Persistent Strain of Salmonella Hadar (REPTDK01) Linked to Backyard Poultry and Ground Turkey
Posted September 14, 2023
Posted September 14, 2023
Food Safety Alert/Investigation Notice
CDC, public health, and regulatory officials in several states, and _____________________________ are investigating a multistate outbreak of Salmonella Infantis infections with this persistent strain linked to ________________. Do not eat, sell, or serve ______________________.
REPTDK01
REPTDK01 is a persistent strain of Salmonella Hadar bacteria that has caused illnesses and outbreaks in the United States.
Illness caused by this strain was first reported to PulseNet in 2019, and the first outbreak was detected in 2020. Illnesses caused by this strain occur year-round but are more common in the spring and summer.
In the past, the REPTDK01 strain has spread to people through animal contact and contaminated food.
This strain is relatively diverse genetically. Bacteria in this strain are within 26 allele differences of one another by core genome multilocus sequence typing (cgMLST), which is more diverse than typical multistate Salmonella 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.
| Bacteria | Salmonella enterica |
|---|---|
| Serotype | Hadar |
| Persistent Strain | REPTDK01 |
| First Illness Detected | July 2019 |
| Illnesses Reported in PulseNet as of July 31, 2023 | 1,899 |
| Outbreaks Investigated | 5 |
| Identified outbreak sources*
*Confirmed sources were implicated by epidemiologic |
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Last Updated: May 1, 2023 |
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Outbreaks and Outbreak-Related Illnesses
Although most enteric illnesses are not part of a known outbreak, investigation of outbreaks provides information that increases our understanding of germs, sources, settings, and factors that contribute to illness. 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 2020, CDC and local, state, territorial, and federal health and regulatory partners have investigated several outbreaks of Salmonella Hadar illnesses caused by the REPTDK01 strain. This strain has been identified in both backyard poultry and food poultry products, but it is not yet understood how this contamination has occurred. Evidence collected during outbreak investigations indicate that this strain is widespread in both industries.
Summary of Selected Multistate Outbreaks
| Outbreak | Dates People Became Ill* |
Outbreak Source† |
Geographic Location of Outbreak Source** |
Reported Illnesses |
Reported Hospitalizations |
Reported Deaths |
Number of States with Illnesses |
More Informationⱡ |
|---|---|---|---|---|---|---|---|---|
| Outbreak A | April 2020– November 2020 |
Backyard poultry (confirmed) | Unknown | 848 | 186 | 0 | 49 | Salmonella Outbreaks Linked to Backyard Poultry | 2020 |
| Outbreak B | December 2020– April 2021 |
Ground turkey (confirmed) | Unknown | 33 | 4 | 0 | 14 | Salmonella Outbreak Linked to Ground Turkey | 2021 |
| Outbreak C | April 2021– October 2021 |
Backyard poultry (confirmed) | Unknown | 364 | 111 | 0 | 45§ | Salmonella Outbreaks Linked to Backyard Poultry | 2021 |
| Outbreak D | April 2022– October 2022 |
Backyard poultry (confirmed) | Unknown | 273 | 74 | 1 | 40 | Salmonella Outbreaks Linked to Backyard Poultry | 2022 |
| Outbreak E | February 2023– May 2023 |
Multiple vehicles (confirmed backyard poultry and suspected ground turkey) | Unknown | 55 | 9 | 0 | 28 |
* 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 the product (i.e., live animals or ground meat) sold from or mixed with other products from multiple suppliers is confirmed as the source, but the evidence cannot implicate a specific supplier. This can also happen when evidence confirms an outbreak source but traceback cannot pinpoint the exact geographic location of the source. Traceback investigations for all outbreaks caused by REPTDK01 have not identified a common source of contamination. Traceback activities within the backyard poultry industry are conducted solely through non-regulatory partnerships.
§ One illness also occurred in Washington, D.C.
ⱡ Web pages describing backyard poultry–associated illness outbreaks do not exclusively present data on Salmonella Hadar but instead report all outbreaks of any Salmonella serotype linked to backyard poultry during that year. As such, numbers of patients, hospitalizations, deaths, and states reported in those web postings will not be identical to the numbers presented here.
Timeline
This chart, called an epidemiologic curve, shows when people got sick.
People with Salmonella Hadar illnesses caused by the REPTDK01 strain, by date illness started and by outbreak, 2019–2023*
Map
This map shows where sick people lived.
Salmonella Hadar illnesses caused by the REPTDK01 strain, by state, 2019–2023*
Laboratory data
Whole Genome Sequencing analysis
Bacteria in this strain are within 26 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 six major subclusters of isolates linked to backyard poultry and one major subcluster of isolates linked to ground turkey. 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
In addition to isolates of this strain that have been detected in humans, isolates have also been detected in food products, animals, and the environment. Some isolates obtained from food products have been detected as part of routine surveillance performed by the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) or as part of surveillance conducted by the Food and Drug Administration (FDA) or USDA branches of the National Antimicrobial Resistance Monitoring System (NARMS).
Overall, this includes 197 isolates detected in food products, 25 isolates detected from backyard poultry or their habitats, and 24 isolates detected in animal cecal (intestinal) contents during 2019–2023. In 2022, one isolate was obtained from a pet dog via endoscopy performed at a veterinary hospital.
Summary of Selected Non-Human Isolates Associated with Outbreak Investigations*
| Year | Number of Isolates | Isolate Type | Geographic Location of Source | Reason Collected |
|---|---|---|---|---|
| 2020 | 4 | Backyard poultry (ducks or chickens) | Kentucky (3 isolates) & New Hampshire (1 isolate) | Outbreak A |
| 2020 | 2 | Environmental (duck habitats) | Kentucky & Oregon (1 isolate each) | Outbreak A |
| 2021 | 13 | Food (ground turkey) | Arkansas (2 isolates), Indiana (3 isolates), Maine (1 isolate), Minnesota (2 isolates), New Jersey (1 isolate), North Carolina (1 isolate), Pennsylvania (2 isolates), & South Dakota (1 isolate) | Routine sampling by USDA-FSIS, included in Outbreak B |
| 2021 | 3 | Turkey cecal contents | Iowa, South Carolina, & Virginia (1 isolate each) | Routine sampling by USDA-FSIS NARMS, included in Outbreak B |
| 2021 | 7 | Food (ground turkey) | Connecticut (3 isolates), New York (1 isolate), & Tennessee (3 isolates) | Routine sampling by FDA NARMS, included in Outbreak B |
| 2021 | 7 | Food (ground turkey) | Pennsylvania | Outbreak B, Frozen, unopened product at home of a patient |
| 2021 | 3 | Backyard poultry (ducks or chickens) | Arizona (2 isolates) & Ohio (1 isolate) | Outbreak C |
| 2021 | 7 | Environmental (duck or chicken habitats) | Arizona (2 isolates) & California (5 isolates) | Outbreak C |
| 2023 | 6 | Backyard poultry (chicks) | Ohio | Outbreak E |
| 2023 | 10 | Food (ground turkey) | Connecticut (4 isolates), Louisiana (1 isolate), New York (3 isolates), Pennsylvania (1 isolate), & Tennessee (1 isolate) | Routine sampling by FDA NARMS, included in Outbreak E |
| 2023 | 2 | Turkey cecal contents | Michigan (1 isolate) & Indiana (1 isolate) | Routine sampling by USDA-FSIS NARMS, included in Outbreak E |
| 2023 | 18 | Food (ground turkey [n=16], turkey carcass [n=1], or chicken carcass [n=1]) | Michigan (2 isolates), Missouri (1 isolate), North Carolina (3 isolates), New York (3 isolates), Pennsylvania (2 isolates), South Carolina (2 isolates), Utah (2 isolates), & Virginia (3 isolates) | Routine sampling by USDA-FSIS, included in Outbreak E |
* Isolates from food, animals, or the environment are only included in this table if they were detected during an outbreak investigation and were considered a source of patient exposure to the outbreak strain. No such isolates were detected in association with Outbreak D.
Genomic information
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information. To view the full SNP cluster, click on the link below; then within NCBI’s platform click the link underneath the “SNP Cluster” column.
SNP Cluster*: https://www.ncbi.nlm.nih.gov/pathogens/isolates/#PNUSAS362655.
* 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 people’s samples most commonly showed resistance to the antimicrobials streptomycin and tetracycline. These findings should not affect treatment for most patients with Salmonella infection caused by REPTDK01.
Collaboration
Interested in collaborating on a project related to this strain? Contact CDC at REPStrains@cdc.gov.