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The Listeria Whole Genome Sequencing Project

Whole genome sequencing improves the detection and investigation of foodborne outbreaks

Whole genome sequencing is a process that uses laboratory methods to determine the complete DNA sequence of an organism’s genome.

Whole genome sequencing is an important tool for disease detectives. It provides genetic information about germs that are making people sick. This information improves our ability to detect, investigate, and stop foodborne outbreaks.

With whole genome sequencing, Listeria outbreaks can be detected when as few as two people have gotten sick. Determining that the same strain of Listeria is making people sick is an indication that these illnesses may have come from the same source – for example, the same contaminated food or the same contaminated food processing facility. Thus, whole genome sequencing can help disease detectives solve outbreaks.

By combining real-time whole genome sequencing with data from patients about the foods they ate and data about Listeria in foods, public health officials can:

  • Detect more clusters (possible outbreaks) of Listeria infections
  • Link cases of Listeria to a likely source
  • Identify unrecognized sources of Listeria
  • Stop Listeria outbreaks while they are still small

Whole genome sequencing prevents Listeria illness

Chart showing how whole genome sequencing prevents listeria illness. # years of data are depicted where the number os outbreaks solved per year has increased and the number of cases per outbreak has decreased. The data starts the year prior to using whole genome sequencing in September 2012 and goes through September 2014.

Moving into the future

Whole genome sequencing alone cannot solve outbreaks, but it has dramatically improved our ability to track Listeria and other germs. Epidemiologic data, such as information about what foods people ate before they got sick, are critical for outbreak investigations. Our ability to solve outbreaks caused by Listeria and other germs will improve as we obtain more epidemiologic data, and thus strengthen the link between epidemiologic and whole genome sequencing data.

Federal agencies collaborate to prevent Listeria infections

Whole genome sequencing of Listeria began as a one-year project in fall 2013 as a collaboration between the Centers for Disease Control and Prevention, U.S. Food and Drug Administration, U.S. Department of Agriculture, National Center for Biotechnology Information, and state and local health departments. The practices developed during the project have now become standard.

Successful investigations depend on drawing data from these laboratory and epidemiological sources:

  • PulseNet, a national laboratory network that collects information about Listeria and other germs isolated from patients
    PulseNet uses pulsed-field gel electrophoresis (PFGE) and now also whole genome sequencing, two types of DNA fingerprinting. Scientists characterize Listeria isolated from a sample of the patient’s blood or other tissue. The DNA fingerprint from a patient’s Listeria is compared with hundreds of Listeria DNA fingerprints from other patients. When PulseNet identifies a cluster of people with related Listeria germs, it notifies epidemiologists, who begin an investigation to look for a common source of the illnesses and check GenomeTrakr to see if there are matches to food isolates. PulseNet is a collaboration among CDC and state and local health departments.
  • The Listeria Initiative, a national epidemiology system that collects reports of Listeria infections in humans
    As quickly as possible after Listeria infection is diagnosed, health officials interview the ill patient using a standard questionnaire about foods recently consumed. When PulseNet identifies a cluster of Listeria isolates that look similar, epidemiologists review the questionnaires from patients in the cluster, and compare foods they ate with foods eaten by patients with Listeria infection who are not part of the cluster. This gives investigators clues about possible sources, and helps to determine the next steps in the investigation. The Listeria Initiative is a collaboration among CDC and state and local health departments.
  • GenomeTrakr, a national laboratory network that collects information about Listeria and other germs isolated from food and the production environment
    When a Listeria isolate from food or the environment is sequenced, GenomeTrakr checks the PulseNet database to identify possible links to Listeria DNA fingerprints from patients. GenomeTrakr is a collaboration among FDA and public health and university laboratories.
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