Data Summary: Persistent Strain of Salmonella Hadar (REPTDK01)

At a glance

_{^* Confirmed sources were implicated by epidemiologic plus traceback or laboratory data. Suspected sources were implicated by epidemiologic data only. More information available in the latest summary of possible multistate enteric disease outbreaks.}

Key findings

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 the data show

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

Timeline

People with Salmonella Hadar illnesses caused by the REPTDK01 strain, by date illness started and by outbreak, 2019–2023

Map

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

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.

Antimicrobial-resistant isolates

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.

Percentage of Salmonella Hadar REPTDK01 isolates from people who were sick that were antimicrobial resistant, by antimicrobial (n = 1,886), as of July 31, 2023 — NARMS

Collaborate with CDC

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

About the data

Summary of selected multistate outbreaks

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 information available in the latest summary of possible multistate enteric disease outbreaks.

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.

In Outbreak C, one illness also occurred in Washington, D.C.

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

N=1,899 for whom information was reported as of July 31, 2023. Some illness onset dates have been estimated from other reported information.

Map

Outbreak dates are estimated, based on reported or estimated illness onset dates.

Summary of selected non-human isolates associated with outbreak investigations

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 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-resistant isolates

Resistance was determined based on the results of antimicrobial susceptibility testing when available (n = 89 isolates); otherwise, resistance was predicted based on whole genome sequencing (n = 1,797).

Ciprofloxacin data includes isolates carrying a single quinolone resistance gene (n = 3; 0.2%); a single gene may result in interpretation of "intermediate" for ciprofloxacin on antimicrobial susceptibility testing.

Resources

Suggested citation

Centers for Disease Control and Prevention. (2024). Data Summary: Persistent Strain of Salmonella Hadar (REPTDK01) Linked to Backyard Poultry and Ground Turkey.