Do Modern Farming Alternatives Reduce the Risk of E. coli?

Learn more about aquaponics and hydroponics, and the pros and cons of these food production methods.
Do Modern Farming Alternatives Reduce the Risk of E. coli?
June 15, 2020

Food-borne pathogens cause millions of illnesses, and even some deaths, throughout Canada every year. In fact, the Government of Canada estimates that there are approximately four million cases per year. The source of these food-borne illnesses are food that is contaminated with pathogens such as bacteria, parasites or viruses. The main way that these pathogens contaminate food is through improper food handling by Food Handlers.

While all of these pathogens present their unique set of symptoms and risks, E. coli is one that is particularly dangerous. It has been responsible for many food-borne illness outbreaks, especially ones which cause severe illnesses and hospitalizations. For example, in 2019, there was an outbreak of E. coli linked to romaine lettuce that sickened 40 people and hospitalized 28. Outbreaks like these point to issues with fresh produce production and lead to questions about alternative growing methods.

E. coli and its risks

Escherichia coli (E. coli) is a large group of bacteria that is found in the intestines of people and animals, as well as the environment such as soil and water. Some E. coli are harmless and are actually good for a healthy human intestinal tract. However, some types of E. coli are dangerous (called pathogenic E. coli) and can cause symptoms such as watery or bloody diarrhea, abdominal pain, nausea or vomiting. Even more serious symptoms like hemorrhagic diarrhoea, kidney failure and Thrombotic thrombocytopenic purpura (blood disorder) can occur, especially for those in high-risk groups.

Pathogenic E. coli can be transmitted through contaminated water, ground beef, unpasteurized dairy products and leafy green produce. For produce, contamination with E. coli often comes from the soil or a contaminated water source. Safety measures and protocols exist to prevent E. coli contamination in traditional farming, but there continue to be many cases causing food-borne illness in Canada.

Some companies are advocating for alternative methods for growing fresh produce and indicate that these methods prevent E. coli infection in these foods. This has raised questions about whether there truly are safer ways to grow produce that eliminate the risk of E. coli infection.

What are the alternatives to traditional farming?

A recent study by Purdue University examined whether there is less risk of E. coli contamination in aquaponic or hydroponic systems. The study looked particularly at E. coli O157:H7, which is one of the more deadly types of bacteria and commonly associated with food-borne illness outbreaks. The results of the study found there is still some risk of E. coli contamination in these systems. However, a growing amount of companies are advocating for aquaponics or hydroponics as a safe and effective alternative to growing fresh produce in the ground.


Aquaponics is a type of indoor farming that involves growing produce and raising fish in tanks to create a co-dependent system. The fish and the growing produce work in symbiosis: the water the fish live in becomes rich with nutrients which is then used to fertilize the produce, while the produce purifies the water for the fish.

The pros of aquaponics include:

  • providing a controlled environment for produce growth
  • allowing for the water source to be more controlled
  • using fish waste as the fertilizer so it is considered all-natural
  • using no soil in the system, which eliminates soil as a possible source of E. coli contamination
  • allowing the growth of produce locally, which reduces the import of produce from other countries with less stringent food safety standards.

Despite the many advantages of an aquaponics system, the study from Purdue University does bring up some interesting considerations. In the study, three aquaponic systems were built in a greenhouse and used to grow lettuce, basil and tomatoes. The study was conducted between December 2017 to February 2018; upon the conclusion of the experiment, samples were taken of the roots and the leaves of each plant, along with samples of the water. Analysis of the samples showed that there was still a presence of E. coli in the feces from the fish as well as the water.

On a positive note, researchers confirmed that the presence of E. coli in the water did not lead to E. coli being detectable in the produce. The researchers stated that the biggest risk of E. coli contamination would come from the splashing of the infected water onto the produce.


Hydroponics is also a type of indoor farming that grows produce without the need for soil. The produce is provided with water and nutrients in order to grow. There are two types of hydroponic techniques: the Nutrient Film Technique and the Neutral Medium Technique. Nutrient Film involves recirculating a water and nutrient mix over the bare root of a plant in a gully. Neutral Medium involves growing produce in a neutral medium, while water supply is provided to the plant through a drip irrigation system.

The pros of hydroponics include:

  • using less water than traditional farming
  • creating a year-round growing season
  • providing faster-growing cycles
  • providing control over water source and environment
  • using no soil, which effectively eliminates soil as a possible source of E. coli contamination

When it came to hydroponic systems in the Purdue University study, the results were comparable to the aquaponic systems. Three hydroponic systems were built in the greenhouse and were used to grow the same produce as in the aquaponic systems. After conducting their analysis, the researchers discovered that E. coli was in the water of the hydroponic systems, however, they indicate that there are a variety of possible reasons for the contamination. They suggested that the bacteria could have been introduced to the water during set-up or due to incomplete sanitation of all the parts.

Food handlers play a vital role

What the research by Purdue University illustrates is that there are many factors at play when it comes to E. coli contamination. Simply choosing one type of growing system over the other does not solve the problem of food-borne pathogens. It is essential that proper health and safety protocols are put in place to maintain food safety, no matter the type of farming.

The results of the study indicate that E. coli could have been transmitted through human activities such as touching the water, feeding the fish (in aquaponics), sample taking or other methods of cross-contamination such as contaminated shoes being worn in the greenhouse. Also, the results show that proper cleaning methods and sanitation of aquaponic and hydroponic systems is needed to reduce E. coli contamination of the produce. Both of these examples illustrate just how easily food workers can decrease — or increase — the risk of E. coli contamination of food. Efforts to eliminate E. coli from the food chain can be hindered if proper food safety protocols and food handling procedures are not followed. The responsibility falls on those who are growing, producing and handling the food to ensure that food safety standards are followed and met.

Contact the Canadian Institute of Food Safety for more information about safe food practices and our online food safety training.