The ability to identify foodborne pathogens quickly can determine whether an outbreak affects a handful of people or spreads across multiple states before its source is discovered. Advances in laboratory diagnostics are changing how public health officials identify infections, recognize emerging outbreaks, and trace contaminated food through the supply chain.
One of the most significant developments is the growing use of culture independent diagnostic tests, commonly known as CIDTs. According to the Centers for Disease Control and Prevention’s preliminary 2024 Foodborne Diseases Active Surveillance Network data, 78% of reported bacterial infections covered by the analysis were diagnosed using CIDTs, compared with 47% during 2016 through 2018. The data exclude Campylobacter because of a change in reporting requirements. The findings demonstrate how rapidly clinical laboratories have moved toward newer diagnostic methods.
This shift matters because traditional laboratory culture methods can require additional time to identify a pathogen. CIDTs can detect genetic material or antigens associated with an infectious organism, often allowing clinicians to identify the likely cause of an illness much sooner. Faster diagnoses can help healthcare providers make treatment decisions and can give public health officials earlier warning that a foodborne outbreak may be developing.
However, the benefits extend beyond speed. When combined with traditional laboratory culture, whole genome sequencing and epidemiological investigations, modern diagnostics can help authorities identify relationships between infections, recognize contaminated products and intervene before additional consumers become sick.
The technology does not automatically prevent foodborne illness, and it does not eliminate the need for traditional laboratory methods. Its greatest potential lies in strengthening the surveillance systems that identify outbreaks and guide food safety interventions. Understanding that potential begins with the scale of the problem.
The Annual Burden of Foodborne Illness in the United States
Foodborne illness remains a major public health problem despite advances in food processing, sanitation, refrigeration and disease surveillance. The CDC estimates that approximately 48 million people in the United States become ill from foodborne diseases each year. Of those, approximately 128,000 are hospitalized and 3,000 die. These estimates include illnesses caused by bacteria, viruses, parasites and other foodborne hazards.
The figures are estimates rather than a count of laboratory confirmed cases. Many people experience diarrhea, vomiting or abdominal pain without visiting a healthcare provider. Others seek medical attention but never receive testing to determine which pathogen caused their illness. Consequently, official outbreak reports capture only part of the overall burden.
The CDC’s more detailed estimates for seven major foodborne pathogens illustrate the scale of the problem. A study using 2019 data estimated that six pathogens caused approximately 9.9 million domestically acquired foodborne illnesses, while illnesses associated with all seven pathogens examined accounted for approximately 53,300 hospitalizations and 931 deaths. Those figures cover a defined group of pathogens and should not be confused with the broader annual estimate of 48 million illnesses. The most common foodborne illnesses are not necessarily those responsible for the greatest number of deaths.
Norovirus causes more foodborne illnesses than any other pathogen. Non typhoidal Salmonella is a particularly important cause of severe illness and foodborne deaths. Campylobacter, Clostridium perfringens and Shiga toxin producing Escherichia coli are also major contributors to the national burden.
These infections arise from different sources and require different prevention strategies. Salmonella can contaminate eggs, poultry, produce and other foods. Campylobacter is commonly associated with poultry. Shiga toxin producing E. coli can be transmitted through contaminated ground beef, produce and other foods. Norovirus can spread through contaminated food, infected food handlers and person to person transmission.
The challenge is not simply identifying these pathogens. Public health officials must determine which infections are connected, which foods caused them and where contamination occurred. That is where faster diagnostic methods can make a difference.
What Are Culture Independent Diagnostic Tests?
Traditional bacterial diagnosis frequently relies on culturing a patient specimen. During culture, laboratory personnel place a sample under conditions that allow bacteria to grow. The resulting organisms can then be identified and characterized.
Culture remains valuable because it produces a physical isolate of the pathogen. That isolate can be used for additional testing, including antimicrobial susceptibility testing, serotyping and whole genome sequencing.
CIDTs approach diagnosis differently. Rather than requiring bacteria to grow in a laboratory, these tests detect genetic material or antigens associated with particular pathogens. Molecular tests, including polymerase chain reaction assays, can identify specific DNA or RNA sequences in a clinical specimen.
Some diagnostic panels can test for multiple pathogens simultaneously. This is especially useful when patients present with gastrointestinal symptoms that could be caused by many different organisms.
A patient with diarrhea and abdominal cramps could have Salmonella, Campylobacter, Shigella, a Shiga toxin producing E. coli infection or another illness. Symptoms alone generally cannot establish the cause. A CIDT can help identify the likely pathogen more rapidly than a diagnostic process that depends entirely on culture.
The CDC explains that CIDTs can be faster, easier and less expensive to use than traditional culture based methods. However, CIDTs do not necessarily provide the information required for detailed pathogen characterization or antimicrobial susceptibility testing. This distinction is essential.
CIDTs improve the speed of detection, while culture and genomic analysis often provide the additional information needed to investigate and control outbreaks. The two approaches are most effective when used together.
The Significance of the 78% Figure
The CDC’s 2024 preliminary FoodNet data show how dramatically diagnostic practices have changed. Among bacterial infections included in the analysis, 78% were diagnosed using CIDTs in 2024. During 2016 through 2018, the corresponding proportion was 47%. The increase means that modern diagnostic testing has become a major part of how bacterial gastrointestinal infections are identified in the FoodNet surveillance area. The findings also reveal a challenge.
In 2024, 41% of bacterial infections were diagnosed by CIDT alone, compared with 21% during 2016 through 2018. Conversely, 22% were diagnosed by culture alone in 2024, compared with 53% during the earlier period.
These figures should not be interpreted as meaning that 78% of all foodborne illnesses nationwide are diagnosed by CIDTs. FoodNet monitors selected pathogens in a defined surveillance population. The percentage refers to the bacterial infections covered by the analysis, with Campylobacter excluded from the overall comparison because of a reporting change. Nor does the 78% figure mean that CIDTs have prevented 78% of infections. It measures the diagnostic method used to identify infections, not the proportion of illnesses prevented.
The public health significance is that faster and more accessible testing can improve the information available to clinicians and investigators. That information can then support earlier interventions.
How Faster Diagnosis Can Accelerate Outbreak Detection
A foodborne outbreak investigation often begins with laboratory findings. When several patients have infections caused by the same pathogen, public health officials examine whether those cases might share a common source. Traditional surveillance depends partly on clinicians ordering appropriate tests, laboratories identifying the pathogen and results reaching public health authorities. If patients are not tested, their infections may never be attributed to a particular organism.
If testing is delayed, investigators may not recognize a cluster until additional people become sick. CIDTs can shorten part of this process by helping laboratories identify likely pathogens more rapidly.
Consider a hypothetical example. Several people in different counties develop diarrhea after eating at different restaurants. Initially, the cases appear unrelated. If their infections are diagnosed quickly and reported to public health authorities, investigators can begin comparing food histories before the cluster becomes substantially larger.
The patients might have eaten at different restaurants but consumed the same packaged ingredient. Alternatively, they might have purchased the same product from different grocery stores. Earlier recognition allows investigators to begin looking for these shared exposures sooner.
The technology does not establish that the cases share a contaminated food source. Epidemiological evidence and additional laboratory analysis are still necessary. Nevertheless, rapid diagnosis can provide an earlier starting point. That can be particularly important when a contaminated product is distributed across several states or incorporated into multiple prepared foods.
Why Faster Diagnosis Does Not Always Mean Faster Source Identification
Although CIDTs can accelerate pathogen detection, identifying the actual food responsible for an outbreak remains difficult. A positive molecular test tells clinicians that genetic material associated with a pathogen has been detected. It does not automatically reveal whether the patient ate contaminated lettuce, undercooked poultry, ground beef, eggs or another food.
Investigators must still conduct interviews, examine purchasing histories, compare restaurant exposures and investigate the distribution chain. The limitations become more significant when a pathogen is common or when people have consumed numerous potentially relevant foods.
Investigators also need to determine whether infections are genetically related. Two people can test positive for the same bacterial species without having acquired it from the same source. For example, Salmonella infections occur regularly in the United States. Finding Salmonella in two patients does not prove that their illnesses resulted from a shared product.
Additional laboratory analysis can help distinguish unrelated infections from those caused by a common contaminated food. This is one reason CIDTs should be considered part of a broader diagnostic and surveillance system rather than a replacement for every traditional method.
The Continuing Importance of Culture and Whole Genome Sequencing
A major challenge associated with the shift toward CIDTs is obtaining bacterial isolates for further testing. An isolate is a sample of the actual organism recovered from a patient’s specimen. It can be used to examine the organism’s characteristics and compare it with bacteria recovered from other patients or contaminated foods.
When a CIDT produces a positive result without a subsequent successful culture, investigators may lose access to information that could help connect cases. The CDC’s 2024 FoodNet report found that among patient samples cultured after a positive CIDT result, 59% yielded positive cultures in 2024, compared with 71% during 2016 through 2018. This decline creates a potential surveillance gap.
If fewer positive specimens produce isolates, investigators may have less information available for serotyping, genomic analysis and other characterization methods. Whole genome sequencing, or WGS, allows laboratories to compare the genetic makeup of pathogens with considerable detail.
Public health officials can use this information to identify clusters of infections that are closely related genetically. Investigators then combine those findings with interviews and food distribution records to determine whether the patients may have been exposed to the same contaminated product.
The CDC explains that genomic surveillance has improved outbreak detection, including the identification of outbreaks that might previously have gone undetected. The implication is clear: rapid diagnostic testing is valuable, but its benefits can be reduced if laboratories cannot obtain isolates for further investigation.
How Diagnostic Improvements Could Reduce Foodborne Illness
CIDTs do not directly prevent bacteria from contaminating food. Their potential to reduce the number of illnesses lies in what public health officials can do with the information they provide.
Several mechanisms are particularly important.
1. Earlier recognition of outbreaks
When infections are identified sooner, public health agencies may recognize a cluster earlier. That can allow investigators to begin identifying common exposures before additional cases accumulate. The earlier the investigation begins, the greater the opportunity to identify a contaminated product while it is still available for removal from commerce.
2. Faster recalls and product removal
Once sufficient evidence links a food to an outbreak, regulators and companies can take corrective action. Depending on the circumstances, that may involve recalling products, suspending production, removing contaminated ingredients, cleaning facilities or correcting sanitation failures. Removing contaminated food from circulation can prevent additional exposures. A recall cannot reverse illnesses that have already occurred, but it can reduce the number of people exposed afterward.
3. Better identification of recurring contamination problems
Improved surveillance can reveal patterns that might otherwise remain hidden. If investigators repeatedly identify infections associated with a particular production process, ingredient or distribution chain, regulators can investigate the underlying problem. The goal is not merely to respond to one outbreak. It is to identify and correct the conditions that allow contamination to recur.
4. More informed food safety policies
Accurate surveillance helps officials identify which pathogens are increasing, which populations are most affected and where prevention efforts may be insufficient. The CDC emphasizes that foodborne illness surveillance helps evaluate whether prevention measures are working and identifies areas where additional action is needed. Better information can help direct limited resources toward the foods, pathogens and production practices responsible for the greatest burden.
5. Improved recognition of less obvious cases
CIDTs may identify infections that would otherwise remain undiagnosed because clinicians did not initially suspect a particular pathogen. Detecting these cases can improve understanding of the true distribution of illness. It may also reveal outbreaks involving people with relatively mild symptoms who would otherwise never have been included in an investigation.
Could CIDTs Help Reduce the 48 Million Annual Illnesses?
The answer is potentially, but the distinction between detecting illness and preventing illness must remain clear. The 48 million annual illnesses estimate includes many infections that are never diagnosed in clinical laboratories.
CIDTs may increase the number of infections that receive a specific diagnosis. As a result, the number of reported cases could increase even if the actual number of people becoming sick remains unchanged. An increase in detected cases does not necessarily mean that food safety has deteriorated. It may mean that surveillance has improved.
Conversely, a decrease in reported infections does not automatically prove that prevention measures are working. Changes in healthcare seeking, testing practices and reporting can influence the number of cases recorded.
The CDC’s 2026 report on Salmonella surveillance specifically highlights this problem. The analysis found that Salmonella diagnostic patterns shifted substantially between 2004 and 2024, with culture diagnosed infections declining as CIDT diagnosed infections increased. The authors warned that increased detection of milder illnesses could obscure changes in more severe infections resulting from prevention efforts. This makes long term surveillance more complicated.
Researchers must account for changes in diagnostic methods when comparing illness rates over time. The more important measure is whether the actual burden of disease decreases, including hospitalizations, severe complications and deaths, rather than whether fewer or more infections appear in laboratory reports alone.
CIDTs could contribute to that reduction if faster detection leads to earlier interventions that prevent additional infections. However, their contribution cannot be quantified simply by comparing the 78% figure with the 48 million annual illness estimate. The two numbers measure different things.
The Economic and Human Consequences of Better Surveillance
Foodborne illness affects more than the immediate health of infected individuals. People who become sick may miss work or school, require medical care or experience prolonged complications. Severe infections can result in hospitalization, kidney damage or other long term health problems. Businesses can also suffer when an outbreak is linked to their products.
Recalls can result in lost inventory, interrupted production, legal expenses and damage to consumer confidence. Small producers may face particularly serious financial consequences. Improved diagnostics could help reduce some of these costs by allowing public health officials to identify problems earlier.
Nevertheless, rapid testing is only one component of an effective response. A positive result must be communicated appropriately. Laboratories must have the resources to perform additional testing. Public health agencies need staff to conduct interviews and trace products. Regulators must be able to investigate facilities and take corrective action when necessary. Without these supporting systems, faster diagnosis may not translate into faster prevention.
Challenges That Must Be Addressed
The growing reliance on CIDTs creates several priorities for laboratories and public health agencies.
- First, laboratories need effective procedures for obtaining cultures after positive CIDT results when appropriate.
- Second, clinicians and laboratories need clear protocols for communicating results to public health authorities.
- Third, surveillance systems must account for diagnostic changes when assessing whether infections are increasing or decreasing.
- Fourth, public health agencies need adequate funding and staffing to investigate outbreaks once they are detected.
- Finally, diagnostic manufacturers and laboratories should continue improving methods that combine rapid detection with the ability to recover and characterize pathogens.
These measures can preserve the speed advantages of CIDTs without sacrificing the information needed for outbreak investigations. The CDC has specifically identified continued surveillance, culture of positive specimens and improved compatibility between CIDTs and culture based methods as priorities for reducing the burden of enteric disease.
Analysis & Next Steps
What’s new: Preliminary CDC FoodNet data show that 78% of bacterial infections included in the 2024 analysis were diagnosed using CIDTs, up from 47% during 2016 through 2018. The finding confirms a substantial shift toward rapid diagnostic methods.
Why it matters: Earlier pathogen identification can help clinicians make decisions and allow public health officials to recognize potential outbreaks sooner. When combined with genomic surveillance, epidemiological investigations and effective recalls, faster detection can create opportunities to prevent additional infections.
Who’s affected: Consumers benefit when contaminated food is identified and removed quickly. Healthcare providers, laboratories, food manufacturers, regulators and public health agencies all play important roles in converting diagnostic information into preventive action.
What to do now: Public health agencies should support rapid diagnostic testing while maintaining the capacity to culture positive specimens and perform genomic analysis. Surveillance programs should account for changes in testing methods when comparing illness rates. Manufacturers and regulators should continue strengthening the processes that identify and correct contamination before food reaches consumers.
Final Note
The CDC’s estimate of 48 million foodborne illnesses each year illustrates why these improvements matter. Even a modest reduction in actual infections could prevent substantial suffering, medical expenses and lost productivity. Yet diagnostic innovation should not be mistaken for a complete solution.
Foodborne pathogens will continue to threaten public health unless contamination is prevented, unsafe products are identified and corrective action is taken throughout the food supply chain. The greatest opportunity presented by CIDTs is their ability to shorten the distance between an infection occurring and public health officials recognizing a potential problem. The ultimate measure of success is not simply how quickly laboratories identify pathogens. It is whether that information helps prevent people from becoming sick in the first place.
