Why Salmonella Dublin poses a food safety threat in beef and dairy

By Dr. Liji Thomas, MDReviewed by Lauren HardakerAug 27 2025

A nationwide genomic study shows that while Salmonella Dublin looks genetically uniform, it hides powerful resistance traits that threaten cattle, people, and the food supply alike.

Study: Genomic evolution of Salmonella Dublin in cattle and humans in the United States. Image credit: Parilov/Shutterstock.com 

The foodborne pathogen Salmonella Dublin shows increasing antimicrobial resistance (AMR). It also spreads in the American food chain, compromising food safety and threatening food security. A recent paper published in Applied and Environmental Microbiology explored biosurveillance data for S. Dublin to understand how it changes in various human and non-human hosts.

Introduction

S. Dublin is a zoonotic microbe that has adapted well to cattle. It contaminates the human food chain and can cause severe disease in cattle and animals. Its scientific name is Salmonella enterica subsp. enterica serovar Dublin (S. Dublin). It is the most common strain obtained from clinical cattle case submissions, and the second-most common from non-clinical cattle submissions, rather than all clinical infections.

S. Dublin contaminates other cattle or humans primarily via the feco-oral route but can also be carried through saliva or milk. Infected calves become severely ill. A high proportion develop septicemia and respiratory disease, leading to death. Survivors may become healthy carriers and shed the microbe at intervals later in life.

Mature cattle develop gastroenteritis following infection, decreasing lactational milk production. Again, they often become healthy carriers, with shedding rates varying with physiological, environmental, and disease-related factors. Their calves are more likely to be infected and develop septicemia.

The USA is the world's largest beef producer and among the top three for major dairy products. Thus, S. Dublin has a documented impact on dairy and beef production.

Raw milk, soft cheeses, and contaminated beef are the primary sources of foodborne S. Dublin outbreaks and contact with infected cattle. It forms an occupational hazard for veterinarians and cattle workers. Humans suffer more severely and require hospitalization more often with S. Dublin infection than from other serovars, and it is more likely to cause illnesses requiring hospitalization.

Antimicrobial resistance (AMR) and multi-drug resistance (MDR) enhance the severity of S. Dublin infections, conferring resistance to fluoroquinolones like ciprofloxacin, or cephalosporins like ceftriaxone. The National Antimicrobial Resistance Monitoring System (NARMS) monitors AMR in this and other pathogens known to infect humans across the USA, especially using whole-genome sequence (WGS) techniques.

This has produced a large amount of publicly available data, which has provided insights into the prevalence or rise of AMR by species, regions, or time periods, singly or in combination. The current study focused on S. Dublin AMR and virulence using public genomic data within the One Health framework.

About the study

The study included data on 2,150 strains of S. Dublin collected from various parts of the USA between 2002 and 2023. About 580 were from infected cattle, 664 from infected humans, but most from environmental sources. The researchers then analyzed the genomes, especially the plasmids, virulence factors, and AMR genes. They assessed phylogenetic relationships using single-nucleotide polymorphism (SNP) differences to compare the genomes.

Study findings

Bovine, human, and environmental samples displayed distinctive features, displaying variations in the AMR potential and the genomic constitution. There were 116 genes that determined various aspects of bacterial virulence. Most of these genes (99) were present in 99% or more strains.

Antibiotic resistance genes were present in 1-10 per strain, out of 49 unique genes identified. Most conferred resistance to specific drugs, a few to metals like copper or gold, and two to biocides. Two genes were common to almost all strains.

AMR prevalence

Interestingly, unlike the global picture, S. Dublin shows a higher AMR potential in the USA, especially in bovine samples collected from clinically infected cattle.

S. Dublin strains from overtly infected cattle had the highest prevalence of AMR genes specific to various drugs. This includes resistance to a critical cephalosporin class used to treat invasive and severe diseases in children and calves. These samples also often showed resistance to florfenicol, which is used to treat calf pneumonia.

Quinolone resistance was most prevalent in environmental strains, likely linked to food supply chain contamination and indirect selective pressures, but not directly attributed to adult human drug use.

Multidrug resistance

Strains from infected cattle also had the highest levels of multidrug resistance plasmid IncA/C2, and the most significant diversity of genes. The fitness cost of acquiring AMR point mutations is less than that of plasmids. Moreover, plasmid acquisition mandates exposure to diverse plasmid-harboring environments and microbial communities. Thus, a less diverse environmental exposure could explain these differences between bovine and other sources.

Genomic stability

This is supported by environmental sources having a higher proportion of core genes and fewer accessory (shell and cloud) genes than clinical strains. Environmental, human, and bovine strains had distinctive features, such as a high proportion of core genes for the environmental vs the least proportion for the bovine strains. The reverse was true of cloud and shell genes. Most functional genes were shared across all strains, irrespective of the source. 

This suggests that clinical disease-causing strains are more adaptable. They cross environmental and host barriers, face immune defenses, and must incorporate into different microbial communities.

Conversely, less adaptable environmental strains from apparently healthy cattle may more easily contaminate post-harvest food supply chains. The food supply chain is also a more closely controlled environment, reducing the need for microbial adaptation.

Human strains cover the midpoint between clinical bovine and environmental strains, perhaps representing a mix. This could indicate adequate S. Dublin adaptation to cause invasive human disease after non-human transmission. Alternatively, they could represent the strains more likely to cause symptomatic illness, as others may have escaped recognition.

Phylogenetic resemblance

Surprisingly, 72% of the strains closely resembled one or more other strains with less than 20 SNP differences, irrespective of the source, period, or geographic location. The phylogenetic tree showed that most were on the same trunk.

Thus, the microbe shows high cross-reservoir genomic similarity, but the study does not establish direct transmission directionally between humans, cattle, and environmental reservoirs. The outcome is the widespread distribution of S. Dublin over the USA through closely related strains over a vast area and over a long period of time.

This “underscores the importance of considering strain source when assessing and monitoring antimicrobial resistance.” The study also highlights the need to improve publicly available databases for better phylogenetic and functional analysis.

Conclusions

“Our analyses of Salmonella Dublin reveal a striking degree of genomic similarity among strains circulating in U.S. cattle, human, and environmental reservoirs. However, this apparent homogeneity masks differences in genomic stability and antimicrobial resistance elements, highlighting distinct evolutionary trajectories within each reservoir.”

Antimicrobial stewardship policies must be uniformly applied to human and animal health practices. Ensuring food safety and biosecurity remains an important field of public health.

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