The Western Center for Food Safety (WCFS) is supported by a cooperative agreement to address the development of research approaches and data critical to high priority public health issues addressing FDA-regulated fresh fruits, vegetables, and tree nuts. Such knowledge is essential to the development of scientifically validated “best practices” for mitigating those risks at the pre- and post-harvest production levels. WCFS scientists work collaboratively with other scientists in universities, industry and governmental agencies across different regions of the United States and internationally. WCFS research and outreach programs in partnership with FDA have played a pivotal role to inform policy related to the development of the proposed and final Food Safety Modernization Act (FSMA) Produce Safety Rule and the proposed and final Preventative Controls Rule under FSMA.

Examples of research projects supported through WCFS and leveraged funding:

California Longitudinal Study


FDA, in collaboration with the California Department of Food and Agriculture, the University of California, Davis’s Western Center for Food Safety, and agricultural stakeholders in the Central Coast of California, is conducting a multi-year study in the Central Coast agricultural region to identify environmental factors that significantly contribute to the introduction, persistence, growth, and spread of foodborne pathogens that could contaminate produce during production and harvest. We are also interested in identifying factors that lead to pathogen die-off.

Agricultural Water


Agricultural water contaminated with microbial pathogens can elevate the risk of foodborne illness when used as source of irrigation water or for other purposes (e.g., crop protection sprays, agrochemical mixtures) that result in contact with the edible portion of the produce.

    • Facilitating implementation of FSMA’s agricultural water quality regulations: Case study for cooperative monitoring
    • Assessment of the benefits of cooperative monitoring in the Gulf South
    • Project feasibility to assess microbial survival on equipment surfaces during long distance transport between southwestern US growing regions and central coastal California
    • Assisting rural communities to comply with FDA’s water quality regulations: Hold-time evaluation
    • Evaluation of the risk of using tail water sources for the production of leafy green lettuces and herbs (also funded through the Center for Produce Safety)
    • Movement of Salmonella through farm ponds, irrigation distribution systems and transfer to fresh produce at medium-size mixed produce farms in Georgia (also funded through Center for Produce Safety)

Biological Soil Amendments


The microbial food safety risks from using raw animal manure and other untreated biological soil amendments of animal origin (BSAAOs) are well documented. Nevertheless, some growers still rely on untreated BSAAOs for economic and practical reasons, and recent research has shown that their use varies widely by geographic region, farm size, and type of crop/manure. The Produce Safety Rule specifies that BSAAOs must be applied in a manner that does not contact covered produce during application, but has reserved the specific harvest interval(s) after application until further research and a risk assessment are conducted. In contrast, application of FSMA-compliant composted or treated BSAAOs to soils for production of fresh produce is expected to result in reduced risk of pathogen contamination with minimal public health risk. But, unexpected risk may occur from cross-contamination or regrowth of pathogens.

    • Evaluation of application intervals for the use of untreated animal manure as a soil amendment in conventional and organic fresh vegetable production (also funded through USDA Specialty Crop Research Initiative and USDA Organic Research and Extension Initiative)
    • Prevalence and levels of Salmonella and STEC in raw manure in different geographic locations of the western and eastern U.S.
    • Persistence and transfer of generic coli and STEC on organic farms that integrate rotational sheep grazing and fresh produce production (also funded through Center for Food Animal Health)
    • Understanding and enhancing the safe use of biological soil amendments: Evaluating potential microbial risks from commercial heat treated poultry pellets

Domesticated Animals & Wildlife


Many of the major enteric foodborne pathogens (Campylobacter, STEC, Salmonella, Cryptosporidium spp., etc.) are zoonotic, meaning that they have animal reservoirs that may shed the pathogen in their feces. Produce-related outbreaks have been caused by fecal contamination of plants or surrounding watersheds by domesticated animals (especially livestock) or by wild or feral animals. Even a low level of contamination from fecal-borne zoonotic enteric pathogens can be a significant public health concern due to the low infectious dose of these pathogens, the potential for attachment and possibly ingress into edible parts of plants, and the lack of a post-harvest “kill step” to destroy pathogens on fresh and minimally processed produce.

    • Strengthening good agricultural practices for reducing bacterial contamination of leafy greens grown in central coastal California
    • Salinas field trials to enhance quantitative microbial risk assessment following simulated wildlife fecal contamination in romaine lettuce fields
    • Sources and modes of transmission of foodborne pathogens in orchards and adjacent concentrated animal feeding operations (CAFO) in central valley California (also funded through Center for Produce Safety)
    • Identification of pre-harvest risk factors for foodborne pathogen transfer to leafy greens grown in the southwestern desert (also funded through Center for Produce Safety)



Postharvest handling of fruits, vegetables, and nuts is the stage of crop production immediately following harvest, including cooling, cleaning, hulling, sorting and packing. Foodborne pathogens can be introduced into the postharvest environment from product contaminated during pre-harvest production or harvest. Contamination may also occur due to unsanitary conditions including pests, dirty equipment, poor microbial water quality, and lack of hygienic practices by workers. Some pathogens (e.g., Listeria monocytogenes, Salmonella spp.) may persist for long periods of time in postharvest facilities, especially if the environment promotes formation of biofilms.

    • Evaluating microbiological food safety risks associated with tree nut harvest equipment
    • Postharvest studies to support the scientific basis for sanitation controls in treefruit packinghouses
    • Postharvest handling of onions
    • Postharvest studies to support the scientific basis for implementation of Produce Safety Rule and Preventative Controls at produce packinghouses and nut hullers and dehydrators

Indoor Agricultural Systems


Indoor agriculture (including aquaponic systems that integrate plant and fish production), are emerging as a sustainable approach to fresh produce production. The unique ability to regionalize these indoor systems (partially independent of acreage and climate), and the potential to serve different populations (urban, peri-urban, rural), make indoor/vertical agriculture increasingly attractive internationally. Best food safety practices outlined in FSMA also apply to these systems, but there is also a need to conduct research and outreach to fill knowledge gaps related to unique aspects of pre- and post-harvest production under these systems.

    • Evaluation of zoonotic food safety risks in aquaponic production of vegetables and tilapia
    • Evaluating microbiological food safety risks associated with condensate that forms in protective or greenhouse structures