Reoccurring, Emerging, and Persisting Enteric Bacterial Strains

Outbreak Investigation Basics

Some enteric bacterial strains cause acute outbreaks linked to specific sources. Other strains, referred to as reoccurring, emerging, or persisting (REP) strains, can reoccur and periodically cause acute outbreaks. They can also emerge and increase in frequency or persist and cause illnesses over periods of months or years, despite investigation and prevention efforts.

Investigators use a laboratory method called whole genome sequencing (WGS) to identify the DNA fingerprints of bacteria from ill people and from foods, animals, and the environment. These DNA fingerprints represent strains of bacteria.

Investigators use these DNA fingerprints to find outbreaks of enteric (gastrointestinal) diseases. When scientists identify a group of people who got sick around the same time with a strain with the same DNA fingerprint, this represents a possible outbreak. Investigators then work to determine what caused the illnesses. These acute outbreaks tend to start off with a significant rise in illnesses followed by a significant decline over a short period of time.

WGS has also enabled investigators to find and investigate groups of illnesses that are caused by the same strain but that occur over time periods longer than an acute outbreak. These strains can reoccur and periodically cause acute outbreaks, emerge and increasingly cause illness, or persist and cause illnesses over periods of months or years. They may continue to cause illnesses despite investigation and prevention efforts.

Identifying a strain as a REP strain is based on many factors, including the number of illnesses, whether illnesses are increasing, the characteristics of the strain (e.g., multidrug resistance, high virulence, increased transmissibility), and whether the strain is the cause of large or frequent outbreaks.

REP Strain Characteristics

  • Reoccurring strains: Strains repeatedly causing acute outbreaks separated by periods during which the strain either does not make people sick or causes illnesses at very low levels.
  • Emerging strains: Previously novel or rare strains that increasingly cause illnesses or show the potential to cause increasing illness.
  • Persisting strains: Strains causing illnesses consistently over a long time.

CDC’s Role

Since 2019, CDC has used the PulseNet system to identify and monitor REP strains of several major pathogens, including Salmonella, E. coli O157:H7, Listeria, and Campylobacter. PulseNet uses a combination of different WGS tools for identifying and tracking these strains and will develop more as new strains are identified and investigated.

CDC uses information gained from investigations of REP strains to better understand their sources, track how they change over time, and collaborate on measures to reduce their spread.

CDC plans to share detailed information about some REP strains. Links will be available on this web page.