Genomic Analysis Tracks a Persistent Salmonella Hadar Strain Through Poultry-Linked Outbreaks
A persistent Salmonella enterica serovar Hadar lineage has now been tied to five multistate outbreaks in the United States, with roughly 2,000 human illnesses reported during 2020 through 2023. The strain, designated REPTDK01 by the Centers for Disease Control and Prevention, sits close enough across the genome to look deceptively uniform at first glance, yet the finer-scale sequence data reveal a split into two clades with different exposure patterns. One clade tracks mainly with backyard poultry and other food sources; the other is linked predominantly to commercial poultry products.
The findings matter because the same serovar moved through both household animal contact and the food supply. In practice, that creates a public health problem that does not respect the usual boundary between animal husbandry and foodborne transmission.
Why This Strain Drew Genomic Scrutiny
Nontyphoidal Salmonella enterica causes more than 1 million human salmonellosis cases each year in the United States. Illness often resolves on its own, but diarrhea, fever, and abdominal pain still carry real consequences, especially in children younger than 5 years, adults older than 65 years, pregnant women, and immunocompromised people, who face greater risk for invasive disease such as meningitis or septicemia.
Poultry remains one of the most important reservoirs. Commercial poultry food products contaminate consumers through ingestion, while backyard poultry can spread infection through direct contact with birds or contaminated environments. REPTDK01 emerged in both pathways, which makes it a useful example of how a single bacterial lineage can circulate across distinct but biologically connected reservoirs.
A particularly important feature of the lineage is persistence. Five outbreaks over several years suggest not a one-time contamination event but an organism able to move repeatedly through poultry-associated networks and remain available for reintroduction into human exposure settings.
Genome Sequencing Revealed Two Related but Distinct Clades
Investigators analyzed 404 genomes subsampled from routine surveillance and outbreak investigations to reconstruct the evolutionary history of REPTDK01. The work relied on molecular clock analysis and phylogenetic methods built on single-nucleotide polymorphism differences, allowing estimation of when the lineage most likely emerged. The most recent common ancestor likely appeared in early 2018.
That timing places the strain’s origin before the earliest recognized outbreaks, leaving a window during which the lineage could have been expanding quietly through poultry-associated reservoirs before public health detection caught up. The genomic tree then separated the lineage into two major clades. Clade 1 aligned with backyard poultry and other food sources. Clade 2 was predominantly associated with commercial poultry products.
The split is clinically useful because it gives epidemiologists a way to read transmission history from sequence data rather than waiting for a complete exposure story from patients alone. When food, animal, and environmental isolates cluster into separate clades, the genome becomes a source-tracking tool, not just an outbreak confirmation tool.
Exposure Patterns Match the Sequence Data
The 404-isolate set was drawn from a larger curated collection of 2,021 isolates collected during 2018 through 2023. Most of the isolates came from 2020 through 2022, the period when REPTDK01 was most active. To avoid overrepresenting closely related genomes, the cohort was stratified by year and randomly subsampled at about 16% per year, while all available isolates from 2018, 2019, and 2023 were retained. After quality control, 8 genomes were excluded, leaving the final subsampled dataset for analysis.
Isolates were categorized by exposure source using epidemiologic information and available metadata: backyard poultry, backyard poultry plus commercial poultry, commercial poultry, beef, pork, and unknown. Within that structure, clade associations lined up with known outbreaks and exposure histories. The backyard poultry signal was not incidental. It appeared repeatedly across illnesses, animal isolates, and environmental samples. The commercial poultry clade showed the same kind of coherence around food-linked exposure.
This is the kind of pattern public health surveillance depends on: a genomic division that mirrors real-world transmission routes rather than one that merely reflects arbitrary clustering.
Clade-Specific SNP Markers May Improve Source Attribution
The study identified two clade-specific single-nucleotide polymorphism markers, and in silico screening of additional isolates supported their potential value for source attribution. In practical terms, those markers could help distinguish whether a new isolate belongs to the backyard poultry-associated lineage or the commercial poultry-associated lineage. For investigators facing a live outbreak, that distinction can sharpen the field response, guide sampling priorities, and focus traceback efforts.
The biology is plausible. Distinct poultry systems differ in scale, breed patterns, husbandry practices, and biosecurity. Shared upstream inputs such as hatcheries, egg suppliers, or feed sources can still connect them, and some distribution practices may move bacteria between species when multiple poultry types are shipped together. Once a successful strain gains foothold in those networks, it can move between birds, environments, food products, and humans with enough continuity to sustain repeated outbreaks.
Public Health Value of the REP Framework
CDC’s reoccurring, emerging, or persisting strain framework was developed after whole-genome sequencing became widely available for outbreak surveillance. The framework recognizes that genetically related isolates may remain relevant over a longer time span than the narrow windows traditionally used in outbreak investigations. For REPTDK01, that approach captured a lineage whose allele differences stayed within the range used to define a REP strain, even as it caused multiple outbreaks across different exposure settings.
The broader implication is straightforward: long-lived enteric lineages can require a surveillance model that looks beyond a single cluster. WGS makes it possible to see a continuing bacterial population rather than a series of isolated incidents. For Salmonella Hadar, that view exposed a strain that appears to have originated in extant commercial poultry populations and later disseminated into backyard poultry environments.
The final constraint is equally clear. The analysis depended on available surveillance isolates and exposure metadata, and the source of each human illness is not always equally well documented. Even so, the combination of molecular clock dating, clade structure, and exposure-linked isolates offers a strong genomic framework for tracking future REPTDK01 detections and separating commercial poultry risk from backyard poultry risk when new cases appear.