, such as FDA and USDA, to find immediate (such as a food recall) and long-term (such as a new production practice) solutions to the problems that cause outbreaks.

Isn’t it better to prevent outbreaks before they happen?

Preventing outbreaks from occurring in the first place is the ultimate goal of food safety policies and programs, including good manufacturing practices, safety inspections, and hazard analysis critical control points (HACCP) plans. But because of the complexity of food production, distribution, and preparation, it is impossible to completely eliminate foodborne disease.
PulseNet, along with other foodborne illness surveillance systems, is our best tool for detecting unrecognized problems within our food safety system. Identifying these problems allows us to take action—and action means progress toward prevention.

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PulseNet in Detail

How does DNA fingerprinting help outbreak investigations?

What we eat and how we eat have changed. Over the past 20 years in the United States, we have observed a shift away from the typical point source, or “summer picnic” outbreak, where many people gather and eat together in the same place—which is relatively easy to detect. Instead, because of larger food processing facilities that distribute products across the country, we have more widespread outbreaks that occur across many communities with only a few illnesses in each community and are more difficult to detect.

However, PulseNet has increased our ability to identify and investigate these outbreaks by

  • Identifying cases that are part of an outbreak. It distinguishes these cases from others that are not part of an outbreak but are naturally occurring at the same time.
  • Detecting outbreaks through surveillance. Fingerprinting links cases that may appear unconnected because they are geographically far apart, because the organism is common and a small increase of cases is not noticed, or because outbreak-related cases and unrelated cases may look the same.

What is Pulsed-field Gel Electrophoresis (PFGE)?

Graphic: The PFGE Process

PFGE Process: Larger View

Pulsed-field gel electrophoresis (PFGE) is a technique used by scientists to generate a DNA fingerprint for a bacterial isolate.

How does PFGE work?

PFGE uses molecular scissors, called restriction enzymes, to cut bacterial DNA at certain locations known as restriction sites. These molecular scissors are selected to generate a small number of DNA pieces that can be separated based on size. Usually these DNA pieces, or restriction fragments, are large and need to be specially treated and separated to generate a DNA fingerprint. First the bacteria are loaded into an agarose suspension, similar to gelatin, then the bacterial cell is opened to release the DNA. Once the DNA is released then the agarose and DNA suspension, also known as a plug, is treated with restriction enzymes. The treated plugs are then loaded onto an agarose gel and the restriction fragments are separated based on size using an electric field. What makes PFGE different from how scientists usually separate DNA is because PFGE can separate several large restriction fragments. To do this an electric field that constantly changes direction to the gel is used to generate a DNA fingerprint.

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PulseNet Participants

Who participates in PulseNet?

Since it began in 1996, PulseNet has expanded to include public health laboratories in all 50 states and food regulatory laboratories within the Food and Drug Administration (FDA) and U.S. Department of Agriculture (USDA).
Partial funding for PulseNet is provided to state participants by the CDC-managed Epidemiology and Laboratory Capacity Cooperative Agreement. Local, state, and federal agencies also support the network to varying degrees, but gaps in the system remain because of limited resources and competing priorities.

What is PulseNet International?

PulseNet International, which now spans more than 80 countries, was born from the success of PulseNet USA to establish similar networks in Canada, Europe, Latin America and the Caribbean, Asia Pacific, the Middle East, and Africa. These networks collaborate with one another and with PulseNet USA.

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PulseNet in the Future

How does PulseNet adapt to changing technology?

As technology evolves, PulseNet is committed to identifying and standardizing the best molecular techniques to identify outbreaks. With the development of next generation sequencing techniques and culture independent diagnostic testing, many changes exist on the horizon for the network. Today, PulseNet is an effective tool to detect outbreaks because it uses bacterial fingerprinting solutions that are:

  • rapid,
  • easily standardized, and
  • able to be performed by laboratory technicians in state and local health departments and by PulseNet international participants.

Any future PulseNet network must also fulfill these requirements.

Culture Independent Diagnostic Tests

Graphic: Test for Foodborne Illnesses

Similarities and differences between culture-dependent and culture-independent tests. Click for larger view.

The scientist takes bacterial cells from an agar plate

The scientist takes bacterial cells from an agar plate.

One way that technology is evolving is the development of new clinical laboratory diagnostic tests, called culture independent diagnostic tests, that do not rely on a pure bacterial culture. PulseNet’s ability to identify outbreaks is challenged when foodborne illnesses are diagnosed using these culture independent diagnostic tests because PulseNet relies on bacteria cultured from clinical specimens, such as stool, to perform DNA fingerprinting. These new tests are quick and inexpensive and may soon replace the techniques that PulseNet has used for decades to identify outbreaks.

To meet this challenge, CDC and its regulatory and industry partners developed an action plan. This plan includes short term activities, such as:

  • Retaining isolates from culture-based methods to support current surveillance technologies, including through reflexive culture of test positive specimens in the clinical laboratories or forwarding these specimens for culture in public health laboratories.

Long term activities include:

  • Assessing the performance of new tests and developing new case definitions for more accurate estimates of disease burden and trends;
  • Partnering with FDA and industry to lessen the negative impacts of the device development and licensure processes; and
  • Developing new technology and surveillance systems to curate epidemiologically relevant information from available samples (typically, specimens containing primary DNA).

As next-generation test use expands, CDC’s national surveillance systems and laboratory infrastructure must keep pace with the changing technology. With modernization, CDC and its public health partners can continue to successfully detect, respond, and stop infectious diseases.

What are the future objectives of PulseNet?

  • Develop and validate new subtyping methods, with focus on next generation sequencing approaches, with the goal of improving the laboratory-based surveillance capacity of the network.
  • Address the role next generation sequencing could play in PulseNet and develop strategies to effectively manage, analyze and archive this type data.
  • Continue working toward improving communication between laboratorians, epidemiologists and other public health partners at the national and international levels
  • Develop subtyping techniques to address the shift from culture-based to culture-independent diagnostic approaches that are proliferating in the clinical laboratory setting
  • Strengthen collaborations and establish partnerships/affiliations with other stakeholders in the world of food safety, including academia and the food industry, as well as non-profit national and international organizations worldwide

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