Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic production vegetable production. However, there is a risk of foodborne pathogen transferring to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may be subsequently transferred to the produce. This dissertation assesses food safety risks in rotational ICLS in organic fresh produce production, by conducting field trials involving small ruminant grazing of winter cover crops established between growing fresh produce within a single field. In Chapter 1, a three-year (2019-2021) organic ICLS field trial was conducted in organically managed plots with three treatments (fallow, cover crop without grazing (non-graze CC), and cover crop with grazing by sheep (graze CC)) in a maize/tomato rotation at the Russell Ranch Sustainable Agriculture Facility, University of California, Davis. The study examined the effect of cover crops and the risk of grazing on soil and produce contamination by foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes). Generic E. coli, as an indicator of fecal contamination, was quantified monthly in the soil to compare its persistence among the three treatments. None of foodborne pathogens was detected from harvested tomatoes in 2020 and 2021. One soil sample was non-O157 STEC positive from the fallow treatment. Soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61–82 days post grazing, but no difference was observed after 96–123 days. According to the results, foodborne contamination of fresh produce was rare under ICLS, with lower levels of generic E. coli in graze CC soils approximately 120 days post grazing. In Chapter 2, environmental risk factors, including meteorological and soil chemical factors, were evaluated for their effect on generic E. coli presence in soil. A two-year (2021-2022) organic ICLS field trial was conducted under two different environmental conditions in California (grazed by sheep) and Minnesota (grazed by goats) with the same study design as in Chapter 1, but with a spinach/cucumber rotation. Foodborne pathogens were rarely detected in soil and produce in either state, but non-O157 STEC presence in fecal samples of grazing animals was linked to its detection in the soil. Concentrations of generic E. coli in graze CC soil returned to levels comparable to non-graze or fallow treatments within 87-147 days post-graze in both years, with a significant decrease predicted after 32 days post-graze. Generic E. coli persistence in soil after grazing was mainly influenced by treatment group or days post grazing. Although the effects of meteorological factors and soil chemical characteristics were not as influential as treatment or sampling day effects, further analyses using zero-inflated negative binomial modeling suggested that regional differences in generic E. coli counts were influenced by maximum air/soil temperatures on the sampling day in graze CC treatment soil. In conclusion, fecal pathogen shedding status of grazing animals and meteorological factors during the growing season were related to the presence of foodborne pathogens and the survival of generic E. coli in soil under ICLS. In Chapter 3, the role of small ruminants in pathogen shedding through grazing, and interaction between fecal and soil microbial communities in ICLS were investigated, using fecal and soil samples collected from Chapter 1 and Chapter 2. A total of 300 fecal samples (148 from sheep and 152 from goats) and 415 soil samples (272 from California and 143 from Minnesota) were analyzed using 16S rRNA amplicon sequencing to assess if feces deposited by grazing affect soil microbiome composition and foodborne pathogen contamination in ICLS. Species of grazing animals and regional differences significantly influence the microbiome dynamics, while short-term grazing by sheep or goats in ICLS fields has minimal effects on fecal or soil microbiome diversity and composition changes. Additionally, no interaction was observed between the post-graze fecal samples and the grazed soil by small ruminants in ICLS, with distinct microbial compositions depending on sample types and regions. This dissertation’s findings provide valuable insights for developing detailed guidelines to ensure safe and sustainable agriculture practices by conducting ICLS field trials. These results support agroecological practices of ICLS, while maintaining food safety in organic fresh produce production. Further studies comparing the genetic relatedness between the foodborne pathogens isolated in fecal and soil samples would be necessary to identify the source of foodborne pathogen contamination. Despite the fact that no interaction between fecal and soil compositions was observed with short term grazing, repeated implementation of grazing under this system will be necessary to evaluate the cumulative effect of grazing on soil microbial communities, and its interaction with persistence of foodborne pathogens in the soil.

The increasing number of diversified small-scale farms (DSSF) and outdoor-raised livestock in California and nationwide, reflects growing consumer interest and demand for organic or sustainably-produced local foods, including humanely-raised animal products such as meat and eggs. However, there is a lack of research evaluating the unique agricultural management practices of DSSF and how these farming systems may involve risk factors that affect the transmission of foodborne pathogens in the food supply.Diversified farms are often small-scale and raise a combination of livestock and produce, or multiple livestock species with the intent of selling specialized animal products directly to consumers. However, livestock are reservoirs for foodborne pathogens like Shiga toxin-producing Escherichia coli (STEC). Additionally, raising pigs outside provides an opportunity for contact with feral pigs, which harbor zoonotic and foodborne pathogens. STEC remains one of the major causes of foodborne outbreaks in the US and STEC outbreaks associated with DSSF are most likely underreported The overall goal of this dissertation focused on evaluating the pre-harvest food safety risks on DSSF in California: Chapter 1 estimated the prevalence of STEC in cattle, goats, sheep and pigs raised on DSSF and evaluated risk factors associated with the prevalence of STEC using a multilevel logistic regression model. Chapter 2 used a species distribution modeling method Maximum Entropy (MaxEnt) to predict suitable habitat for feral pigs in California. Then the MaxEnt prediction map was overlapped with the location of over 300 outdoor-raised pig operations (OPO) in California to create a risk map, identifying areas most at risk for disease transmission between these two growing swine populations. In the past few decades, California has experienced an increase of feral pigs and a resurgence of outdoor-based domestic pigs and this trend has implications for pathogen transmission in the wildlife-livestock interface. The feral pig–outdoor-raised pig risk map built in Chapter 2 identified counties to target for a STEC prevalence study in Chapter 3. Fecal samples from both feral pigs and domestic pigs raised outdoors were collected in counties that had a higher risk for contact between feral pigs and domestic swine raised outdoors. The overall goal of Chapter 3 included assessing the prevalence of STEC in those counties as well as using a multilevel logistic regression model to assess risk factors associated with the presence of STEC in fecal samples. Although consumers perceive small-scale farms or outdoor-raised meat as safer or more natural, these three studies together demonstrated that livestock raised outdoors on small-scale farms are reservoirs for STEC and indicated the need for more studies to ascertain risk factors of foodborne pathogens on DSSF. As the number of DSSF farms continues to grow, evaluating risk factors and management practices that are unique to these small operations will help identify risk mitigation strategies and develop extension outreach materials to keep food safe from farm to fork and protect California’s agricultural economy.