Persistent Strain of Salmonella Enteritidis (REPJEG02)

At a glance

_{*Also known as decreased susceptibility to ciprofloxacin (DSC).}

Key findings

REPJEG02 is a persistent strain of Salmonella Enteritidis bacteria that has caused illnesses and outbreaks in the United States.

Illness caused by this strain was first reported in 2016.

Multiple sources

REPJEG02 has spread to people through contaminated chicken and shell eggs, contact with backyard poultry, and international travel.

Genetically diverse

REPJEG02 is more genetically diverse than typical multistate Salmonella Enteritidis foodborne outbreak strains based on results from whole genome sequencing (WGS).

Genetic diversity can increase over time as strains pass among human hosts, animal hosts, and environmental settings—each with different selective pressures. Understanding this genetic diversity helps public health officials identify related illnesses and better understand how these strains continue to spread and persist over time.

What the data show

Illnesses and outbreaks

Outbreaks and other investigations

Although most enteric illnesses—including those caused by REPJEG02—are not part of an outbreak, investigation of outbreaks provides information that increases our understanding of germs, sources, settings, and factors that contribute to illness.

Starting in 2020, CDC and local, state, and federal public health and regulatory partners have investigated several outbreaks of Salmonella Enteritidis illnesses caused by the REPJEG02 strain.

REPJEG02 has been identified in both backyard poultry and food poultry products, but it is not yet understood how spread between these industries occurred. Evidence collected during outbreak investigations indicates that this strain is widespread in both industries

Summary of selected multistate outbreaksA

Selected publications about REPJEG02 investigations

• Emergence of Salmonella Enteritidis with decreased susceptibility to ciprofloxacin in humans and poultry in the United States (2026)
• Chicken vaccination reduces colonization and dissemination of Salmonella Enteritidis with decreased susceptibility to ciprofloxacin (2026)

Timeline

Map

Laboratory data

Whole genome sequencing analysis

Isolates that meet the REPJEG02 strain definition are genetically related as determined by core genome multilocus sequence typing (cgMLST), and have a genetic mutation GyrA (D87Y) that causes nonsusceptibility to ciprofloxacin. Additionally, isolates within REPJEG02 fall into the single nucleotide polymorphism (SNP) cluster PDS000065758 on NCBI.

REPJEG02 is more genetically diverse than typical multistate Salmonella Enteritidis foodborne outbreak strains, in which bacteria generally are within 3 allele differences of one another.

Genetic diversity can increase over time as strains pass among human hosts, animal hosts, and environmental settings—each with different selective pressures. Understanding this genetic diversity helps public health officials identify related illnesses and better understand how these strains continue to spread and persist over time.

Isolates from food, animal, and environmental samples

Information from 1,913 REPJEG02 isolates from non-human sources has been reported to PulseNet, with the earliest in 2017. Most isolates are from chicken samples collected by the USDA Food Safety and Inspection Service (USDA-FSIS), including 1,486 from FSIS sampling of food and food products and 62 from FSIS sampling of intestinal (cecal) content.

Other non-human sources of this strain, with WGS data submitted to PulseNet, include

• Environmental swabs (174 isolates)
• Turkey (18 isolates)
• Eggs (9 isolates)
• Beef or cattle (6 isolates)
• Pork or swine (4 isolates); and
• Other food and animal sources (23 isolates).

Although WGS data from U.S. Food and Drug Administration (FDA) samples have not always been submitted to PulseNet, more than 200 food and environmental isolates collected through FDA sampling programs are highly related to REPJEG02 isolates by WGS. These include many samples from retail chicken products.

More information about these isolates can be found through the National Center for Biotechnology Information or the NARMS Now: Integrated Data platform.

Genomic information

The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information.

Antimicrobial resistance

The National Antimicrobial Resistance Monitoring System (NARMS) is a national public health surveillance system that tracks antimicrobial resistance for certain intestinal bacteria from ill people (CDC), food animals (USDA), and retail meats (FDA) in the United States. The NARMS program helps protect public health by providing information about emerging antimicrobial resistance, the ways in which resistance spreads, and how resistant infections differ from susceptible infections.

Bacteria from all ill people's samples had a mutation in GyrA (D87Y), predicting nonsusceptibility to ciprofloxacin (expected MIC ≥0.12 µg/mL) This is also known as decreased susceptibility to ciprofloxacin (DSC).

Only a small proportion of samples (0.2%) had more than one quinolone resistance determinant. Fewer than 1% of ill people's samples showed resistance to other antibiotics.

Most people with Salmonella illness recover without antibiotics. However, if antibiotics are needed, REPJEG02 illnesses may not be treatable with ciprofloxacin and may require a different antibiotic choice. When possible, healthcare providers should use antimicrobial susceptibility testing results to guide treatment.

Collaborate with CDC

Interested in collaborating on a project related to this strain? Contact CDC at REPStrains@cdc.gov.

About the data

Resources

Suggested citation

Centers for Disease Control and Prevention. (2026). Persistent Strain of Salmonella Enteritidis (REPJEG02).