California Longitudinal Study (2020 – present)

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The Central Coast of California is farmed year-round and supplies a large portion of the nation’s leafy greens. It also produces artichokes, broccoli, cauliflower, celery, strawberries, wine grapes, and other crops. It is precisely because the region, sometimes called the “salad bowl of the world,” grows so much produce, that researchers are interested in studying it. There have been periodic foodborne illness outbreaks associated with the region, including several between 2016 and 2020 caused by the same E. coli O157:H7 strain, so increasing our understanding of the ecology of this growing region as it pertains to foodborne pathogen persistence is of great benefit to consumers, producers, cooperative extension specialists, and food safety officials.

Study Description

In 2020, FDA, in partnership with the Western Center for Food Safety at the University of California, Davis, the California Department of Food and Agriculture, and members of the agriculture industry, launched a multi-year environmental study in the Central Coast of California. This longitudinal study followed an adaptive research design in which sample collection matrices, sites, and frequencies were continually assessed and refined to obtain maximum useful, practical information to help identify environmental factors contributing to the introduction, persistence, and movement of foodborne pathogens that could contaminate produce prior to harvest.

Between August 2020 and May 2025, the research team conducted 40 multiday sampling events within an approximately 7,000 square-mile area. Sample collection sites included 80 public access areas, 14 livestock ranches, five produce farms, two composting facilities, and two vineyards. A total of 6,134 unique samples were collected, including 704 surface water, 237 biological soil amendment, 1,425 soil, 1,057 sediment, 312 air/dust, 923 livestock feces, 942 wildlife feces, and 32 composited insect samples. Each sample was assessed for the presence of E. coli O157:H7 and other Shiga Toxin-producing E. coli (STEC). A subset of samples was also analyzed for Salmonella spp., Campylobacter spp., total coliform, fecal coliform, and generic E. coli. In addition, metadata, including weather conditions, land use, and matrix-specific characteristics were recorded. Metagenomic analyses were used to characterize the microbial communities within select samples. It was also used to identify or confirm the animal associated with wildlife fecal samples. In total, 486 STEC isolates were recovered and underwent whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analyses to evaluate genetic relatedness. Genetic relatedness results were used to determine the distribution of individual STEC strains across sample types, time, and geographical location. Over five years of sampling, the research team observed trends in STEC presence that provided insightful information on STEC prevalence and location, as well as factors that may potentially influence STEC persistence, such as seasonality, weather conditions, and domestic and wild animal activities on adjacent and nearby land.

As of March 2026, the research team is currently analyzing Salmonella spp. and Campylobacter spp. data. To date, 606 Salmonella and 428 Campylobacter isolates have been recovered and are undergoing WGS. Below are initial key findings related to E. coli O157:H7 and other STEC.

Key Findings

STEC Diversity, Persistence, and Movement

In total, 68 STEC serotypes were isolated, including six serotypes considered highly pathogenic to humans (O157:H7, O26:H11, O103:H2, O111:H8, O121:H19, and O145:H28). Some strains of these serotypes persisted for nearly two years. Two serotypes, O157:H7 and O26:H11, were not found in air, but were isolated at least once in other sampled matrices (i.e., surface water, soil, sediment, livestock feces, and wildlife feces). Notably, 12 different E. coli O157:H7 strains were isolated; however, the strain (REPEXH02) responsible for recurring outbreaks between 2018 and 2020 was not recovered.
STEC isolated from wildlife feces genetically matched strains isolated from cattle feces, other wildlife feces, and in some cases, surface water, sediment, and soil. The same strain was isolated from samples collected at a geographic distance of 70 miles apart and, in some cases, from collections made up to 15 months apart, providing evidence that wildlife may contribute to the movement of STEC in the region.
Analyses of rangeland beef cattle and wildlife fecal samples from one livestock ranch revealed three consecutive annual E. coli O157:H7 infection events that were associated with different strains. Strains introduced each year were detected in both cattle feces and wildlife feces, suggesting transfer between these populations.

Animal Sources of Contamination

The overall prevalence of STEC was higher in wildlife fecal samples than in other sample types, except for livestock feces. Wildlife fecal samples were identified using mitochondrial DNA matching via metagenomic sequencing, which included 54% of the STEC positive samples, or by visual inspection. A higher prevalence of STEC was observed in wildlife feces from feral pigs, deer, birds, and coyote compared to other wildlife. Bird species positive for STEC based on mitochondrial DNA analysis of fecal samples were crow, raven, dove, and hawk. STEC was also detected in feces from bobcat and elk, but sample sizes were not robust, thus prevalences for these animals are uncertain.
Highly pathogenic STEC serotypes O157:H7 and O26:H11 were isolated from feral pig, coyote, and bobcat feces. STEC O26:H11 was also isolated from bird, elk, deer, squirrel, and rabbit fecal samples. Overall, 29 different STEC serotypes were recovered from wildlife fecal samples, including some considered highly pathogenic to humans.
Rangeland beef cattle fecal samples had a much higher STEC contamination level than fecal samples from sheep and horses. STEC was detected in bison feces, but from a limited number of samples, thus a reliable prevalence could not be determined. Overall, 46 different STEC serotypes were recovered from livestock feces including O157:H7, O26:H11, O103:H2, and O111:H8.
Both fresh and older, dry animal fecal samples were collected throughout the study. E. coli O157 and other STEC were isolated from fresh and older, dry feces from livestock and wildlife, suggesting that STEC may remain viable in fecal material for extended periods and may introduce risk if disturbed through animal actions or weather events.

Environmental Sources of Contamination

E. coli O157:H7 and other STEC were observed more frequently in water and sediment samples from rivers and creeks compared to tailwater and tailwater sediment (accumulations of field runoff from irrigation practices).
STEC prevalence in surface water and sediment samples collected at public sites close to both cattle rangelands and riparian zones was higher than in samples collected at sites distant from both these environments. These findings indicate that surface water and sediment adjacent to animal habitats may provide an environment for STEC persistence and movement.
Repeated sample collection from a publicly accessible ditch adjacent to a produce field and vineyard, and downhill from cattle rangeland, revealed a high prevalence of STEC in sediment and water over a 3.4-year period. Mitochondrial DNA analysis suggested cattle and feral pigs may have contributed to the presence of STEC in several of these water and sediment samples.
Air samples were repeatedly collected throughout the study area. Viable STEC was isolated from less than 1% of passive air samples collected, suggesting air is not as significant a vector for movement of STEC in the Central Coast agricultural region of California as it was in a previous study near a large cattle feedlot in the southwest United States.
STEC was isolated from 1% of soil samples, indicating that soil is not a significant STEC reservoir in this region. Although the overall prevalence was low, STEC was isolated slightly more frequently in field soils nearer to either riparian habitats or cattle rangeland. Metagenomic sequencing of soil samples at one produce ranch corroborated these results.
No consistent relationship was observed between STEC presence and soil moisture content, although seasonal variation was observed in STEC prevalence and soil microbiomes.
Intense sampling of soil at one produce ranch adjacent to the Salinas River revealed a higher STEC incidence in soil when their field was flooded. Additionally, several tailwater samples collected four weeks post-flooding were STEC positive.
STEC was rarely isolated from either finished or unfinished compost.

Discussion and Future Analyses

While the results of the California Longitudinal Study are regionally specific, the findings address knowledge gaps, particularly concerning animal activities on adjacent and nearby land. They also reinforce the One Health interconnectedness among people, animals, and the environment, and how each can influence food safety. Similarly, just as collaboration across the California Central Coast agricultural community was key to the development and execution of this study, continued collaboration among stakeholders including livestock managers/producers, fresh produce growers, vintners, composters, academia, cooperative extension specialists, retailers, and federal, state, and local government partners will be important to help mitigate potential contamination via environmental transmission.

The research team intends to present additional details about this study during the Western Food Safety Conference in Salinas, CA, in May 2026, and the International Association for Food Protection annual meeting in New Orleans, LA, in July 2026. Once final data analyses are completed, manuscripts on this study will be published in the scientific literature. Additional information and publications will be added to this longitudinal study webpage as they become available.

Study Related Announcements

Study Collaborators

FDA
California Department of Food and Agriculture
University of California, Davis, Western Center for Food Safety
Local members of the produce, viticulture, livestock, and compost industries

Post-Study Actions

California Agricultural Neighbors, a large and diverse group of agricultural stakeholders across the California Central Coast agricultural region, has committed to continuing to explore the findings from this study and identifying ways to improve the safety of food grown in this region. As more analyses are completed and made available, FDA plans to engage with stakeholders to further discuss the data and information gathered during this study and assist stakeholder efforts.