There are several common sources of pathogens that you should be aware of. The ones discussed in this article include irrigation water, soil, animals, insects, the processing environment, air and fomites. Understanding how these sources cause infection and illness may help to keep us safe.

Irrigation water

Waterborne pathogens may live on plant surfaces and may also get internalized in stems and leaves. Such pathogens include Escherichia coli (E. coli), Salmonella, Salmonella typhi, Shigella spp., Campylobacter, Vibrio cholera, Hepatitis A, and Norovirus. By ensuring the safety of water used on farms, produce safety can be improved. Therefore the FDA has set guidelines on the minimum amount of E. coli that is allowed in irrigation water. Water used for irrigating sprouts must be free of E. coli. The presence of E. coli is an indication of fecal contamination and the likely presence of other pathogens. Water used for irrigating other produce may contain E. coli, but within the required limit. The water supply must be tested initially and annually to ensure safe E. coli concentrations. Greater frequency is required for surface water (e.g. from rivers and lakes) compared to ground water (wells). Where limits are not met, corrective actions may include establishing water treatment or allowing enough time interval between application of irrigation and harvest, or between harvest and end of storage. In 2018 a national outbreak of E. coli 0157:H7 in romaine lettuce from California sickened 210 people, hospitalized 96, and killed 5. Eighty seven percent of individuals interviewed indicated that they ate romaine lettuce the week before they got sick. Genome sequencing of the bacteria indicated that the most likely source of the bacteria was an irrigation canal used to irrigate seeds during germination, and later in the growing season to dilute pesticide spray via areal application. 


Soil is a natural source of bacteria. Many of them are helpful as they have a role to play in soil formation, nutrient recycling, and maintaining soil fertility. However, many are pathogenic, including several bacteria, protozoa, fungi, and helminths (parasitic worms). There ability to survive in the soil outside of a human host can range from weeks to several months. Agricultural soil may become infected by contaminated water, feces of wild animals in the field, contaminated compost, and raw manure. Under the Food Safety Modernization Act (FSMA), the FDA requires that compost used to amend soil be prepared in a manner to prevent detectable levels of Listeria monocytogenes, Salmonella spp., and E. coli O157:H7. Under the act, the FDA does not object to farms following the USDA’s Organic Program Standard of maintaining at least a 120-day time interval between application of raw manure and harvest when the edible portion of the produce is in contact with the soil; and a 90-day interval when the edible portion is above the ground. In 2011, soil contamination with E. coli was suspected by the UK’s Health Protection Agency (HPA) to be the cause of an outbreak associated with potatoes and leeks that sickened 250 people across England, Wales and Scotland. Seventy-four of these people were hospitalized and one with an underlying condition died. To avert occurrences like these, consumers are encouraged to wash fruits and vegetables properly., especially if they are eaten raw.  


Diseases that affect animals and can be transferred to humans are called zoonotic diseases. These include anthrax, ascariasis, Lyme disease, trichinosis, listeriosis, salmonellosis, bovine spongiform encephalopathy (BSE), and many more. BSE, also known as mad cow disease, is a slowly progressive degenerative disease of the central nervous system in adult cattle. It causes abnormal behavior, tremors, nervousness, and difficulty walking. It is the result of alternation and accumulation of an abnormal-shaped protein called a prion in the brain caused from feeding cattle with meat and bone meal (MBM). A human version of mad cow disease called variant Creutzfeldt-Jakob disease (vCJD) is caused by eating beef with mad cow disease. Symptoms include depression, loss of coordination, dementia, and a prognosis of death in as little as 13 months. Mad cow disease was a big problem from the mid-1980s to 1990s after its outbreak in the UK. However, UK cases have significantly tapered down from 14,562 cases in 1995 to only 2 in 2015. Only 6 cases have been found in the United States occurring between 2003 and 2018. Precautions taken by the federal government to prevent mad cow disease in the US include prohibiting the importation of certain live animals, meat, meat products, and pet foods from counties where mad cow disease is known to exist. In addition, high-risk animals are prohibited from entering the food supply. Today, the removal of the central nervous system in cattle is a standard protocol. The Illinois Office of the Vice Chancellor for Research and Innovation provides excellent suggestions on how to prevent zoonotic diseases. These include steps to ensure good personal hygiene practices when handling live animals, maintaining a clean and healthy environment for farm animals and proper herd maintenance.   


Insects are well known as vector-carrying agents responsible for spreading bacteria, viruses, and parasitic protozoa. They are problematic since they are small enough to easily get into processing facilities. Of these, cockroaches and houseflies are among the most problematic. Both carry pathogens on their surfaces, in their saliva and alimentary canal. The most common cockroaches found in food facilities include the German cockroach (Blatella germinica), the American cockroach (Periplaneta americana), and the Oriental cockroach (Blatta orientalis). Cockroaches can get into food plants through unsecured openings and utility piping including drains and sewer pipes. They may also be hitchhikers on raw material, packaging materials, pallets and personal items of workers. During the day, they stay out of sight by hiding in cracks and crevices, preferably where it is warm (>70 oF), dark and moist. At night they come out to feed. They do not need much to feed on. Small food scraps and residue in poorly sanitized areas, rodent droppings, and mold provide enough nutrients for them to grow and thrive. As they crawl in dirty, dingy places they pick up germs. They are then able to shed those germs by touching food, expelling saliva to “taste” their environment, and defecating along their travel paths. Common pathogens associated with cockroaches include Salmonella, Listeria, and Campylobacter. Like cockroaches, house flies live in close proximity to humans. They breed rapidly using garbage, sewage, and germ-infested decaying materials as prime media for laying their eggs. Unlike cockroaches though, they are most active during the day,  making contact with food as they feed, shedding germs from their surface, vomitus and excreta. Their contact may result in intestinal, eye, skin infections, and polio. Controlling flies and cockroaches in food establishments requires a combination of physical blocks to prevent entry such as screens, insecticides, traps, cleaning and sanitation, and elimination of breeding grounds in and outside the food facility. 

The Processing Environment

The environment where food is produced is a major source of food contamination. Environment typically refers to the cleanliness of food-contact and non-food contact surfaces; building and equipment integrity, design, and layout; air; and water quality. However, food handlers may also be added to this list. Poor personal hygiene such as improper or failure to wash wands can result in the infection being passed from workers to food. Transmission of infection is especially heightened during times of illness. Hence, the FDA requires that food handlers should not report for work or should be sent home if they are showing symptoms of diarrhea, vomiting or jaundice. If they have a sore throat with fever and are already at work, they may be sent home or immediately reassigned to a job that does not involve coming in contact with food or food contact surfaces. Food handlers must not be allowed to return to work until symptoms have disappeared for at least 24 hours. No worker should be allowed to handle food with open soars, boils, bruises, or cuts.


Pathogens, especially viruses can be inhaled due to aerosolization. Improper or inadequate cleaning and sanitation, and failure to cover or remove garbage promptly will lead to unsafe air quality. Hence, proper cleaning and sanitation, and garbage control will be critical in keeping the air clean and free of germs. In addition, air entering the facility must be adequately filtered and air pressure managed to prevent air from flowing from dirtier areas (e.g. toilets, raw materials handling and slaughtering) to cleaner areas (e.g. mixing, filling and packaging rooms). Food handlers may also be a source of contaminated air. For example, rotaviruses are respiratory viruses that cause diarrhea and can be transmitted when sick workers sneeze, cough or talk. To avoid transmission, it is essential that food handlers stay home when sick. 


The term fomite is used to describe any contact surface that may have germs that can be passed on to food after touching. For example, a restaurant worker touching a dirty door handle and then making a sandwich for a customer without wearing gloves. To prevent transfer via fomites, it is important to practice proper cleaning and sanitation, and personal hygiene.

Reference: Stein, R. A. & Chirila, M. (2017). Routes of transmission in the food chain. In C. E. R. Dodd et al. (Eds.), Foodborne diseases (3rd ed.). Philadelphia, PA: J.B. Lippincott. 


  • Courtney Simons

    Dr. Courtney Simons has served as a food science researcher and educator for over a decade. He holds a Bachelor of Science in Food Science and a Ph.D. in Cereal Science from North Dakota State University.