Precision detection of foodborne illness pathogens

How pathogens adapt and thrive

Many foodborne pathogens have evolved sophisticated survival mechanisms, allowing them to thrive in diverse and often hostile environments, including within food products. These highly resilient microorganisms adapt to conditions that inhibit or kill less-hardy bacteria.

For example, Listeria monocytogenes can grow at low temperatures in refrigerated foods that are typically considered safe from bacterial growth. The ability of Listeria to thrive in cold environments poses a serious food safety threat, particularly in ready-to-eat foods like deli meats, cheeses and salads. This resilience makes it especially hazardous for vulnerable groups like pregnant women, the elderly and immunocompromised individuals, who can develop severe infections such as meningitis and septicemia.

Salmonella and E. coli are also resilient to harsh conditions. Salmonella can survive in a dormant state in dry conditions on kitchen surfaces and utensils, from which it can easily contaminate food. E. coli, on the other hand, can withstand acidic environments, enabling it to pass through the stomach to the intestines and cause infection. These adaptations highlight the challenge of controlling foodborne pathogens and underscore the need for advanced detection and prevention strategies.

The role of bacterial toxins in foodborne illness

The virulence of foodborne pathogens like Salmonella and Shiga toxin-producing E. coli (STEC) is driven by their ability to produce potent toxins that can cause severe gastrointestinal illness. Salmonella adheres to the intestinal lining, invading epithelial cells and producing an inflammatory response. This causes symptoms like diarrhea and abdominal pain and helps the bacteria spread within the host. Some Salmonella strains produce enterotoxins that disrupt intestinal function, leading to fluid loss and severe dehydration.

STEC, on the other hand, is infamous for producing Shiga toxins, some of the most potent bacterial toxins known. These toxins can enter the bloodstream and damage the endothelial cells lining blood vessels, particularly in the kidneys. This can result in hemolytic uremic syndrome (HUS), a life-threatening condition that can cause kidney failure, particularly in children and the elderly. Thus, advanced detection and disease control can prevent outbreaks and reduce their impact.

The viral and parasitic threats to food safety

Foodborne viruses and parasites present additional challenges to food safety. Viruses like Norovirus and hepatitis A, along with parasites such as Toxoplasma gondii, can cause widespread illness, often without the host realizing they are infected. Plus, these organisms are more difficult to culture than bacteria. Their low concentrations in food samples along with the complexity of identifying them further complicates efforts to ensure food safety.

Norovirus is the leading cause of foodborne illness globally, responsible for millions of cases of gastroenteritis each year. It is highly infectious – fewer than 20 viral particles can cause infection – leading to rapid and widespread outbreaks that are difficult to control. The highly resilient Norovirus can survive in water or food for extended periods. This durability and rapid transmission make it a persistent challenge in outbreak management and routine food safety practices.

Hepatitis A virus (HAV) poses another serious risk, particularly in areas with poor sanitation. HAV contamination often occurs through improper food handling or contact with contaminated water. Once ingested, the virus targets the liver, causing symptoms that range from mild flu-like illness to severe liver disease. Its long incubation period (typically 15 to 50 days) means that symptoms can take weeks to appear, making it difficult to trace the contamination source and prevent further spread.

Parasites like Toxoplasma gondii add another layer of complexity to food safety. Toxoplasma can infect a wide range of warm-blooded animals, and humans can become infected by consuming undercooked meat containing tissue cysts or by ingesting oocysts from contaminated water or surfaces. While infections are often mild or asymptomatic in healthy individuals, Toxoplasma poses severe risks to pregnant women and immunocompromised individuals, potentially leading to congenital infections or neurological disorders.

From bacteria and viruses to parasites, foodborne pathogens come in many forms, each with unique traits that can cause illness. Here are some of the most common and dangerous microbes responsible for foodborne illnesses:

• Aeromonas caviae, Aeromonas hydrophila, and Aeromonas sobria: All of these bacteria can survive in fresh and brackish water alike. They're commonly associated with gastrointestinal illnesses and, at times, can cause wound infections. Their typical telltale symptoms are diarrhea, nausea and abdominal discomfort. While usually mild, the illness can become more severe for individuals with a compromised immune system or those with open wounds exposed to contaminated water.
• Aliarcobacter butzleri: This hardy bacterium can thrive in various environments, including contaminated water and food. It typically triggers gastrointestinal illness, with symptoms like diarrhea, abdominal pain and fever. While most cases are mild, some can develop into more serious illness.
• Bacillus cereus: This bacterium is known for producing two distinct types of toxins – one that causes vomiting and another that results in diarrhea. It can survive harsh conditions, like high temperatures, which makes it a common issue in improperly stored food. Starchy foods, like rice, are often linked to the vomiting type, while the diarrhea-causing strain is found in meats and vegetables. The illness is typically mild, albeit uncomfortable and short-lived.
• Campylobacter jejuni: One of the leading bacterial causes of diarrhea worldwide, Campylobacter jejuni, survives in bird digestive systems, making undercooked poultry a frequent source of infection. It releases toxins that cause gut inflammation, leading to symptoms like bloody diarrhea, abdominal pain and fever. While most cases are mild to moderate, severe cases are possible and on rare occasions, it can trigger complications like Guillain-Barré syndrome.
• Clostridium perfringens: This bacterium is able to form spores, helping it survive harsh environments such as heat and low oxygen. When consumed through inappropriately cooked or stored meats, it produces toxins in the intestines, leading to food poisoning. Symptoms include sudden cramps and watery diarrhea. Though the illness mostly resolves quickly and is usually mild, it can be more severe in the elderly or immunocompromised individuals.
• Corynebacterium ulcerans: While it's rare to contract Corynebacterium ulcerans through food, this bacterium can produce a toxin similar to the diphtheria toxin and cause respiratory illness or skin infections. Symptoms range from mild sore throat to severe respiratory distress, making swift treatment crucial for this potentially serious pathogen.
• Coxiella burnetii: Known for causing Q fever, Coxiella burnetii is extremely resilient and can survive in harsh environments like dust and soil for extended periods. It's mainly spread through raw milk or by inhaling contaminated aerosols from infected animals. Symptoms typically mimic the flu, including high fever, headache and muscle aches. In some cases, it can cause pneumonia or hepatitis. While many cases are mild, chronic Q fever can lead to serious complications, such as endocarditis.
• Enterovirus: This group of viruses, which includes the well-known poliovirus and enterovirus D68, can persist in harsh environmental conditions, including low pH levels. Enteroviruses are linked to a variety of illnesses, from mild respiratory infections to more severe conditions like meningitis or even paralysis, as seen with poliovirus. Symptoms can include fever, muscle aches, respiratory issues and neurological symptoms, depending on the strain.
• Escherichia coli (General): Although many E. coli strains are harmless, pathogenic strains can produce toxins or adhere to intestinal walls, causing illness. Symptoms range from mild diarrhea to more severe cases of bloody diarrhea and abdominal cramping. In severe cases, particularly with Shiga toxin-producing E. coli (STEC), the illness can progress to kidney failure, known as hemolytic uremic syndrome (HUS).
• Escherichia coli Shiga toxins (stx1 and stx2): Shiga toxins (Stx1 and Stx2) are key virulence factors produced by Shiga toxin-producing E. coli (STEC) strains, including E. coli O157 and non-O157 serogroups like O26, O45, O103, O111, O121 and O145. These toxins damage the intestinal lining, causing symptoms such as bloody diarrhea. Stx2, in particular, can enter the bloodstream and lead to hemolytic uremic syndrome (HUS), which is a serious condition involving acute kidney failure, hemolysis and low platelet counts. 
• Escherichia coli virulence factors (eae and rfbE): The eae gene, found in both STEC and enteropathogenic E. coli (EPEC), codes for the intimin protein, which helps the bacteria attach to intestinal cells causing damage known as attaching and effacing lesions that destroy small structures on the cell surface that help absorb nutrients. This leads to significant intestinal inflammation and diarrhea. The rfbE gene is unique to E. coli O157 and is involved in producing the O157 antigen. While not a direct virulence factor, rfbE is an important marker for identifying this specific serogroup.
• Hepatitis A virus: Hepatitis A is highly resilient, able to survive for extended periods in contaminated food or water. It targets the liver and causes symptoms such as jaundice, nausea and fatigue. While the illness usually resolves on its own within weeks, it can lead to severe liver inflammation, particularly in older adults or those with pre-existing liver conditions.
• Hepatitis E virus: Similar to Hepatitis A, Hepatitis E is transmitted through contaminated water and affects the liver, causing symptoms like jaundice, fatigue and nausea. In most cases, the illness is self-limiting, but it can be severe in pregnant women, sometimes leading to acute liver failure.
• Human rotavirus A: This virus is a leading cause of severe diarrhea in young children, often leading to dehydration. Rotavirus infects the intestinal lining, resulting in vomiting, diarrhea and dehydration that can sometimes require hospitalization. While generally not life-threatening in developed countries, it can be fatal in areas with limited medical resources.
• Listeria monocytogenes: This bacterium is notable for its ability to thrive at cold temperatures, making it a significant threat in refrigerated foods like deli meats and cheeses. Once it invades intestinal cells, it can spread to the bloodstream, causing listeriosis, a serious infection. Symptoms include fever, muscle aches and gastrointestinal issues. The infection is particularly dangerous for pregnant women, the elderly and those with compromised immune systems, potentially leading to miscarriage, meningitis or septicemia.
• LT E. coli heat-labile enterotoxin and ST E. coli heat-stable toxin: These enterotoxins, produced by certain strains of E. coli, disrupt the intestines' balance of water and electrolytes, leading to watery diarrhea and dehydration. Symptoms are often more severe in young children and the elderly.
• Norovirus (GI and GII): Norovirus is highly contagious and resilient, capable of withstanding a range of environmental conditions. It spreads easily through contaminated food and water, with only a few viral particles needed to cause illness. Symptoms include vomiting, diarrhea and stomach pain. While the illness is usually short-lived, Norovirus can cause severe dehydration, especially in young children and the elderly.
• Plesiomonas shigelloides: Found in contaminated water and seafood, Plesiomonas shigelloides causes gastrointestinal illness with symptoms such as watery diarrhea, abdominal cramps and vomiting. The illness is generally mild but can become more severe in individuals with weakened immune systems.
• Salmonella spp.: Often associated with contaminated poultry, meat and eggs, Salmonella invades the intestinal lining and can survive in low-oxygen environments. Symptoms include diarrhea, fever and abdominal cramps, with most cases resolving on their own. However, severe infections can spread to the bloodstream and may require treatment. Salmonella enterica and its subspecies are particularly concerning, as they produce toxins that disrupt intestinal function, causing inflammation and food poisoning. In severe cases, the infection can lead to life-threatening complications like sepsis.
• Shigella dysenteriae and Shigella sonnei: Shigella species are notorious for causing dysentery, a severe form of diarrhea that often contains blood and mucus. The bacteria invade the intestinal lining and produce Shiga toxins, leading to severe inflammation and tissue damage. Symptoms can range from mild to life-threatening, particularly in young children and the elderly.
• Staphylococcus aureus: This bacterium produces heat-stable toxins in improperly stored food, making it a common cause of rapid-onset food poisoning. Symptoms such as nausea, vomiting and abdominal cramps can appear within hours of consuming contaminated food. While the illness is generally short-lived and not serious, it can cause significant discomfort.
• Vibrio cholerae: The bacterium responsible for cholera, Vibrio cholerae produces a toxin that causes the intestines to secrete large amounts of water, resulting in severe diarrhea and dehydration. Without prompt treatment, cholera can be fatal, especially in areas with limited access to clean water and healthcare.
• Vibrio parahaemolyticus and Vibrio vulnificus: These bacteria are often found in raw or undercooked seafood, particularly shellfish. Vibrio parahaemolyticus causes gastrointestinal illness, while Vibrio vulnificus can lead to more severe bloodstream infections, particularly in individuals with compromised immune systems. In severe cases, Vibrio vulnificus infections can be life-threatening.
• Yersinia enterocolitica and Yersinia pseudotuberculosis: These bacteria, often linked to undercooked pork and contaminated food, cause gastroenteritis. Symptoms include fever, diarrhea and abdominal pain, which can sometimes mimic appendicitis. While most cases are mild, severe infections can lead to complications such as septicemia.

The invisible threat: Detecting low-abundance pathogens

Detecting low-abundance pathogens within complex food matrices is one of the toughest challenges in food safety. Even trace amounts of these pathogens can pose serious health risks, making highly sensitive detection methods a must. Plus, the diverse composition of food – packed with organic and inorganic compounds – often complicates sample preparation, making it difficult to isolate and purify contaminants for accurate testing. If not properly addressed, these matrix components can carry over into the final sample and interfere with detection methods. This is where technologies like NGS and dPCR come into play, offering the precision and sensitivity needed to spot even the smallest traces of contamination, stopping potential outbreaks before they become full-blown crises.

Navigating contaminations and mixed infections

Detecting multiple pathogens coexisting in a single food sample adds another layer of complexity to food safety efforts. These mixed infections often arise when food is contaminated multiple times in the supply chain or when various pathogens flourish under similar conditions. Differentiating and accurately measuring each microorganism is critical for understanding the full extent of contamination. NGS and dPCR deliver precise and detailed results that ensure effective control of all potential threats.

Tackling the rise of antibiotic-resistant pathogens

The rise of antibiotic-resistant bacteria, like Salmonella and E. coli, poses a serious threat to both treatment and detection efforts. These pathogens often carry resistance genes that make standard treatments less effective, increasing the risk of severe illness. Therefore, food safety protocols must go beyond just identifying pathogens; they must also analyze their genetic makeup, including resistance profiles. NGS and dPCR have the potential to transform this process: NGS provides a comprehensive view of resistance genes across entire microbial populations, while dPCR delivers precise quantification of specific known genes. Together, these technologies can help shape smarter and more effective food safety management strategies.

Comprehensive profiling with NGS: Capturing the entire pathogen landscape

NGS, particularly through metagenomic sequencing, is a powerful tool for comprehensive pathogen profiling, especially when dealing with complex food samples with unknown or difficult-to-culture contaminants. By sequencing the entire microbial community within a sample, metagenomics enables the detection of a wide range of pathogens in a single run. This approach is increasingly used for outbreak investigations and routine food industry surveillance. It provides detailed strain typing to trace contamination sources and monitor the evolution of pathogens over time. This resolution is crucial for identifying emerging threats and shaping public health responses.

Precision detection with dPCR: When every pathogen counts

dPCR delivers absolute quantitation of pathogens, making it essential for food safety testing where exact numbers matter. Its high sensitivity allows for detecting even trace amounts of pathogens, ensuring food products meet strict safety standards. This level of accuracy, combined with a rapid turnaround time, makes it invaluable for routine testing, where quick and precise results are critical. Its speed and efficiency in absolute quantification of known targets often makes it more practical and cost-effective than NGS for targeted applications. Plus, dPCR’s ability to detect specific genes, including those linked to virulence or antibiotic resistance, makes it an indispensable tool for comprehensive food safety monitoring.

Maximizing detection using an integrated approach

Combining NGS and dPCR is an increasingly valuable strategy for pathogen detection in food safety testing. NGS provides a broad survey of the pathogen landscape within a sample, identifying known, unexpected and emerging threats. Once identified, dPCR can precisely quantify specific pathogens to ensure their levels meet regulatory safety standards. This integrated approach leverages the strengths of both technologies – NGS’s broad detection capabilities and dPCR’s precise quantification – offering enhanced detection accuracy and supporting more robust food safety protocols to safeguard public health.