Genomic tracing links South Korea’s Salmonella Infantis rise to humans, poultry, and wastewater
Salmonella enterica serovar Infantis is no longer moving through South Korea as a single, easily traceable lineage. Whole-genome sequencing of 65 bla CTX-M-65–positive isolates collected from humans, poultry, and wastewater during 2022–2024 showed a strain population with close genomic ties across sectors, multidrug resistance, and evidence of multiple introductions rather than one local expansion event.
The pattern matters because this serovar sits at the intersection of food production, clinical infection, and environmental contamination. Poultry remains the major reservoir, but wastewater now appears to be part of the same transmission web, providing a genomic snapshot of how resistant Enterobacterales can circulate through the human food chain and back into municipal effluent.
A resistant lineage circulating through food, clinic, and environment
The isolate set included 45 human samples, 16 poultry samples, and 4 wastewater samples collected through national and municipal surveillance systems. Human isolates came from EnterNet and PulseNet Korea; poultry isolates came from chicken fecal samples gathered through foodborne pathogen monitoring; wastewater isolates came from influent at two public treatment facilities in Incheon. From 2,817 human Salmonella isolates collected during 2022–2024, 258 were identified as Salmonella Infantis, and all 45 ESBL-producing isolates available for the study were included.
The resistance profile was broad. Every isolate was multidrug resistant, commonly to aminoglycosides, β-lactams, quinolones, tetracyclines, amphenicols, and folate pathway inhibitors. In practical clinical terms, this is the kind of phenotype that narrows oral treatment options and raises the stakes for susceptibility-guided therapy, especially when a foodborne strain is already carrying an ESBL determinant.
One sentence captures the public health problem: the same resistant lineage was found in patients, poultry, and wastewater.
Whole-genome sequencing showed intermingled clades across sectors
Whole-genome sequencing and phylogenomic analysis revealed high genetic similarity among isolates from all three sectors. Human, poultry, and wastewater strains were not segregated into cleanly separated clusters; instead, they were intermingled within monophyletic clades with strong bootstrap support, signaling close genomic relatedness rather than distant coincidence.
That structure is exactly what a One Health investigation is designed to detect. When strains from clinic, farm, and sewer share the same genetic neighborhood, transmission is no longer a theoretical concern. It becomes an inference supported by sequence data, even if the exact direction of movement cannot be assigned to a single route from the available isolates alone.
The study also placed the South Korean isolates into a larger global frame. Bayesian phylogeographic reconstruction suggested multiple introductions during 2018–2022, including one lineage related to isolates from the United States, designated clade I, and other lineages related to isolates from the United Kingdom, designated clade II. Rather than a single importation followed by domestic spread, the genomic picture points to more than one entry event, each leaving a separate trace in the national collection.
pESI-like plasmids likely helped the strain persist and diversify
The biology behind this spread is familiar in Salmonella Infantis. The serovar has repeatedly demonstrated an ability to acquire large plasmids that bundle resistance and virulence traits together. Earlier work identified the approximately 280-kb pESI megaplasmid, which carries genes linked to tetracycline, trimethoprim, sulfamethoxazole, antiseptic, and heavy-metal resistance, along with virulence determinants such as the yersiniabactin operon and fimbrial loci. Those accessory genes improve survival under antimicrobial and environmental pressure, giving the bacterium a clear fitness advantage in poultry production systems and along the food chain.
In this study, pESI-like plasmid markers were used to characterize the resistant isolates, and long-read sequencing was performed on one human isolate and one poultry isolate from clade II to better define plasmid context. For clade I, previously reported complete genome sequences from retail chicken meat in South Korea were used to assess plasmid context. The analytical strategy was designed to answer a central epidemiologic question: whether the same mobile genetic backbone was traveling with the organism across different reservoirs.
Wastewater added an environmental readout of the same epidemic
Wastewater surveillance gave the study a useful environmental dimension. The influent samples from public treatment facilities contained ESBL-producing S. Infantis, and those isolates fit into the same broader genomic picture as the human and poultry strains. In a resistant enteric pathogen, wastewater is not a passive endpoint. It can function as a community-level composite sample of shedding from infected or colonized hosts, especially when the same clone is already moving through food animals and patients.
The presence of related isolates in wastewater also strengthens the case for integrated surveillance. Clinical laboratories may see only the tip of the iceberg, while wastewater can reveal whether a circulating lineage has become embedded in a wider population ecology. When the same resistant strain appears in all three sectors, ignoring any one of them weakens outbreak detection and source tracking.
Surveillance gaps remain despite the clearer genomic map
South Korea has seen an increase in Salmonella Infantis through national gastrointestinal infection surveillance since 2022, and bla CTX-M-65–positive isolates have been increasingly identified in poultry. Human genomic data, however, had been sparse before this analysis, with only one human isolate previously reported. That gap delayed a full understanding of how the lineage was assembling and moving within the country.
The present genomic set closes part of that gap, but it does not close the case. The study defines relatedness, suggests multiple introductions, and supports cross-sector circulation, yet it does not by itself identify a single dominant source or transmission route for every isolate. The clusters are genetically close; the ecology is distributed; the movement is likely bidirectional across the food-environment-human interface.
From a clinical perspective, the important signal is resistance embedded in a successful serovar. ESBL production, broader multidrug resistance, and evidence of clonal persistence together create the kind of strain profile that can complicate enteric infection control, especially when exposure pathways extend beyond the hospital and into poultry production and wastewater systems.
Genomic surveillance now functions as an infection-control tool
The strongest message from the study is operational rather than abstract. Whole-genome sequencing can connect the dots between patient isolates, poultry strains, and environmental sampling before conventional epidemiology fully resolves the picture. In a pathogen with strong food-chain fitness and a mobile resistance platform, that kind of surveillance is no longer optional background work; it is the core method for recognizing emergence early.
The investigators’ comparisons with global genomes also place South Korea’s isolates in a broader international context, with related lineages tied to the United States and the United Kingdom. That finding reinforces the mobility of bla CTX-M-65–positive Salmonella Infantis and argues for continued sequencing across sectors, not just in clinical cases that reach diagnostic attention.
The next challenge is not whether this lineage can spread. It already has. The more difficult question is how early genomic and environmental surveillance can detect the next wave before resistance becomes further entrenched in poultry production and community transmission.