Research

We are seeking integrated livestock farmers for a study assessing the dynamics of foodborne pathogens (e.g. shiga toxin producing E. coli (STEC) and Salmonella) in integrated crop-livestock systems involving grazing in orchards (fruit & nut trees).

For more information, click here: Orchard Research Flyer

The increasing popularity of small-scale farms and integrated crop-livestock systems reflects growing consumer interest in local, organic food production and sustainability. Dr. Pires’s research and extension focus is focused on food safety issues unique to small-scale farms including integrated farms that grow livestock/poultry and crops on the same land. However, potential food safety risks, associated with the interface of animals and crops on these mixed crop-livestock farms, are largely unknown. Dr. Pires’ research and outreach work has focused on characterizing the unique features of these diversified systems and identifying mitigation strategies to reduce the spread of foodborne pathogens in pre-harvest small farm environments. 

Many certified organic producers and small-scale farms rely on the use animal-based soil amendments (i.e., manure, compost) to improve soil fertility and quality. To reduce the microbial contamination of produce, a minimum waiting time is required between the use of soil amendments and crop harvest. One of the goals of our research is to characterize and identify risk mitigation strategies to reduce the risk of microbial contamination from foodborne pathogens commonly associated with human illness in fresh produce organically grown with animal-based soil amendments. Our ongoing projects are collaborative and involve the participation of the farmers, organic industry members, farm advisors (UC ANR CE), non-profit organizations (e.g. The Organic Center, Organic Trade Association), extension educators, researchers (University of Minnesota, University of Maine Extension, Cornell University, UC Davis (SVM, WCFS)), and state and national governmental agencies (e.g. USDA-ARS, USDA-ERS). The results of the data collected from our research directly benefits organic farmers and consumers by creating strategies to continue utilizing raw manure while limiting food safety risks. Moreover, our research will provide science-based recommendations to create new metrics for appropriate time-intervals used between untreated manure and harvest, and will inform ongoing FDA risk assessments and the organic and fresh produce industries.

Click here to learn more about the Multi-Regional Risk Analysis of Farm Manure Use.

Grazing Soil Health Factsheet 2023 Integrated crop-livestock growers diversify their production systems by including a rotation of livestock in crop fields (i.e. re-integrating animals back into cropland), which provides numerous benefits. However, these systems face challenges, including potential food safety risks and compliance with the federal regulations. Our research focuses on applying epidemiological quantitative tools and laboratory methods to characterize these systems and identify mitigation strategies to reduce food safety risks, particularly for those farms that integrate animals and produce production. Some of the various aspects of food safety that our projects are looking at include: 1) prevalence and risks factors associated with major foodborne pathogens in diversified farms, 2) prevalence of Shiga-toxin producing E. coli (STEC) in sheep and survival of generic E. coli in the soil in farms integrating crops with rotational grazing, 3) ecological dynamics of Campylobacter on diversified farms raising multiple livestock species, and 4) food safety risks and Salmonella prevalence in products sold in farmers markets. Our projects provide critical information that can be incorporated into statewide and nationwide guidelines aimed towards developing best practices for risk mitigation of foodborne pathogens and improving animal health on alternative agricultural systems.  

Click here to learn more about one of our ongoing projects!

See grazing cover crops fact sheet for our ongoing project results Grazing Soil Health Factsheet 2023

The increase in the number of small-scale livestock farms and backyard livestock production in the US may create an increased risk for zoonotic, foodborne and/or emergent pathogens, and drug residues in food supply, as well as increased animal health and welfare concerns. Our lab has developed outreach and mitigation tools that farmers, extension educators (advisors and extension specialists), government agencies, and veterinarians may use for education, good management practices, and animal health surveillance. We have partnered with state universities (Washington State University, Colorado State University, and Oregon State University) and state and federal governmental agencies to synergize research and extension efforts to characterize and evaluate the disease risk of livestock raised on small-scale farms or in backyard premises.

In addition to our outreach tools, one of our ongoing projects is focused on evaluating the implications for disease transmission in the wildlife-livestock interface. Evaluating the interface between wildlife and livestock is crucial in keeping the food supply safe and protecting California’s agriculture. Our project assesses the distribution of domestic swine raised outdoors in California and evaluates the disease risks associated with the interface with feral pigs.

Cooperative Extension Specialists focus on applied research and extension in several areas including animal agriculture, environment and natural resource management and 4-H youth programs.

For more information, visit their website.