Persistent Strain of E. coli O157:H7 (REPEXH01) Linked to Multiple Sources
Posted February 8, 2023
Posted February 8, 2023
Food Safety Alert/Investigation Notice
CDC, public health, and regulatory officials in several states, and _____________________________ are investigating a multistate outbreak of E. coli O157: H7 infections with this persistent strain linked to ________________. Do not eat, sell, or serve ______________________.
REPEXH01 is a persistent strain of Shiga toxin-producing E. coli O157:H7 bacteria that has caused illnesses and outbreaks in the United States.
Illness caused by this strain was first reported to PulseNet in 2017. Illnesses caused by this strain occur year-round but are less common in winter.
In the past, the REPEXH01 strain has spread to people through contaminated food and contaminated recreational water.
This strain is relatively diverse genetically. Bacteria in this strain are within 21 allele differences of one another by whole genome sequencing, which is more diverse than typical multistate foodborne outbreaks where bacteria generally fall within 10 allele differences of one another.
What is a persistent strain?
CDC uses “persistent” to describe some strains of bacteria that have caused illness for years. The strains continue to cause illness, even though the number of illnesses they cause might vary over time. The strains are sometimes linked to more than one source, making them harder to control.
|Shiga Toxin Type||Stx2a and/or Stx2c|
|First Detection||April 2017|
|Illnesses Reported in PulseNet||634|
|Identified outbreak sources*
*Confirmed sources were implicated by epidemiologic
Last Updated: September 2, 2022
Outbreaks and Outbreak-Related Illnesses
Although most enteric illnesses – including those caused by REPEXH01 – 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. Moreover, lab-confirmed cases comprise only a small portion of the true number of illnesses that occur because most people do not seek medical care and even fewer submit a stool specimen.
Starting in 2017, CDC and local, state, and federal health and regulatory partners have investigated several outbreaks of E. coli O157:H7 illnesses caused by the REPEXH01 strain.
Summary of Selected Multistate Outbreaks
|Geographic Location of
|Number of States
|Outbreak A||July 2017||Recreational water
|Outbreak B||March 2018–
|Outbreak C||August 2018–
|Outbreak D||October 2018–
|Outbreak E||May 2019–
|Outbreak F||December 2020–
|Unknown||Unknown||22||7||CDC Investigation Notice|
|Outbreak G||April 2021–
* Outbreak dates are based on reported or estimated illness onset dates.
† Confirmed sources were implicated by epidemiologic plus traceback or laboratory data. Suspected sources were implicated by epidemiologic data only. More info
** The geographic location of a confirmed outbreak source may not always be known. This can happen when a food containing multiple ingredients (e.g., bagged salad blend) is confirmed as the source, but the evidence cannot implicate a specific food, or when evidence confirms an outbreak source but traceback cannot pinpoint the exact geographic location of the source.
This chart, called an epidemiologic curve, shows when people got sick.
People with E. coli O157:H7 illnesses caused by the REPEXH01 strain, by date illness began and by outbreak, 2017–2022*,†
This map shows where sick people lived.
E. coli O157:H7 illnesses caused by the REPEXH01 strain, by state, 2017–2022*
Bacteria in this strain are within 21 allele differences of one another by core genome multilocus sequence typing (cgMLST), which is more diverse than typical multistate foodborne outbreaks where bacteria generally fall within 10 allele differences of one another.
This strain includes two major genetic subclusters. Each has caused at least two outbreaks linked to different sources and geographic regions. Possible reasons for the differences among genetic subclusters are still being investigated. More research is needed to determine if any genetic subclusters are associated with specific foods, animal populations, or geographic regions.
Isolates from food, animal, and environmental samples
|Isolate Type||Geographic Location
|2017||1||Goose feces||California||Outbreak A|
|2017||2||Lake sediment||California||Outbreak A|
|2017||4||Lake water||California||Outbreak A|
|2019||1||Ground beef||California||Routine Sampling|
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information.
SNP Cluster*: PDS000059979.158
* The SNP (Single Nucleotide Polymorphism) tree provided by NCBI’s Pathogen Detection Pipeline in the link above may include isolates that are not considered part of this strain. The difference in thresholds and allele/SNP differences occur because NCBI’s Pathogen Detection Pipeline uses an analysis pipeline different from CDC PulseNet. The link is provided to give context to the overall genetic relatedness of the strain reported on this page, as well as to provide links to raw sequence files. Moreover, the SNP trees on NCBI’s Pathogen Detection Pipeline are updated more frequently than this web page.
Antimicrobial resistance information
The National Antimicrobial Resistance Monitoring System (NARMS) is a national public health surveillance system that tracks antimicrobial resistance for certain intestinal bacteria from sick people (CDC), retail meats (FDA), and food animals (USDA) in the United States. The NARMS program helps protect public health by providing information about emerging antimicrobial resistance, the ways in which resistance is spread, and how resistant infections differ from susceptible infections.
Bacteria from most sick people’s samples showed resistance to the antimicrobials chloramphenicol, streptomycin, sulfisoxazole, tetracycline, and trimethoprim-sulfamethoxazole. These findings do not affect treatment guidance because antimicrobials are not recommended for patients with E. coli O157:H7 infection.
Interested in collaborating on a project related to this strain? Contact CDC at REPStrains@cdc.gov.