Emerging Foodborne Pathogens Public Health Officials Are Monitoring
Foodborne illness remains a pervasive public health challenge worldwide, affecting millions of people annually and imposing significant health, social, and economic burdens. Traditional foodborne pathogens such as Salmonella, Escherichia coli, Listeria, and Campylobacter are well-known targets of surveillance and control efforts by public health agencies such as the U.S. Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA). However, beyond these familiar agents, health officials are increasingly concerned about emerging and re-emerging foodborne pathogens, microorganisms that are newly identified, exhibiting new modes of transmission, expanding their geographic range, or demonstrating resistance to conventional control measures.
Emerging pathogens arise due to complex ecological, technological, and sociocultural forces, including globalization of food supply chains, changes in consumer behavior, microbial adaptation, and limitations in surveillance infrastructure. Scientists and health agencies invest substantial resources in monitoring these threats, aiming to detect and respond to outbreaks sooner, characterize shifts in disease patterns, and inform prevention strategies.
Defining “Emerging” Foodborne Pathogens
Emerging foodborne pathogens include organisms that are:
- Newly recognized as causes of human disease (e.g., newly described bacteria or viruses)
- Increasing in incidence or geographic range
- Developing new characteristics, including antimicrobial resistance or expanded host range
They may be completely novel to science or newly associated with food transmission after initial recognition in other contexts (such as environmental or animal reservoirs). According to foundational infectious disease research, emergence is driven by demographic change, human behavior, globalization, microbial adaptation, and shifts in the food system, factors that intersect with both microbial evolution and food production practices.
These pathogens can include bacteria, viruses, parasites, biotoxins, and even unconventional agents such as prions. Some may cause sporadic illnesses, while others have the potential to trigger large outbreaks. Discoveries of new foodborne agents frequently occur in the context of outbreak investigations, where epidemiological and laboratory evidence first links specific microbes to contaminated food vehicles.
Traditional Pathogens as Evolving Threats
Before exploring truly novel agents, it is important to recognize that many familiar foodborne pathogens continue to pose evolving threats. These organisms remain high-priority for surveillance even as they undergo genetic shifts, develop antimicrobial resistance, or are found in new food vehicles.
Salmonella and E. coli
Well-established pathogens like nontyphoidal Salmonella and Shiga toxin–producing E. coli (STEC) remain leading causes of foodborne illness and hospitalization in the United States. Data from CDC estimates indicate that Salmonella and related organisms are responsible for millions of domestically acquired foodborne illnesses each year, alongside other major pathogens including Campylobacter and Listeria. Even within these groups, specific serotypes continue to emerge or re-emerge, as seen in historical outbreaks like the E. coli O104:H4 outbreak in Germany linked to fenugreek sprouts, where a hybrid strain acquired Shiga toxin genes.
Increased Antimicrobial Resistance
Microbial adaptation through antimicrobial resistance is a significant concern for many established pathogens. For example, research has explored resistance trends in Campylobacter, demonstrating increased resistance to fluoroquinolones and other drugs, which complicates treatment and shifts pathogen dynamics. Antimicrobial resistance can transform previously manageable infections into serious public health threats and warrants continued surveillance.
Emerging or Re-Emerging Threats of Current Concern
Beyond the traditional set of foodborne bacteria, several pathogens have emerged or re-emerged as causes of concern for public health officials:
Cyclospora cayetanensis
The parasite Cyclospora gained international recognition in the mid-1990s following outbreaks traced to imported raspberries, linking it conclusively to foodborne transmission. It remains a monitored pathogen due to its ability to persist in environmental reservoirs and its association with produce outbreaks.
Norovirus
Although known primarily as a cause of viral gastroenteritis outbreaks, norovirus is sometimes transmitted through contaminated food and is considered one of the leading causes of domestically acquired foodborne illness. CDC data indicate it causes the largest share of domestically acquired foodborne illnesses annually.
Clostridium perfringens
C. perfringens exemplifies an emerging pathogen that, while recognized for many years, remains an evolving threat because of its spore-forming ability and adaptability across diverse environments, including soil, animal intestinal tracts, and food. It is one of the most frequent causes of bacterial foodborne illness and contributes significantly to hospitalizations and deaths each year.
Non-O157 STEC and Other Novel Serogroups
While STEC O157:H7 remains infamous, non-O157 STEC serogroups have gained prominence as recognized foodborne pathogens. These organisms can cause severe disease, including hemolytic uremic syndrome, and are actively monitored through laboratory surveillance systems.
Parasites and Other Agents
Parasites such as Toxoplasma gondii, though not always symptomatic, are included in models estimating foodborne disease burden due to their impact on hospitalization and mortality. Norovirus and parasites that do not always receive routine clinical surveillance still contribute significantly to illness.
Drivers of Pathogen Emergence
Understanding why foodborne pathogens emerge or re-emerge aids in designing effective prevention strategies. Several key drivers include:
Globalization of Food Supply
Global food distribution networks have expanded, increasing the chances that contaminated products will cross borders and reach diverse populations. New food vehicles or distribution chains amplify opportunities for pathogens to spread widely, sometimes before detection.
Technological and Behavioral Shifts
Changes in food processing, preparation habits, and dietary trends, such as increased consumption of raw or minimally processed foods, can expose consumers to infectious agents that survive traditional safeguards. For example, fresh produce has become a common vehicle in outbreaks due to contamination in the field or processing environment.
Microbial Adaptation
Microbes evolve continually. Genetic changes can enhance virulence, survival in food environments, or resistance to antimicrobials. Such adaptations have contributed to the rise of resistant strains of Salmonella, Campylobacter, and other pathogens.
Surveillance and Detection Technology
Improved surveillance and diagnostic methods, including culture-independent diagnostic tests (CIDTs), whole genome sequencing, and active pathogen genome projects (such as the 100K Pathogen Genome Project), have increased detection sensitivity and the ability to identify distinct pathogen strains. Surveillance networks like PulseNet, which shares genetic fingerprints of pathogens across laboratories, have enhanced outbreak detection and linkage capabilities.
These tools, while boosting detection, can also reveal previously undetected or underappreciated foodborne threats.
Public Health Surveillance Infrastructure
FoodNet and Active Surveillance
Active surveillance systems such as FoodNet play a central role in monitoring foodborne disease trends and detecting emerging threats. FoodNet conducts routine surveillance for multiple enteric pathogens and supports epidemiologic investigations of foodborne disease incidence across participating states.
However, changes in surveillance scope have recently raised concerns. In mid-2025, CDC reduced mandatory active surveillance within FoodNet to focus only on Salmonella and STEC, leaving other pathogens such as Campylobacter, Listeria, Shigella, Vibrio, Cyclospora, and Yersinia optional for reporting by participating states. Public health experts warned that this might hinder early detection of emerging trends in those pathogens.
Laboratory Networks and Molecular Tools
Networks like PulseNet and projects like the 100K Pathogen Genome Project enhance detection by enabling rapid strain identification and comparison across outbreaks. These platforms accelerate the recognition of patterns indicative of emerging pathogens before widespread illness occurs.
These surveillance infrastructures are essential for rapid response and containment of outbreaks linked to emerging pathogens.
Recent Emerging Pathogen Trends and Outbreaks
2024–2025 Multistate Outbreaks
Recent outbreaks demonstrate the evolving landscape of foodborne pathogens. CDC maintains active outbreak investigation dashboards that show Salmonella, Campylobacter, STEC, and Listeria remain frequent causes of multistate outbreaks, with ongoing investigations into multiple active clusters.
Novel Outbreak Vehicles
Outbreaks linked to Salmonella in unexpected vehicles, such as raw oysters, illustrate how new food products and distribution chains can reveal emerging risks. Recent multistate Salmonella outbreaks tied to raw oysters infected dozens across numerous states, illustrating uncommon vectors of disease transmission.
Analysis & Next Steps
What’s New
Emerging foodborne pathogens continue to evolve in response to ecological, technological, and social forces. Even long-recognized pathogens such as Campylobacter and Salmonella are subject to shifting epidemiology due to antimicrobial resistance and novel food vehicles. Advanced molecular surveillance, including genomic sequencing and active pathogen databases, is improving detection and characterization of emerging threats, but changes in surveillance programs such as FoodNet’s reduced coverage have sparked concern about detecting a full spectrum of pathogens.
Why It Matters
Emerging pathogens can cause severe disease, broader outbreaks, and higher healthcare costs if not detected and controlled promptly. The dynamic nature of food systems and pathogen adaptation means that risks are constantly shifting, requiring vigilant monitoring and updated public health strategies.
Who’s Affected
Consumers at all risk levels can be affected by emerging foodborne pathogens, but young children, older adults, pregnant individuals, and immunocompromised persons face the highest risk of severe illness. Food producers, regulators, and healthcare providers also bear critical roles in surveillance and response.
What To Do Now
- Support and maintain robust surveillance systems such as FoodNet and PulseNet to track a broad range of pathogens.
- Invest in molecular and rapid diagnostic technologies that allow earlier detection of novel or emerging pathogens.
- Strengthen international and state–federal collaboration to share data on emerging threats promptly.
- Educate food supply chain stakeholders on evolving risks associated with emerging pathogens and best food safety practices.
Final Note
Emerging foodborne pathogens are a dynamic and evolving public health challenge. Public health officials monitor both new and re-emerging agents, supported by surveillance networks, laboratory innovations, and epidemiological research. The integration of advanced genomic tools with active surveillance promises to improve early detection and response, but sustained commitment to broad pathogen monitoring remains essential to protect public health in an increasingly interconnected and complex food system.
