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Food System Primer

Food Safety


The U.S. food supply has often been described as “the safest in the world.” The truth in such claims has been challenged1 and raises the question: What does it mean for food to be “safe”?

Food safety involves protecting the food supply from contamination and—if that fails—preventing people from getting sick as a result of eating contaminated food. Food supplies are susceptible to many different types of contaminants, including:

  • Pathogens, which are disease-causing organisms, such as certain bacteria, viruses, and parasites.
  • Biological toxins, such as those produced by some algae, fungi, and bacteria.
  • Naturally occurring chemicals, such as arsenic, that are present at very low levels in most soils.
  • Chemicals from human activities, such as pesticides used in agriculture and heavy metals from coal-fired power plants.

Pathogens and biological toxins in food generally cause illness within hours or days of exposure. Most chemical contaminants in food are associated with health conditions such as cancer that develop gradually and persist over time, usually as a result of longer-term, repeated exposures.

Food can be contaminated at multiple points along the supply chain, including during production, processing, transport, storage, preparation, and handling. Keeping food safe from contamination is a complex challenge that requires vigilance on the part of industries, consumers, and government agencies.

Foodborne illness

TP Chart

The four leading causes of foodborne illness in the U.S., 2000–2008.3

When people experience cramps, nausea, vomiting, and diarrhea, they often blame it on “stomach flu.” The actual cause rarely has anything to do with influenza and is usually the result of some other viral or bacterial infection. ­­­Noroviruses, for example, are easily transmitted through contaminated food or utensils.

Image credit: Brent Kim, Johns Hopkins Center for a Livable Future, 2013.

Dairy lot

Dairy cattle on a feedlot. Yuma, Arizona.

Many of the bacterial pathogens responsible for foodborne illness live in the guts of animals and may be passed in the animals’ waste. Grasses are the natural diet of cattle; feeding them grain—standard practice in industrial operations—changes their gut environment in ways that increase populations of certain pathogens.14

Photo credit: Jeff Vanuga. USDA National Resource Conservation Service, 2012.

Chicken process

Poultry processing plants can legally operate at very high speeds—up to 140 birds moving down the line per minute—allowing just a fraction of a second to identify and remove contaminated carcasses before they enter the food supply.15 The large volume of carcasses handled by these plants also presents frequent opportunities for cross-contamination.16

Photo copyright.


The Hazard Analysis and Critical Control Points (HACCP) process is a prevention-based approach required by the USDA (for meat) and the FDA (for juice and seafood) that monitors food safety hazards at key points along the supply chain.17 HACCP procedures, for example, might involve checking temperatures during cooking, or checking to make sure containers are properly sealed during food packaging. 

Photo copyright.

Click images for captions

Foodborne illness, or “food poisoning,” is the result of eating food contaminated with pathogens (disease-causing organisms) or biological toxins. The common symptoms of foodborne illness, vomiting and diarrhea, are thought to be evolutionary defense mechanisms designed to expel—sometimes violently—these foreign invaders.2

Each year, there are an estimated 48 million cases of foodborne illness in the U.S., affecting one in six Americans. More serious cases—around 128,000 per year—require  hospitalization, and roughly 3,000 are fatal.3 Infants, young children, the elderly, and people with weakened immune systems are particularly vulnerable to foodborne illness.4

How does food become contaminated with pathogens?

Many of the bacterial pathogens responsible for foodborne illness, such as Salmonella and E. coli, live in the guts of animals, and may be passed in the animals’ manure. Pathogens in manure can contaminate food crops in several ways, for example:

  • when manure is applied as a fertilizer to produce fields,5
  • if manure is transported by runoff onto nearby produce fields,5 or
  • if manure contaminates water sources used for irrigating produce fields.5,6

The age-old practice of applying manure to crop fields is an important method of cycling nutrients and organic matter. Farmers following agroecological methods can take steps to reduce pathogens in manure, such as composting it or applying it several months before planting.7 Industrial meat, dairy, or egg operations, however, generate manure in such large quantities that it becomes difficult to safely manage. Research has also shown that manure from these operations may contain more dangerous, antibiotic-resistant strains of pathogens,8–12 in addition to a range of chemical contaminants.12

Further down the supply chain, at slaughtering facilities, employees and food safety inspectors must take steps to prevent and respond to cases when the animals’ guts are accidentally severed, spilling the pathogen-rich contents and potentially contaminating entire batches of meat.

Food can also become contaminated in restaurants and home kitchens. Norovirus, for example—the leading cause of foodborne illness in the U.S.3—is easily spread through food, drinks, or utensils that were handled by infected people. Raw meat and eggs frequently harbor pathogens, which can be transferred to other foods through cutting boards, countertops, and other surfaces. To help prevent foodborne illness, people who prepare or handle food should wash their hands, disinfect surfaces, keep raw meat separate from other foods, thoroughly cook meat and eggs, and refrigerate or freeze perishable foods to slow the growth of pathogens.13

Chemical contaminants in food

Power Plant

Emissions from a coal-fired power plant.

Some of the chemicals that may contaminate food, such as arsenic, occur naturally in the environment. Human activities, however, are often responsible for dispersing them into air and water. Globally27 and in the U.S.,28 coal-burning power plants are the largest human-caused source of airborne mercury emissions, in addition to releasing large amounts of arsenic, cadmium, chromium, and lead.

Photo credit: Emilian Vicol. Public domain.


In the U.S., growth-promoting hormones are administered to most beef cattle29 and an estimated one-third of dairy cattle.30 The evidence is unclear as to what effect these hormones may have for people who consume beef and dairy products. Some studies suggest a possible link to increased cancer risk.30

Photo credit: Len Rizzi. National Cancer Institute, 1990. Public domain.


Advertisement for Flit, an insecticide formulated with DDT. Dated between 1930 and 1940.

Theodore “Dr. Seuss” Geisel is best known for his children’s books, but earlier in his career, he illustrated advertisements for insecticides. His cartoons helped popularize the use of insecticides in American households before their health and ecological effects were widely understood. The Lorax, the Dr. Seuss tale about protecting the environment, may have been Geisel’s way of making amends for promoting hazardous chemicals.31

Image source: Dr. Seuss Collection, Special Collections & Archives, University of California, San Diego. Used with permission.

Rachel Carson

“If we are going to live so intimately with these [pesticides]—eating and drinking them, taking them into the very marrow of our bones—we had better know something about their nature and their power.”32

Rachel Louise Carson (1907–1964) was a marine biologist, author, and conservationist. Her book Silent Spring drew public attention to the impact of pesticides on health and ecosystems. Her work has been credited with advancing the global environmental movement.

Photo credit: USDA. Creative Commons CC BY 2.0.

Click images for captions

How do harmful chemicals wind up in our food?

Natural gas fracking, mining, coal burning, and plastics manufacturing are just a few of the industrial activities that release chemicals into our environment. Many are known to be harmful, while the health effects of thousands of others are not yet understood. Because these chemicals are present in air, water, and soil, they can make their way into our food supply.

Some contaminants, such as arsenic in poultry meat,18 may be present in food as an indirect result of industry practices—feeding certain drugs to animals, for example. Other harmful chemicals, such as caramel color in soft drinks,19 are present in food or beverages because manufacturers add them directly to the product.

Pesticide use is another contributor to chemical contamination of food. DDT, for example, was among the earliest synthetic chemicals to be used as an insecticide. First used during  World War II to combat malaria and other insect-borne diseases,20 DDT’s initial success led to its being promoted as the simple solution to any insect problem. Hailed as the “atomic bomb of the insect world”,21 DDT quickly became widely used in controlling agricultural, household, and garden pests.22

In her book Silent Spring, biologist and ecologist Rachel Carson drew public attention to evidence that DDT was impacting wildlife and putting human health at risk. Despite strong opposition from the pesticide industry, in 1972 the U.S. government banned the use of DDT.22,23

Almost 30 years after the ban, a study identified DDT, along with several other pesticides and industrial chemicals, as among the most problematic chemical contaminants in the U.S. food supply, based on their toxicity and the amounts of them Americans consume in food. The lion’s share of exposure to these chemicals is through seafood, beef, and other animal products.24 DDT is among many synthetic chemicals that persist in the environment (they last many years before breaking down) and accumulate in the tissues of animals.

Fruits and vegetables may also contain chemical residues, particularly if they were grown using pesticides25 or in contaminated soil.26 Consumers can reduce their pesticide exposure by washing produce thoroughly, peeling root vegetables, or choosing organic varieties. Eating nonorganic fruits and vegetables, however, is recommended over not eating them at all—the health benefits of diets rich in fruits and vegetables generally outweigh the risks from pesticides.


The following list of suggested resources is intended as a starting point for further exploration, and is not in any way comprehensive. Some materials may not reflect the views of the Johns Hopkins Center for a Livable Future.

For teachers

Reports and other documents

Academic journal articles


1. Wirt K. Another myth: American agriculture yields world’s “cheapest, safest” food. 2004.
2. Nesse RM, Williams GC. Why We Get Sick: The New Science of Darwinian Medicine. Random House; 2012.
3. Centers for Disease Control and Prevention. Vital Signs: Incidence and Trends of Infection with Pathogens Transmitted Commonly Through Food --- Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 1996--2010. Morb Mortal Wkly Rep. 2011;60(22):749-755.
4. McCabe-Sellers BJ, Beattie SE. Food safety: emerging trends in foodborne illness surveillance and prevention. J Am Diet Assoc. 2004;104(11):1708-1717.
5. Erickson MC, Doyle MP. Plant Food Safety Issues: Linking Production Agriculture with One Health. In: Improving Food Safety Through a One Health Approach: Workshop Summary. Washington DC: National Academies Press; 2012.
6. Solomon E, Yaron S, Matthews K. Transmission of Escherichia coli 0157:H7 from contaminated manure and irrigation water to lettuce plant tissue and its subsequent internalization. Appl Environ Microbiol. 2002;68(1):397-400.
7. University of New Hampshire Cooperative Extension. Guidelines for Using Animal Manures and Manure-Based Composts in the Garden. 2013.
8. Price LB, Lackey LG, Vailes R, Silbergeld E. The persistence of fluoroquinolone-resistant Campylobacter in poultry production. Environ Health Perspect. 2007;115(7):1035-1039.
9. Sapkota AR, Curriero FC, Gibson KE, Schwab KJ. Antibiotic-resistant enterococci and fecal indicators in surface water and groundwater impacted by a concentrated Swine feeding operation. Environ Health Perspect. 2007;115(7):1040-1045.
10. Casey JA, Curriero FC, Cosgrove SE, Nachman KE, Schwartz BS. High-Density Livestock Operations, Crop Field Application of Manure, and Risk of Community-Associated Methicillin-Resistant Staphylococcus aureus Infection in Pennsylvania. JAMA Intern Med. 2013;21205(21):1980-1990.
11. Graham JP, Evans SL, Price LB, Silbergeld EK. Fate of antimicrobial-resistant enterococci and staphylococci and resistance determinants in stored poultry litter. Environ Res. 2009;109(6):682-689.
12. Graham JP, Nachman KE. Managing waste from confined animal feeding operations in the United States: the need for sanitary reform. J Water Heal. 2010;December:646-670.
13. USDA Food Safety and Inspection Service. Be food safe: four easy lessons in safe food handling. 2007.
14. Callaway TR, Elder RO, Keen JE, Anderson RC, Nisbet DJ. Forage feeding to reduce preharvest Escherichia coli populations in cattle, a review. J Dairy Sci. 2003;86(3):852-860.
15. Zuraw L. Reactions Vary to USDA’s Poultry Inspection Rule. Food Saf News. 2014.
16. Baron P. The Fast and the De-Feathered: Proposed Processing Rule Puts Health at Risk. Livable Futur Blog. 2012.
17. Kevin Keener. Safe Food Guidelines for Small Meat and Poultry Processors: Overview of HACCP. Purdue Extension; 2007.
18. Nachman KE, Baron P a, Raber G, Francesconi K a, Navas-Acien A, Love DC. Roxarsone, inorganic arsenic, and other arsenic species in chicken: a u.s.-Based market basket sample. Environ Health Perspect. 2013;121(7):818-824.
19. Smith TJS, Wolfson JA, Jiao D, et al. Caramel Color in Soft Drinks and Exposure to 4-Methylimidazole: A Quantitative Risk Assessment. PLoS One. 2015;10(2).
20. National Pesticide Information Center. DDT Technical Fact Sheet. 2000.
21. Dumanoski D. The End of the Long Summer: Why We Must Remake Our Civilization to Survive on a Volatile Earth. New York: Random House; 2009.
22. The Pesticide Action Network. The DDT Story. 2013.
23. U.S. Environmental Protection Agency. DDT - A Brief History and Status. 2012.
24. Dougherty C. Dietary Exposures to Food Contaminants across the United States. Environ Res. 2000;84(2):170-185.
25. Environmental Working Group. EWG’s 2013 Shopper's Guide to Pesticides in Produce. 2013.
26. Kessler R. Urban gardening: managing the risks of contaminated soil. Environ Health Perspect. 2013;121(11-12).
27. UNEP Chemicals Branch. The Global Atmospheric Mercury Assessment: Sources, Emissions and Transport. Geneva, Switzerland; 2008.
28. U.S. Environmental Protection Agency. Mercury: Basic Information. 2013.
29. Johnson R, Hanrahan CE. The U.S.-EU Beef Hormone Dispute. 2010.
30. California Breast Cancer Research Program. Identifying Gaps in Breast Cancer Research. 2007.
31. Allen W. The War on Bugs. White River Junction, VT: Chelsea Green Publishing Company; 2008.
32. Carson R. Silent Spring. New York: Houghton Mifflin; 1962.