Microbial contamination of food, particularly with Escherichia coli, Listeria or Salmonella, is frequently the culprit behind food recalls and outbreaks of foodborne illnesses. In 2024, the U.S. Food and Drug Administration (FDA) issued 241 food and beverage recalls-an 8% increase from 2023. There's a more concerning trend within the recall increase: those caused specifically by E. coli, Listeria or Salmonella increased sharply in 2024, making up 39% of the 296 recalls issued by the FDA and the U.S. Department of Agriculture (USDA) combined, and the number of people who were hospitalized or who died after getting sick from contaminated food doubled. While contamination often occurs during food processing or preparation, it can also happen before animals or produce items ever leave the farm. Chickens, for example, can pass diseases through to eggs, both on the shell and in the egg itself, and contaminated water used for irrigation can flood the surfaces of fruits or vegetables with bacteria before they're harvested. A critical step to reducing the possibility of contamination is to address the issue during the first stage of food processing-production-or in the case of produce specifically, pre-harvest.
In the session "Pre-Harvest Produce Contamination: How Microbial Research Facilitates an Understanding of Outbreaks" at ASM Microbe 2025, Faith Critzer, Ph.D., Steven Bowden, Ph.D. and Angineh Parsadanians will discuss the challenges and new developments in addressing pre-harvest contamination.
Whether your research focuses on produce contamination, agricultural production or other areas relating to the microbial sciences and food safety, connect with peers working on cutting-edge research in your field at ASM Microbe 2025.
In the Field: Sources of Pre-harvest Contamination
Why is addressing pre-harvest contamination so important if there are so many other stages at which produce can be contaminated? If produce contaminated during pre-harvest makes contact with surfaces during the harvesting process, either on equipment, storage items or the glove or hand of a worker harvesting the produce, the bacteria can spread further. If the equipment or storage materials aren't properly cleaned, the bacteria can persist and continue to contaminate later harvests. On the other hand, when measures are taken to prevent contamination during the pre-harvest process, it is easier to mitigate contamination down the line of the food production chain, and, ultimately, to avoid outbreaks of foodborne illness.
Pre-harvest contamination can come from soil, water, wild and domesticated animals, insects, equipment and human handling. Soil quality, type and texture, water chemistry and salinity, or seasonal factors, like temperature and humidity, can also influence what pathogens are present and how well (or poorly) they survive in the field. However, these diverse factors make studying microbes in the pre-harvest environment a challenge.
"It can be harder to detect foodborne pathogens present in pre-harvest environments because they typically exist at very low concentrations," said Parsadanians, a graduate research assistant and Ph.D. candidate in the School of Plant and Environmental Sciences at Virginia Tech in Blacksburg. "When these pathogens are in a non-host environment, such as a crop field, they are distributed unevenly, their survival is shorter, and they often fall below detection thresholds."
Agricultural Water
Even for just one of those potential sources of contamination-water-measuring and detecting pathogen presence, let alone identifying the introduction point of those pathogens, can be difficult. This is, in part, because the water gets used in so many systems to support crop growth. For instance, water can be used for normal irrigation, for the application of a spray that protects against plant pathogens or insects or for temperature protection. Strawberry farmers will sometimes use irrigation systems to intentionally develop ice casings over strawberry plants to protect the plant, flowers, buds or fruit from frost and freezing temperatures. However, the water volume required to execute this ice-encasing process successfully is high, so even if the water source the farmers are using is well-filtered and of high quality, like groundwater, they may need to pump and store it somewhere (e.g., a retention pond) so they have enough water to use when needed. Doing so introduces another potential entry point of contamination.
"As soon as the groundwater is pumped into that pond, it takes on the microbial community profile more similar to that of other surface water sources," said Critzer, professor and undergraduate coordinator at the University of Georgia, Athens. "But because farmers can't pump directly from the groundwater source at the rate their irrigation demands, they have to put it in this reservoir to fulfill the quantity of water they need at one time." Additionally, some systems are able to recover irrigation water and put it back into retention to make the system more sustainable, and that can also carry different microbes back into the pond. If the farm has animals, such as chickens, cows or horses, in addition to crop fields, there's the added risk of agricultural runoff (i.e., water containing E. coli or other fecal bacteria or viruses from animal waste, such as Highly Pathogenic Avian Influenza A) contaminating the crops or the retained water used to irrigate them.
Soil Amendments
Produce can also be contaminated in the field by soil amendments, such as raw or treated manure. Passive treatments (e.g., ensuring the manure is well-aged and decomposed before it is applied to field crops, or allowing time for it to be exposed in the field to natural ultraviolet radiation from the sun) can kill pathogens and reduce the pathogen load in manure. Active treatments, such as heat-drying or alkali stabilization, can also be used, but they're more expensive. However, both treated and untreated manure must be managed, handled and applied carefully to avoid produce contamination.
The Cost of Contamination Prevention
The hurdles farmers face in preventing crop contamination with E. coli, Salmonella, Listeria or other microbes that can cause foodborne illness vary depending on the size of the farm; its location; the crops being grown; water source, pH and salinity; ambient temperature; humidity; fertilizer or pesticide application and a litany of other factors. Unfortunately, this means there isn't a one-size-fits-all recommendation for the best way to go about contamination prevention, and farmers must rely on a combination of different strategies that best align with the parameters of their farm and finances.
According to Bowden, an assistant professor at the University of Minnesota Twin Cities, even as new strategies become available, such as commercially available cocktails of bacteriophages used to fight plant disease (e.g., fire blight in apple trees) supply and affordability remain an issue. "Though it's ready and available as an agricultural biocontrol method, it's less common, and it's competing against cheaper technology. Farmers might choose to use a pesticide like peracetic acid, for example, because it's more affordable than a newer method," Bowden said. Patented in 1950, peracetic acid (also called peroxyacetic acid or PAA) is an antimicrobial approved by the USDA, FDA and Environmental Protection Agency (EPA) for a variety of uses in the produce industry. It's been in use for decades, and has long since passed the approval process, while newer technologies still require review and may be a pricier option even after they are approved.
Farmers also have to address pathogens that harm the plants, deplete crop yield, impact produce quality or quicken spoilage. This can include using insecticides to prevent infestation with pests like aphids, whiteflies or psyllids, which both eat the plants and carry damaging plant pathogens. Or, they may use suppressive soil that has microbes that are antagonistic to phytopathogenic fungi to protect plants against fungal infection. Mitigating the spread of pathogens that cause foodborne illness is important, but those efforts are moot if there's no viable produce to sell at the end of the process.
"Some growers, to stay financially viable, really can't take the hit of having an outbreak associated with them," Critzer said. It could hurt the farm's bottom line if buyers are hesitant to purchase from a grower that turned out to be the reason behind a recall, or they may outright refuse to buy from a grower that doesn't have a food safety plan in place. Having a food safety plan in place to prevent the spread of foodborne pathogens includes establishing hygiene protocols for agricultural workers, regular equipment sanitization or water testing and treatment. And while farms (depending on size, production type or other parameters) may not be required by law to take certain food safety measures, the pre-harvest investment of time, energy and resources can avoid profit loss for the farm later on.
There are non-mandatory food safety organizations, such as the California Leafy Green Products Handler Marketing Agreement, that farmers can voluntarily join to implement food safety practices specific to their crop.
The Role of Regulations
Outside of the responsibilities of the individual farmers, the U.S. FDA, USDA and the EPA all have parts to play in agricultural production. Products applied to crops, like fertilizers, pesticides or antimicrobials, have to be reviewed and approved by the necessary agencies before they can be used on crops. The FDA Food Safety Modernization Act established rules to ensure the safety of the food supply. It included specific guidance about pre-harvest agricultural water that went into effect July 5, 2024. According to these guidelines, farms covered in the language of the final rule are required to take timely action (based on risk, and under certain circumstances) to test pre-harvest agricultural water to identify and eliminate known routes of microbial contamination.
Still, a lack of data makes the development of universal recommendations or requirements to prevent or cut down on pre-harvest contamination difficult. "There is limited data on the microbial quality of water from diverse agricultural settings," Parsadanians said, "including small farms, urban farms or organic farms, where irrigation practices might differ."
What's more, even with these interventions the crops and raw commodities grown in a farm environment will be repeatedly exposed to a variety of pathogens with dust, dirt, insects and wildlife constantly entering and exiting the environment. "It's impossible to entirely eliminate contamination risk, but what we can do is try to reduce pathogen load," Critzer added. Understanding the typical microbial community composition can help identify concerning shifts that potentially require swift action to prevent an outbreak, such as a sudden spike in E. coli concentrations or detection of HPAI(H5N1). Yet, Critzer cautioned that, "as we do that, it's also important to also understand treatment efficacy and any unintended consequences, like impacting soil health."
Even as researchers work to address the knowledge gaps, there's still the matter of developing guidance to help farmers ensure food safety once the data are available, and it takes time and expertise to create and implement that guidance. In March 2025, both the USDA National Advisory Committee on Microbiological Criteria for Foods and the National Advisory Committee on Meat and Poultry Inspection were eliminated. As more data become available on the pre-harvest environment and microbial contamination, particularly with E. coli, Salmonella and Listeria, farmers will need updated guidance-and the expertise of microbiologists-on best practices to help prevent foodborne illness outbreaks while accounting for the unique circumstances of each farm.
The American Society for Microbiology and the International Union for Microbiological Societies released Microbial Solutions for Climate Change, a report developed by their scientific advisory group of experts (SAG). The report includes microbe-based solutions that can help address food security issues and underscores the urgent need for coordinated cross-sector global action.
