Emerging Food Safety Risks from Biological Contamination

Food safety is one of the largest challenges facing the global food system. It is not only about supplying enough to eat for a growing population, but also ensuring the integrity of food.

Emerging food safety risks of biological origin

Since early days, mankind had to find ways of overcoming the potential harmful effects of biological contamination of food, leading to spoilage, poor quality and, even worse, to illness and death. Today’s world relies on industrial food processing and a global supply chain in order to nourish a growing urban population, but food safety remains a constant challenge. Food safety hazards of biological origin still count to the main risks around the globe.

Mycotoxins are a silent threat for humans and animals

The Food and Agriculture Organization of the United Nations (FAO) estimates that 25% of food crops are contaminated by mycotoxins. These are poisonous chemicals formed by fungal mould which grows on crops like maize, wheat, rice and other grain staples. Also nuts, in particular peanuts, and dried fruit are frequently affected. Mycotoxin contamination of feed and food is the third most frequent hazard reported in the European Rapid Alert System for Food and Feed (RAFFS). Globally, 80% of animal feed is contaminated, because mycotoxins are concentrated in the side streams from grain processing which are diverted into feed[1]. Although mycotoxin is considered a chemical hazard, the route cause is fungal growth on raw material on the field or during storage due to poor agricultural practices, insect infestation and poor post-harvest handling. Many fungi are known to form mycotoxins under hot and humid conditions, and overall more than 300 of these toxic compounds have been described.

Risk map showing estimated prevalence on maize for Europe

Climate change increases the risk of aflatoxin, the most toxic mycotoxin. The risk map shows the estimated prevalence on maize for Europe for three different climate scenarios (a) present, (b) +2°C, (c) +5°C. Image from reference[2].

Aflatoxin is the most toxic mycotoxin and maximum limits exist around the world for feed and food in the range of 0.1 to 20 μg/kg, while the contamination of raw materials may be 10 to 100 fold higher. Also cow milk may be affected by aflatoxin as a result of carryover of contaminated cattle feed. Acute intoxications of humans by high levels of aflatoxin leading to death are rare. However, prolonged exposure to this tasteless and colourless compound is a silent threat for humans and animals, as aflatoxin is the most potent natural carcinogen known. Around 4.5 billion people, mainly in developing countries, are continuously exposed to cereals contaminated with aflatoxin and other mycotoxins like fumonisin and deoxynivalenol.

It is estimated that aflatoxin accounts for up to 150 000 cases of liver cancer, mainly in Asia and Africa[3]. An emerging concern is the role of mycotoxins as factor contributing to stunted child growth[4] on top of poor nutrition and infections. Stunting of children is manifested by impaired infant growth and diminished cognitive and physical development. The World Health Organization (WHO) judges childhood stunting is one of the most significant impediments to human development, globally affecting approximately 162 million children under the age of 5 years. Likewise, livestock health and productivity is severely impaired by the continuous exposure of animals to mycotoxin contaminated feed.

Mycotoxin prevention means post-harvest protection of crops

Mycotoxins are relatively heat stable compounds which cannot be eliminated by thermal processing. Containing the risk of mycotoxins means preventing fungal growth on the field and in storage. Aflatoxin is a typical storage mycotoxin, and the most effective prevention is drying of crops directly after harvest, as fungal moulds stop growing at moisture levels below 14%. Furthermore, safe storage that protects the crop from rain and pests is necessary.

An effective measure to reduce the level of mycotoxins is the removal of highly affected grain fractions. The uneven distribution of aflatoxin is a typical feature of this kind of contamination, where a few highly contaminated grains within 10 000 grains destroy the value of a lot. Eliminating the highly contaminated grains by cleaning and sorting is a key measure for safe food. The cornerstone of mycotoxin reduction is high capacity optical grain sorting to identify and remove the discoloured, shriveled and broken grains, which are the typical signs of fungal infection. For moderately contaminated grain it allows processors to recover over 95% of a lot for safe feed and food.

Nuts, spices and cereals may carry harmful bacteria

Most foodborne diseases are caused by bacteria, viruses and parasites causing around 230 000 deaths per annum according to WHO. The public health burden is highest for low income regions and for children under the age of 5. Microbial contamination of food can also strike more affluent societies. In Europe 23 million people fall ill and 5 000 die every year. The Center of Disease Control (CDC) estimates that in the United States 48 million people get sick and 3 000 die of foodborne diseases. According to the US Department of Agriculture (USDA) foodborne illnesses cost USD 15.6 billion each year.

Food of animal origin and water are still the main vehicles of contamination. However, in the past 15 years foods of plant origin have increasingly been associated with foodborne illnesses due to microbial contamination. Besides fresh fruit, sprouts and vegetables, dry foods like nuts, sesame, spices, cereal flour and chocolate are today seen as potential carriers of harmful bacteria like Salmonella spp., Listeria monocytogenes, E. coli, etc. High profile foodborne outbreaks and product recalls in Europe and the United Stated could be traced back to these ingredients by applying modern methods of DNA fingerprinting. New scientific evidence has led to a reassessment of food safety risks related to dry plant-based foods[5]. It is known today that many raw food materials can be contaminated with pathogenic bacteria trough unclean water, birds, rodents or unhygienic handling. Although the number of harmful bacteria may be small, they pose a hazard as they may well survive in dry environments and start multiplying in contact with moisture. The threat is even higher where the infectious dose leading to illness is as low as a few cells, which has been documented for fat-rich products like peanuts, almonds or chocolate contaminated with Salmonella spp. Modern urban lifestyle features ready-to-eat foods for snacking on the go and convenience in the kitchen. A good example are snack bars based on dry fruit, nuts, seeds, cereal flakes and chocolate, all these ingredients being potential vectors of microbial contamination.

The biggest risk for global public health are pathogenic bacteria that carry antimicrobial resistances (AMR). They mainly evolve due to overuse of antibiotics in livestock production, and are spreading into the whole food supply chain. When humans are infected with AMR bacteria, antibiotics fail to cure, resulting in the death of 25 000 people every year in Europe and the United States. It is estimated that by 2050, more than three million will lose their lives to one bacterial infection: drug-resistant E. coli[6] which is primarily transmitted by contaminated food.

Global use of antimicrobials in livestock

Antimicrobials – mainly antibiotics - are used in animal food production, and a strong increase is predicted with rising meat demand[7]. This practice increases the risk of AMR as recently detected for Salmonella isolated from broiler meat in Europe[8].

Almonds should also be pasteurized

Protecting consumers from microbial contamination of food means implementing preventive measures along the value chain from farm to fork. Good post-harvest practices are key to minimize the risk of all kinds of biological contamination. In addition, at one point in food processing the pathogenic bacteria have to be reduced to safe levels by washing, cooking or chemical decontamination. Cooking methods like boiling, steaming or frying are very effective to inactivate or kill bacteria. The process where pathogenic bacteria are inactivated is also called pasteurization. While pasteurization of milk or cooking of meat is well known to avoid the transmission of bacteria to end consumers, the inactivation of bacteria in plant-based foods is a new processing target. The first dry plant-based food for which pasteurization has become mandatory in the United States are almonds for direct consumption. Thus, there is a need to upgrade food processing like roasting of nuts, extrusion of breakfast cereals, high-temperature drying of fruits or steam treatment of cocoa into trusted microbial inactivation steps. The same applies for feed processing for inactivation of pathogenic bacteria to protect the health of animals, eliminate antibiotics and ultimately to reduce the risk of AMR bacteria in the food chain.

Thermal food processing for decontamination purposes is effective and the preferred method where a heat treatment is needed for generating the desired texture and flavour, and to enhance digestibility. An example is the extrusion of cereal flour into breakfast cereals, where the combination of high temperature and pressure is applied for short time under low to medium moisture conditions, resulting in a puffed and crispy cereal, but also in an effective bacteria inactivation. As a rule, dry heat treatments are less effective killing bacteria, which needs to be compensated by longer exposure times, higher temperatures or by the addition of moisture in the form of steam. The downside of heat are potential changes in quality like browning, loss of nutrients or the development of rancidity.

Microbial food safety is the game changer in dry food processing, but also the opportunity to design thermal processes based on scientific data and models of bacteria inactivation and quality changes. The benefit is precision processing to optimise microbial inactivation and food quality. An important paradigm change is that the proof of safe food processing is no longer based on merely testing the end products. Best practices and regulation such as the US Food Safety Modernization Act (FSMA) require process validation of microbial inactivation steps. Validation is the scientifically documented evidence that the process consistently delivers the defined level of bacteria kill and includes process monitoring. For examples, roasting of nuts can be upgraded into a microbial inactivation step provided that the process has been validated. Modern roasting technology relies on monitoring and control systems that include the intelligence on microbial inactivation for real-time process validation for safety, efficiency and due diligence. Finally, all operations following the inactivation step have to be carried out under high hygiene conditions. Hygienic design of production facilities and equipment are important to minimize the risk of contamination of food and contribute to efficient cleaning.

Non-thermal bacteria inactivation for safety and sustainability

There is an increasing demand for microbial decontamination of food ingredients to reduce food safety risk without inducing undesired quality changes. Dry foods like spices, herbs, seeds for sprouting, and nuts are examples of these ready-to-eat foods or ingredients. Effective decontamination of dry food in the early stage of the value chain is an opportunity for innovation in food processing. The ideal solution is non-thermal, a continuous process not requiring the addition of water, environmentally friendly, able to handle high capacities, and cost effective.

Many new technologies are in development, low-energy electron beam being one of the most promising technologies for non-thermal decontamination of dry foods. The technology is scalable as proven by the recent breakthrough application for the sterilization of packaging materials in filling machines for beverages[9]. The same principle can be implemented in compact equipment for dry food decontamination. The opportunity for small and large food processors lies in applying low-energy electron beam for gentle surface decontamination of foods without impacting the quality of the inner food matrix.

Like for all game-changing technologies a careful assessment of potential risks and benefits is mandatory. The primary benefit is protecting consumers from biological contamination risks. Equally important is the assessment of decontamination technologies regarding sustainability aspects like energy demand and the potential to reduce food losses and waste due to spoilage and contamination. The adoption of new technologies addressing emerging food safety risks calls for a dialogue involving all stakeholders in the value chain including regulators and consumers to create awareness, inform about new technologies and to leverage scientific and technological developments for sufficient, safe and sustainable food for all.


  1. Kovalsky P. at al., Toxins, 8, 2016
  2. Battilani, P. et al., Sci. Rep. 6, 24328; 2016
  3. Liu Y. & Wu F., Environ. Health Perspect. 118, 2010
  4. Smith, L. E. et al., Clinical Infectious Diseases 61, 2015
  5. Beuchat L.R. et al., J Food Prot., 76, 2013
  6. O’Neill, J., Tackling drug-resistant infections globally: final report and recommendations. The review on antimicrobial resistance, 2016
  7. Van Boeckel T.P. et al., Global trends in antimicrobial use in food animals, Proc, Natl. Acad. Sci. USA, 112, 2015
  8. EFSA Journal 14, 2016
  9. Fletcher I., Electron Beam Packaging Sterilization Yields Huge Benefits, Food Online, July 15, 2015



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