Scientists say animal operations near leafy greens fields are a food safety problem

Research published this week shows that animal feeding operations continue to be a problem in terms of E. coli outbreaks linked to leafy greens.

As evidenced by outbreaks from Shiga toxin-producing E. coli (STEC) from 2009 to 2021, leafy greens growing fields can be contaminated in a variety of ways related to animal operations such as feedlots and grazing pastures, according to a study published in the Journal of Food Protection.  

From 2009 through 2021, there were 49 leafy greens STEC outbreaks, with 37 linked to a specific type of leafy green — romaine lettuce. Traceback investigations were conducted for 25 of the outbreaks, and farm investigations for 17. Seven outbreaks were traced back to a single farm, and 10 were traced back to multiple farms. 

Environmental samples collected for investigations increased over time, and farm investigations since 2018 included a more diverse collection of environmental sample types because of advancing technology. The study includes a summary of the results obtained from the samples collected, including leafy greens, air, water, sediment, animal feces and soil. 

The outbreak strain was identified in 6 of 17 investigations by genomic analysis. Sample and testing methods changed over time, increasing the sensitivity for pathogen detection. Those changes allowed for more specific tracing of pathogens to specific products. 

The researchers said improved traceability in the supply chain can help with several aspects of food safety related to leafy greens:

• Identification of single farms for investigations and focused product actions; 
• continued grower outreach and education and adoption of regulations and best practices can help improve leafy green safety; and 
• research to address food safety gaps can help minimize the impact of future outbreaks. 

However, enforcement of the new traceability rule has been delayed by President Trump’s Administration.

The Food and Drug Administration has traditionally worked with the Centers for Disease Control and Prevention and with state officials to investigate foodborne illness outbreaks. Federal staffing and budget cuts may seriously curtail these efforts. 

The CDC identified 40 outbreaks of STEC infections linked to leafy greens between 2009 and 2018 in the United States and Canada. Those outbreaks sickened 1,212 people, caused 77 cases of hemolytic uremic syndrome, which is a type of kidney failure that often results in the need for transplants, and caused eight deaths. 

“Collectively, these outbreaks shed light on the need for changes to improve safety during production, harvesting, and processing of leafy greens; enhancements in traceability of product through the supply chain; the identification and reduction of production risks proactively; better understanding of STEC survival in the environment; and mitigation of potential contributing factors to reduce contamination from the environment and adjacent lands, most notably in Arizona and California, where the majority of leafy greens consumed in the U.S. are grown,” according to the study’s authors.

“While traceback can identify the locations where contamination may have happened, further investigation is needed to determine how the contamination occurred. The collaborative efforts of the FDA Coordinated Outbreak Response & Evaluation (CORE) Network and other FDA experts, the CDC, and state and local partners through epidemiologic and traceback investigations help inform the FDA Produce Safety Network — a network of regional produce safety experts that support farmers, regulators, and other key stakeholders — where farm investigations should be conducted.” 

According to the research report, the primary environmental reservoir for STEC is ruminant animal feces, particularly cattle, and the overlap of animal carriers of STEC directly with leafy greens or through an environmental intermediary such as water, dust and manure. 

The specifics of the investigations
Traceback detectives were a key component in the investigation of the 49 STEC outbreaks linked to leafy greens from 2009 through 2021. They found 37 of the outbreaks were epidemiologically linked to consumption of a specific leafy green type — romaine lettuce.

Thirteen of 25 outbreaks were traced back to multiple farms, one of which was a single state outbreak, while the rest were multistate outbreaks. Farm investigations were conducted for 10 of these outbreaks at a total of 46 farms. The type of leafy greens implicated in these 10 outbreaks included romaine lettuce, romaine or iceberg and spinach. Seven of these 10 outbreaks were linked to leafy greens sourced from California, one from Arizona, one from Arizona and California, and one from Oregon and California. Nine outbreaks were linked to leafy greens that were harvested during fall, while one was linked to leafy greens harvested during spring. E. coli O157:H7 caused all 10 of these outbreaks.

Five of the 10 farms were irrigated with surface water, one used well water exclusively, and one used a combination of well and surface water as agricultural water sources. One farm used a reservoir to store water sourced from an irrigation canal. Shiga toxin-producing E. coli (STEC) has been found in open irrigation canals near or adjacent to feedlots, as well as in dust and runoff from those kinds of animal operations, according to the researchers.

Some farms used a combination of overhead sprinkler, furrow, or drip irrigation. Three farms used only overhead irrigation throughout the duration of the crop cycle. Three farms transitioned from overhead irrigation to furrow, while one transitioned from overhead to drip. Water was also used in diluting agrichemicals and fertilizers prior to application to crop plants. 

“Information on the proximity of livestock operations was available for five of seven outbreaks. These operations included a Concentrated Animal Feeding Operation (CAFO) within 8-11, 0.25, and 2 miles from outbreak investigations, respectively, and the presence of grazing cattle within a mile of the farm for two investigations,” according to the research report.

Adjacent and nearby land uses 
Farm investigations are one tool used by food safety regulators to confirm the source of contaminated produce in an outbreak and to identify potential root causes. The uses and characteristics of land adjacent to leafy greens fields have been identified as potential sources of contamination in investigations. The presence of nearby animal industry such as CAFOs or grazing cattle, and/or wildlife and their corresponding feces were observed for all seven investigations with a single implicated farm. 

Animal fecal samples were collected during farm investigations and yielded non-outbreak STEC for many outbreaks as well as the outbreak strain — cattle manure on adjacent land. Animal fecal matter has been a significant contamination issue in leafy greens as shown during outbreak investigations before 2018. The researchers said this stresses the importance of adjacent or nearby land use, including those not under the growers’ control, which can serve as a source of contamination for leafy greens. 

Conditions and practices on adjacent or nearby lands were identified as a contributing factor for at least six outbreaks associated with leafy greens, including four outbreaks between 2018 and 2020. Some of these included the presence of domesticated animals, animal housing, animal waste, and related practices; agricultural water sources; practices related to the applications of soil amendments, manure, or biosolids; land features; weather events; and others, according to the FDA.

The preliminary findings from an FDA study in the Southwest growing region demonstrated that air samples collected yielded viable pathogen results indicating that bacteria can survive in the air and that dust can act as a transfer mechanism for pathogens from adjacent and nearby land to water, soil and plant tissue. This is consistent with other findings when collecting air samples near beef cattle feedlots in Imperial Valley, CA, showed higher odds of recovering generic E. coli from samples in close proximity to feedlots.

Surface water that is located near feedlots or other animal operations can become contaminated with STEC, from dust in the air or sub-surface ground water. Preliminary findings showed that surface water experienced a change in water quality and an increase in the prevalence of STEC as water moved past a nearby feedlot for one of the large, multi-farm outbreaks, even though there was an absence of surface run-off or other direct contamination. Researchers said this suggests that dust or sub-surface water from the feedlot may be a potential contributing factor in the contamination of the irrigation water and/or produce in outbreak associated growing regions.

The study’s authors said the recovery of outbreak strains from irrigation water and sediment was a significant finding during farm investigations. 

“This highlights the importance of collecting a more comprehensive set of environmental samples, including sediment in which enteric pathogens can persist for months or even years, as well as using the large-volume more than 50 L ultrafiltration sampling methods for increased pathogen detection sensitivity.” according to the research report.

The research showed that some pesticides can stimulate the growth of human pathogens if contaminated water is used in their preparation. This mode of contamination was one of the hypotheses of what led to the 2018 outbreak of E. coli O157:H7 infections linked to romaine lettuce from Yuma, AZ.

The Produce Safety Network
The finalization of the Produce Safety Rule in 2015 led the FDA to create the Produce Safety Network (PSN), made up of produce safety experts from the Center for Food Safety and Applied Nutrition and investigators from the Office of Regulatory Affairs. The future of the PSN is unclear amid the staffing cuts at the FDA.

Before 2018, FDA primarily sampled finished product, which was not consistently available in the investigation phase of outbreaks and did not provide information as to the source of contamination. Once the agency transitioned to collecting and analyzing additional environmental samples, such as field soil, agricultural water, soil surface drag swabs, and animal feces, the number of samples collected during farm investigations increased. 

With the establishment of the PSN, the FDA now has consistent access to a high level of experience and expertise from produce safety specialists. The PSN helped improve investigational planning and data collection, identification of outbreak contributing factors, and identified opportunities for prevention. 

“The PSN also serves as a resource for farmers and their partners to help them achieve compliance with the Produce Safety Rule, and thus aids growers in the development of practices that reduce hazards and opportunities for contamination,” according to the report authors. “While the outbreaks discussed in this review from 2009 to 2013 included limited sampling information, there was a significant increase in samples taken during on farm investigations from 2018 to 2021, coinciding with the establishment of the PSN.”

In addition to the work of the PSN, there are CDC staff from the National Center for Emerging and Zoonotic Infectious Diseases, Division of Foodborne, Waterborne, and Environmental Diseases who have had a direct role in the farm investigations of the major STEC outbreaks linked to leafy greens during the 2018-2020 timeframe. 

Specifically, the introduction and optimization of collection and analysis of certain samples was critical in expanding the sample types collected by FDA. Two outbreak investigations that show the benefits of the PSN, according to the researchers, in collaboration with CDC and state partners, were the outbreaks of reoccurring STEC strain associated with romaine lettuce from Yuma, AZ, and Santa Maria, CA, growing regions in 2018 and Salinas Valley in 2019 in California. 

The outbreak strain was isolated from irrigation water and sediment samples in 2018, a water sample collected from a cattle trough in adjacent farmlands in 2019, and from romaine-containing products in 2019. 

It is unclear what impact the Trump Administration’s staffing cuts at the FDA and the CDC will have on food safety testing programs such as the PSN.

Collaboration and data sharing
The reoccurring nature of STEC outbreaks in leafy greens illustrates the importance of developing programs to foster the collection of more data by industry to help identify and mitigate risks to prevent or reduce illness, according to the research report. Transparency is another key factor. 

“Data sharing among industry and with federal partners could help industry collectively learn effective ways to improve safety of leafy greens. Such work could allow for a rapid characterization of field contamination and inform what mitigation steps are needed,” according to the study. 

The FDA has traditionally provided technical assistance to private industry supporting efforts that identify improvements across the leafy green supply chain and assist in outbreak prevention efforts. Similarly, the CDC provides technical assistance to private industry by collaboratively developing resources to support environmental sampling and surveillance efforts. These industry aids could be impacted by cuts to the FDA and CDC budgets.

Nearness of livestock
A survey comparing growers’ produce safety practices from 1999 to 2016 showed an increase in the number of produce fields that are located adjacent to commercial livestock operations. 

The researchers say outbreaks such as those in described in their report suggest that additional awareness of the livestock-produce interface among both leafy green growers and livestock operators is needed. Information about adjacent or nearby land use such as how and where manure is stored on the nearby land, and how manure runs off livestock operations to nearby lands can help leafy green growers implement effective mitigation strategies. 

One stumbling block is the fact that neither the FDA nor the CDC have the authority to access private land used for livestock operations during outbreak investigations. This was shown during investigations in recent years and highlighted FDA’s limited authority on lands outside the scope of implicated leafy green farming operations.

The recovery of outbreak strains from water sources near animal operations demonstrates the importance of using safe agricultural water, according to the study. 

“These findings support systems-based pre-harvest agricultural water assessments to identify conditions that can introduce hazards into or onto produce or food contact surfaces, and to determine mitigation measures for minimizing risks associated with pre-harvest agricultural water,” according to the study’s authors. 

“These investigations showed that the outbreak strain can be found throughout the lifespan of leafy greens products, from the agriculture water used for the leafy greens, sediment from irrigation reservoirs, manure in nearby land, to retail product.”

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Source: https://www.foodsafetynews.com/2025/05/scientists-say-animal-operations-near-leafy-green-fields-are-a-food-safety-problem/