Source: UNIVERSITY OF FLORIDA submitted to
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2024
Grant Year
Project Director
Danyluk, M. D.
Recipient Organization
Performing Department
Non Technical Summary
Many studies have addressed specific aspects of pathogen contamination and control in produce production, but most have focused on a single step in the food chain or on a single pathogen in a single crop. An integrative framework applicable to different food-pathogen combinations is not currently available to support produce safety decisions. The need for a systematic validation of food safety metrics is articulated by white papers, metrics from commodity groups, and opinions expressed by food safety regulatory agencies. This project will focus on the following objectives to develop and implement decision-making tools to enhance produce safety:Find approaches to decrease introduction of microbial food safety hazards onto specialty crops from agricultural water.Discover new strategies to reduce introduction of microbial hazards into specialty crops via biological soil amendments of animal origin during production.Evaluate the risk of current on-farm preharvest and harvest practices for potential contamination of specialty crops with microbiological hazards.Determine the harborage, sources and patterns of contamination, and mitigation strategies for specialty crop contact surfaces in packinghouses to quantify risks.Create quantitative farm-to-fork risk assessment models of pathogens on produce.Develop models for the evaluation of economic costs and benefits associated with produce pathogen reduction strategies.Extend knowledge and awareness of the study outcomes through a translational bridging and leadership role.The project will be highly integrated, with stakeholder input guiding the goals, risk assessments, economic analyses, and extension activities, and provide an ongoing platform for stakeholder interaction.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
This proposal provides the specialty crop industry with tools to effectively manage risks while making most efficient use of available resources. Our approach will provide objective assessment of health, economic, and risk impacts of food safety systems. We will identify the most important factors that drive food safety risks by explicitly acknowledging and analyzing uncertainty. We will help the specialty crop industry 1) develop and validate scientifically supportable food safety metrics that are applicable in a variety of growing regions, commodities, and farm sizes; 2) provide scientific and technological knowledge to develop metrics important to enhancing produce food safety; and 3) identify improved approaches and techniques that allow the attainment of the metrics to be verified and cost effective. Achieving these goals are critical for specialty crops as produce-borne outbreaks and food recalls have caused serious public health problems and devastating economic impacts to individual businesses which extend across the produce industry.The key rationale behind this project is to provide a systems-based decision-support framework to evaluate measures for controlling pathogens on produce that will support an integrated view and decision-making roadmap for all vested parties.
Project Methods
This project will be carried out by a consortium of ten universities and one federal agency that have been selected in part for their geographical locations and expertise in specific specialty crops. The work is envisioned to include diverse farms and facilities of varying sizes, including consideration of both conventional and organic practices, and perennial and annual crops, grown close to and above the soil (including, leafy greens, tomatoes, cucurbits, berries, and tree fruit). The research team is capable of employing a full range of appropriate methods, from microbiological culture and non-culture based methods to molecular biology to highly sophisticated mathematical modeling methodologies. The philosophy underlying the research proposed in this project is to find practical and scalable solutions for real problems. The approaches employed will focus on translating research into practices that are feasible to implement within various pre-and postharvest sectors. Each of the research sub-project will be conducted in at least two locations and on at least two crops to ensure effective consideration of regional and seasonal differences. Careful attention will be paid to identifying and testing appropriate technologies and protocols for small-, medium-, and large-size farms and facilities. This includes addressing appropriate economic and regulatory feasibility assessments to adequately address the transdisciplinary nature of the problems. Frequent communication with our stakeholders is one of the key factors for success of this project.

Progress 09/01/20 to 08/31/21

Target Audience:Produce researchers and growers, Extension Agents, Extension Specialists,Researchersstate/federal agencies, Government officials, Producers, Processors, Packers, Consultants, Buyers, etc.? Changes/Problems:Due to ongoing COVID challenges, all objectives began slower than anticiapted during preparation of the proposal. This included being able to be in the laboratory & complete experiments, hiring staff and students, establishing field trials, and in person meetings including extension events. We used this opportunity to spend more time interacting with our Produce Advisory Committee, and ground truthing all experiments and experimental designs with them, which included pivoting as necessary, and interacting as a larger group in an online forum. Specific objective changes/problems in approach and the resasons for these changes include: 1: The inability to get students and staff into the laboratory to conduct experiments due to Covid protocols delayed the onset of bench-top research, however, it allowed our team to better prepare for research execution, SOP development, and data sharing platform refining. 2: The hiring of personnel at USDA ARS (a post-doctoral research associate) has been delayed due to the COVID-19 pandemic and USDA staffing limitations. 3: Time during this period included a focus on group collaboration, QMRA framework planning, and experimental design development due to constraints regarding COVD and staffing limitations. 4: PI Critzer, leading objective 4, changed positions on August 1, 2021 moving to a research and teaching faculty appointment at the University of Georgia. Therefore, Washington State University will no longer be a subaward for the project moving forward, but representatives from the tree fruit industry will continue to provide insights and expertise on the PAC. 5: Florida team was not able to recruit a qualified graduate student to participate in the risk assessment activities. The position has been changed to a post-doc position and the application procedure is in the final stage. 6: We discovered that we will likely not be able to use Neilson data for 6.2 due to licensing issues. Instead, we will use similar IRI data that is available for purchase through USDA. 7: n/a What opportunities for training and professional development has the project provided?Online, asynchronous course on Environmental Monitoring Programs Foundations (Levels 1-3) in development (working group meeting 11/3/21; learning objectives outlined How have the results been disseminated to communities of interest? Produce Safety Webinar Series (November 4, 2021, December 3, 2021, monthly in 2022 Jan-May, Sept-Dec); 1.5 content (1 h presentation, 30 min live Q & A) November 4th, 2021 Webinar featured Dr. Trevor Suslow 535 registrations, 276 unique viewers, 358 total users Produce Safety Science Social media platforms for direct outreach and dissemination of results/information (official launch November 1, 2021) Twitter profile: 78 followers, daily posting since November 1, 2021 Instagram profile: 50 followers, daily posting since November 1, 2021 Contact Website Resource page: each week posting open access research and extension articles detailing produce safety topics; every month posting a key takeaways summary of the Produce Safety Webinar Series presentations What do you plan to do during the next reporting period to accomplish the goals?1: During the next reporting period, each regional sub-lead under Objective 1 will have begun generating log reduction data for both Salmonella and E. coli for two water sources. We will also have begun aligning field design for agricultural water treatment experiments conducted at field scale. 2: Field studies at three sites will be conducted evaluated survival of E. coli and transfer to crops. Laboratory data will be utilized to simulate field conditions using a suite of pathogens across all CONTACT objectives. 3: Within the next reporting period, field trials will be conducted across four states. These studies will be used to improve approaches and understanding regarding persistence of protozoa and viruses in vegetative matter and soil; assess the risk of crops in contact with soil or plastic mulch; and determine patterns of bacterial survival and transfer to crops from bacteria introduced by wildlife intrusion. 4: Work will commence with team members executing the agreed upon experimental designs in the coming reporting period. 5: Continue collecting water quality data from produce growing throughout different regions in the US and analyze these data using statistical, machine learning and mechanistic modelling approaches. Literature will be surveyed for available QMRA models for produce safety and combining these in an initial farm-to-fork model. We will develop a baseline risk assessment model to estimate the burden of foodborne illnesses due to consumption of contaminated fresh produce. We will develop modules for the QMRA to specifically incorporate new data generated by obj. 1-4. We will continue to support obj. 1-4 in study design, data management and data analysis, as well as interact with investigators from obj. 6 and 7 to support their work. 6: Over the next reporting period we will continue to focus on building and conducting empirical analyses based on secondary data. By the end of the period, we expect to have 2-3 publications submitted or in preparation for submission to peer reviewed journals. We will also continue to work with other objective teams to ensure that the data we receive from them will be useful. Additionally, we will continue to develop, implement, and monitor data governance practices across the project. 7: Develop social media accounts ( and A Twitter Produce Safety Science (PS_SCI) account will be created to communicate and interact with public (78 followers, active since Nov 1, 2021) and an Instagram Produce Safety Science (PS_SCI) account was created to communicate and interact with public (50 followers, active since Nov 1, 2021). As well as a new Produce Safety Webinar Series, planned each Jan-May, Sept-Dec with summer months off. Each month a timely produce safety topic will be dissected and covered in a 1 h presentation or panel format followed by 30 min of live question and answer with all attendees. Our first Produce Safety Webinar series #1 (November 4, 2021) had 535 registrations, 276 unique viewers, and 358 total users-(which includes call-in's).Continue social media campaign of daily posting M-F (research and extension updates/behind the scenes Monday; meet the team Tuesday; highlight webinar/active trainings/news Wednesday; dissecting the FSMA Produce Safety Rule Thursday (or clarifying a confusion topic); best thing we've read this week Friday (highlighting a research or extension open access resource - which is also posted on our website under the resource tab. Continue Produce Safety Webinar Series (#1 Nov - Adjacent Land Use; #2 Dec - Agriculture Water Treatment; #3 Jan - Risk Modeling; #4 Feb - Agricultural Teas; #5 Mar - Cyclospora; #6 Apr - Data Sharing; #7 May - Supply Chain; Break for the summer production season; picking back up in Sept #8 - Audits; TBD. Each webinar series consists of 1 h presentations/panels with a 30 min live Q & A. After each webinar, a short white paper on key takeaways is drafted and posted on social media/website for all registered attendees to access/use for review/recap/etc.

What was accomplished under these goals? 1: The team has currently focused on aligning each regional lead and laboratory to begin bench-top agricultural water treatment experiments. This includes the preparation and sharing of E. coli and Salmonella cultures for distribution and treatment evaluation. Additionally, the team has identified water treatment chemistries most often utilized by industry and has selected those that will be used for evaluation. Historical data sets are also being shared with the modeling team to support hazard risk assessment objectives. 2: We have identified an experimental framework to address critical produce safety data gaps through coordinated scientific approaches. Efforts have focused on the collection of field and laboratory data that can be easily transferred machine learning models to attain metrics that can be used either in national or regionally specific approaches. Specifically, common field and laboratory methodology across sub-objectives has been planned and formalized. Because of the 2020 outbreak of Salmonella Newport associated with onions, transfer of pathogens to onions from amended soils is going to be evaluated. Repeated outbreaks of E. coli O157:H7 for leafy greens refined the focus of sub-objective 2.3 to investigate pathogens in soil/manure generated dust Laboratory methods to evaluate these events, along with reasonable experimental parameters for soil and amendment matrices. 3: We have identified an experimental framework to address questions pertinent to the discovery, validation, and implementation of metrics used to enhance produce food safety pertaining to 1) persistence of protozoa and viruses in vegetative matter and soil; 2) the impact of ground contact on drooping or dropped crops; and 3) risks associated with animals in protected agriculture. In achieving this accomplishment, treatments and parameters necessary to improve knowledge and develop appropriate metrics were determined. 4: The team members working on objective 4 coordinated with the PAC to determine details of the experimental approach for both subobjectives which orient around management of postharvest water in dump tanks and flumes (4.1) and food contact surfaces encountered at harvest at during postharvest handling (4.2). Data from this work will provide scientific and technological knowledge to develop metrics important to enhancing produce safety, specifically with the aim of quantifying risk of bacterial and viral foodborne pathogen transfer to produce during postharvest washing under industry-relevant conditions (4.1) and quantifying the transfer of bacterial foodborne pathogens to harvest and postharvest food contact surfaces as well as produce (4.2). The team also coordinated with objective 7 to create two draft surveys on environmental monitoring programs and sanitation that will be released for stakeholder participation in the next reporting cycle. 5: A postdoc was hired to specifically develop water quality models. Literature related to the survival of pathogens in soil, and transfer from soil to fresh produce has been collected. We developed a conceptual model for the microbial risk assessment framework and interacted frequently with objectives 1-4 to align experimental and observational study plans with the plans for QMRA. This has resulted in draft statements of purpose for the risk assessment. We developed database sheets to share water quality data from previous studies and received four datasets from different regions in Florida. Analysis of these data has been initiated. 6: Subobjective 6.1: Focus on model building, literature review and exploration of potential data sources. A basic empirical framework was built for assessing burden of illness and updated estimates for cost-of-illness was collected from literature. Design of food attribution models for identified pathogens has begun. Subobjective 6.2: Completed a literature review to examine potential models for use in our analysis, collected outbreak and recall data for leafy greens contaminated with dangerous pathogens and identified scanner data from IRI that will be purchased and merged with event data to allow for evaluation of the effect of food safety events on product prices and demand. Subobjective 6.3: Estimated consumption for rarely consumed raw produce commodities using NHANES data using different assumptions. Subobjective 6.4: Sought to work with other objective teams to ensure we will be able to complete future analyses that are dependent on the data they generate. We have worked most closely with objective 5 to give input on the risk assessment. Data Governance: Our data governance efforts have worked towards creating a shared set of protocols for the collection and handling of data. Specifically, we examined data governance models for food safety data, including developing a cross-sectional survey to assess current data collection and management practices within the private sector. We also provided input on development of study protocols and selection of REDCAP as data tool (a pilot tool is currently under team review). Finally, we conducted webinars on calculating sample sizes and data management, including tidy data. 7: Efforts were focused on virtual or online activities and outreach due to the COVID pandemic. An online, anonymous survey was distributed to the produce community to capture the top produce safety concerns. N=311 de-identified responses were collected. Survey data is being analyzed; publication pending, estimated Feb 2022.


  • Type: Journal Articles Status: Published Year Published: 2021 Citation: azquez*, K.M, R. Mu�oz-Carpena, M.D. Danyluk, A.H. Havelaar. 2021. Parsimonious mechanistic modeling of bacterial runoff to inform food safety management of agricultural water quality. Appl. Environ. Microbiol. 87(15):e00596-21. doi:10.1128/AEM.00596-21.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Howell, A.; Kowalcyk, B.B. (2021). Analysis of Methodology Used to Classify Produce Commodities as Rarely Consumed Raw. International Association for Food Protection Annual Meeting.