Food Safety
Not All Salmonella Are Equal: What Virulence Can Tell Us About Food Safety Risk
Not All Salmonella Are Equal: Understanding Virulence and Food Safety Risk
Salmonella is a diverse group of bacteria, and not all strains are associated with the same level of human health risk. Traditional Salmonella testing determines whether the organism is present, while serotyping identifies specific serotypes. Emerging molecular approaches can go a step further by detecting genetic markers associated with virulence, providing additional information about the pathogenicity profile of a Salmonella-positive sample and supporting research into more risk-informed food safety.
A positive Salmonella result answers an essential food safety question: Is Salmonella present? But it can also raise another question: Does every Salmonella-positive sample represent the same level of potential risk? Increasingly, research suggests the answer is more nuanced.
Salmonella remains a significant public health challenge. CDC estimates identify Salmonella as one of the leading contributors to domestically acquired foodborne illness and the leading cause of deaths among the major foodborne pathogens included in its latest burden estimates.
Yet Salmonella is not a single, uniform threat. Serotypes and strains differ in how frequently they are associated with human illness, and advances in genomic and molecular sciences are moving researchers beyond simply detecting Salmonella toward characterizing which subtypes carry the greatest human health significance.
For food safety professionals, this opens a new way of thinking about Salmonella testing: not replacing prevalence data but adding an additional layer of information.
Not all Salmonella contribute to human illness
There are thousands of recognized Salmonella serotypes, but the burden of human illness is concentrated among a much smaller group.
CDC's latest foodborne illness burden estimates identify Enteritidis (23% of Salmonella infections), Newport (14%), Typhimurium (11%), I 4,[5],12:i:- (7%) and Javiana (7%) as the five leading Salmonella serotypes causing foodborne illness in the United States. Together, those five account for roughly 62% of cases.
FoodNet surveillance tells a similar story. In 2024, Enteritidis was the most common serotype among culture-positive infections reported through FoodNet, followed by Newport, Typhimurium, and Javiana.
This concentration of illness raises an important question: If different Salmonella populations are associated with different public health outcomes, can testing provide more information than presence or absence alone?
Serotype and virulence are not the same thing
Serotyping has long played an important role in Salmonella surveillance, epidemiology and outbreak investigation. CDC's national surveillance system, for example, collects serotype information from public health laboratories to understand which Salmonella populations are associated with human infections.
But serotype and virulence answer different questions.
A serotype helps classify Salmonella based on specific surface antigens. This can help identify and track populations associated with illnesses and outbreaks.
Virulence, on the other hand, refers to characteristics that contribute to an organism's ability to colonize a host, survive, invade cells or cause disease.
The distinction matters. FSIS has acknowledged that Salmonella serotypes are not equally associated with human illness, while also noting that the reasons for those differences are complex and cannot necessarily be attributed to serotype-specific human virulence alone. Virulence can involve multiple genetic and biological mechanisms, including differences in genes, gene expression and mobile genetic elements.
So knowing the serotype provides valuable information, but it is not the same as directly examining genetic characteristics associated with pathogenicity.
The Salmonella risk landscape is not static
There is another challenge with focusing exclusively on serotype identity: the Salmonella populations associated with human illness can change.
CDC surveillance has documented changes in the incidence of individual serovars over time. For example, between the 2016–2018 baseline period and 2021, the incidence of Salmonella enterica serovar infantis increased, while S. enterica serovars typhimurium and enteritidis decreased.
Salmonella infantis provides a particularly useful example of why ongoing surveillance matters. CDC is currently tracking a persistent multidrug-resistant strain of S. infantis that has been associated with illnesses and outbreaks in the United States and globally, including transmission through contaminated chicken.
The takeaway isn't that serotyping has become less useful. It is that the risk is dynamic.
A testing strategy built around a fixed list of serotypes may tell you whether those particular targets are present. But emerging strains, changing prevalence and evolving epidemiology create a reason to investigate whether there are other ways to characterize the potential risk represented by a Salmonella-positive sample.
Looking beyond identity to virulence
This is where virulence-detection becomes particularly interesting.
Instead of asking only which Salmonella is present, researchers can examine genetic markers associated with pathogenicity, a strain's capability to cause illness.
USDA-FSIS has already incorporated genomic differentiation of Salmonella virulence into its poultry risk-assessment resources, reflecting the broader scientific interest in understanding differences among Salmonella populations.
Bringing virulence-marker research into the food safety laboratory
Hygiena developed the BAX® System Real-Time Highly Pathogenic Salmonella Assay in collaboration with the USDA Agricultural Research Service's U.S. Meat Animal Research Center, using genomic information from Salmonella strains to identify genetic markers associated with pathogenicity. The result is a highly multiplexed real-time PCR assay that brings this emerging approach into a practical molecular testing workflow.
Designed as a reflex test following a positive BAX® System Real-Time Salmonella result, the assay uses the same lysate from the initial positive sample. It detects three proprietary HPS markers associated with pathogenicity alongside a Salmonella spp. target.
The BAX® System Q7 then automatically interprets the combination of detected markers to provide a pathogenicity profile, rather than simply returning another Salmonella-positive result.
The assay is not simply identifying a predefined list of high-risk serotypes. Instead, it looks for genetic markers associated with pathogenicity across Salmonella populations.
That provides a different lens through which to understand a Salmonella-positive sample.
The assay is designed for research and investigational applications using poultry, beef and pork enrichment cultures. It detects Salmonella spp. plus up to three virulence-associated genetic markers: B, A and X. The 96-reaction, lyophilized assay integrates into the BAX® System workflow, includes an internal positive control and delivers results in under 90 minutes.
It is intended for use only after an initial positive BAX® System Salmonella spp. screening result has been obtained, using the same lysate or isolated suspect colonies. Results are intended exclusively for research and ecological surveillance and must not be used for food safety, regulatory or product-release decisions.
What could risk-based Salmonella testing mean for food safety?
Food safety testing has traditionally been built around clear questions: Is the pathogen present? Does the sample meet a specification? Should product be held, released or investigated?
Those questions remain essential. Detection remains the foundation. A rapid Salmonella PCR assay helps food safety teams determine whether the organism is present and take appropriate action. The opportunity is what happens after that positive result.
But advances in molecular testing are creating opportunities to generate more information from the same testing workflow.
For Salmonella, understanding virulence-associated markers could help food safety professionals build a more complete picture of a positive sample and support research into more risk-informed approaches to pathogen management.
It represents an important shift in what a Salmonella PCR assay can potentially tell us.
Prevalence tells us whether Salmonella was detected. Virulence-marker detection raises another question: Does the Salmonella that was found carry markers associated with strains that cause human illness?
As our understanding of the genetics of foodborne pathogens continues to evolve, that additional layer of information may become increasingly important for linking pathogen detection to public health risk.
