S1077: Enhancing Microbial Food Safety by Risk Analysis

(Multistate Research Project)

Status: Active

S1077: Enhancing Microbial Food Safety by Risk Analysis

Duration: 10/01/2018 to 09/30/2023

Administrative Advisor(s):

NIFA Reps:

Statement of Issues and Justification

The Centers for Disease Control and Prevention (CDC) estimates that one in six Americans becomes sick each year from eating contaminated food, with about 48 million cases of foodborne illness, 128,000 hospitalizations, and 3,000 deaths occurring each year from foodborne pathogens in the U.S. (Scallan et al., 2011). Norovirus is the leading cause of foodborne illness cases in the U.S., accounting for 5.5 million annual cases (58%), followed by non-typhoidal Salmonella (1.0 million, 11%), Clostridium perfringens (1.0 million, 10%), and Campylobacter spp. (0.8 million, 9%). The USDA Economic Research Service estimates that the economic burden of 15 leading foodborne illness acquired in the U.S. is $15.5 billion. Salmonella, Toxoplasma gondii, Listeria monocytogenes, norovirus, and Campylobacter are the top 5 contributors, costing $3.6, 3.3, 2.8, 2.3, and 1.9 annual billion, respectively (Hoffmann et al., 2015). Poultry, complex foods, pork, produce, and beef rank as the top five food commodities most commonly implicated in foodborne illness, with Campylobacter-poultry, T. gondii-pork, L. monocytogenes-deli meats, Salmonella-poultry, and L. monocytogenes-dairy as the leading the pathogen-food combinations with the highest cost of illness burden (Batz et al., 2012).


The long-term goal of this project is to perform comprehensive and integrative risk-based research, education, and outreach to improve food safety and advance public health. The project establishes multi- and trans-disciplinary teams of academics, food producers/processors, retailers, consumers, and local, state, and federal agriculture and health officials. The research conducted under this project contributes to the understanding of foodborne pathogen ecology and transmission—including the emergence and spread of antimicrobial resistant bacteria--in fresh and processed foods so that more effective mitigation strategies can be designed and applied at various stages of the farm-to-table continuum.


The food industry faces problems that are sufficiently complex to render effective research-based solutions are beyond the scope of any single researchers programmatic outputs. Therefore, these complex issues are most efficiently addressed through multidisciplinary efforts by experts in risk analysis, microbial ecology, epidemiology, food safety microbiology, experimental design, data analysis, and other complementary research areas. This project has been specifically designed to address critical needs of the fresh and processed food industries by developing a thorough understanding of how foods become contaminated with foodborne pathogens and how transmission can be further reduced.


Outreach objectives have been developed and integrated into the overall program design to support these research efforts. These objectives include communication of risk-based management recommendations to stakeholders as well as to those who interact with stakeholders. Communication strategies are precisely tailored to farmers, processors, distributors, retailers, and consumers. Message content focuses on risk-based strategies for microbial control deemed critical for each target audience to achieve the greatest strides in improving food safety. Outreach to those who advise producers and consumers (e.g. educators, extension personnel), but who are not part of the project, will be achieved through ongoing professional development opportunities to disseminate key information as outlined in the “Milestones” section.


The results of this project will directly impact industries that handle foods most commonly implicated in foodborne disease outbreaks, including low-moisture foods (especially spices, nuts, and dried fruits); fresh, minimally, and shelf-stable processed produce; dairy; fresh and further processed seafood, meat, and poultry products (including fully cooked and ready-to-eat products subject to post-process contamination), as well as other multi-component and processed foods. Moreover, the threats and specific needs for food safety in the food industry are constantly evolving and require continued risk-based solutions in the face of these changes. Therefore, the project proposes risk-based solutions for the effective control of foodborne pathogens across food commodities in the U.S.

The data generated by this project serves as the foundation for the development of predictive models that can be used to better understand pathogen contamination at specific points of food production and for validation of pathogen reduction interventions. Furthermore, this group will work to standardize protocols among laboratories so that research results can be more easily and directly compared. These outcomes will contribute to the long-term profitability and sustainability of the food industry by providing enhanced tools for microbial control and mitigation.


Having a mechanism to establish formal collaborations under the umbrella of a single goal will enable scientists in this group to access external funding more successfully than if collaborations were formed ad hoc because of the multi-disciplinary nature of food safety research. Furthermore, the scientists in this project are highly committed to 1) the recruitment of a diverse student population, 2) responsible research conduct, 3) outreach and education to communicate current research, and 4) the advancement of food safety science by keeping one another accountable for their share of results.


This multi-state project also proposes integrative and innovative approaches to teaching food safety at the undergraduate and graduate levels. Students will be exposed and trained in the use of modern molecular techniques such as next generation sequencing, metagenomics, and bioinformatics. Partnerships with industry colleagues will allow students to work on current and emerging food safety challenges and to think creatively and critically to solve them.


The need for training programs to support the next generation of food safety professionals and to increase the ethnic and cultural diversity among food safety researchers to better reflect the demographic composition of the U.S. population is clear. Greater diversity is critical from the perspective of educational opportunity, but also relative to food safety and public health because various regional and ethnic groups may face different food safety challenges. Cultural and personal sensitivity and competence among food safety professionals is necessary, and the project proposes to train a new generation of food safety students with both a strong technical background and the soft skills needed to help them succeed in their future careers.

Related, Current and Previous Work

Current Work, S1056 March 2013-September 2018. Since 2013, members of the previous S1056 group have authored over 525 peer-reviewed papers on the subject of food safety. Findings described in these publications have improved the understanding of the microbial ecology, survival, inactivation and biology of foodborne pathogens. All these inputs are essential for informing risk analysis and assist with food safety policy development. The focus on risk communication of S1056 has resulted in more than 130 peer-reviewed extension publications, which are written for lay audiences to describe outcomes of research, practical applications of these findings, and development of food safety plans to mitigate risk with in the food industry.

While the research and extension outputs of S1056 members are notable, the collaborative efforts (defined as funded projects, extension activities, or co-authored publications) between members speaks to the strengths of this multi-state project. There were more than 150 collaborative efforts between members at 39 different institutions over the previous five-year period which encompasses the active dates of S1056 (see Table 1 in the Additional Documents Section). There have been 14 new institutions which have joined S1056, creating 59 collaborations. Actively recruiting members from Kansas State, North Dakota State University, New Mexico State University, Oregon State University, University of Arkansas- Pine Bluff, University of Connecticut, University of Illinois, University of Maine, University of Maryland, University of Massachusetts, University of Puerto Rico, University of Wisconsin, and Wayne State University speaks to the efforts of the previous S1056 project to further extend collaboration amongst members of the project moving forward. Active recruitment of members from minority serving institutions including New Mexico State University, University of Arkansas at Pine Bluff, and University of Puerto Rico, also demonstrates the dedication to expanded inclusion of faculty from all institutions where food safety research is being conducted.

Food safety is an important public health and economic concern in the U.S. and worldwide. As such, there are regional, domestic, and global research emphases to better understand foodborne pathogens, disease transmission and prevention. For example, in 2017 alone, there were nearly 40,000 research papers published on the topic of the most common foodborne pathogens (11 bacterial, 3 parasitic, and 1 viral) occurring in the US (See “Table 2” in the Additional Documents Section). Federal funding for agricultural research in the past few years has not kept pace with increasing demands, but resources for food safety research have been prioritized. The availability of resources for food safety research has attracted a large number of investigators not traditionally trained or previously involved in this field. This influx of new researchers brings exciting new ideas and approaches, along with the opportunity for novel interdisciplinary strategies to address some of the most pressing food safety challenges. However, the competition for available resources has increased, and the new cohort of food safety researchers may not be fully aware of past food safety efforts and advances from a practical and applied perspective.

We recognize the vast amount of food safety research currently conducted around the world. It is the purpose of this multi-state project to contribute to the coordination of food safety efforts performed at land grant institutions in the United States. The networking capability of this group permits the formation of multi-state, regional, or other appropriate teams that build on the strengths of different individuals to develop innovative approaches to food safety that also limits the redundancy in research focus. At the same time, this multi-state project provides investigators new to the field mentoring opportunities to better understand stakeholders’ needs and challenges involved with the conduct of applied research.

The objectives of our new proposal are the natural continuation and expansion of the work completed on S1056. These objectives reflect a commitment to addressing current and emerging food safety concerns in 2018 and beyond. While the membership has grown extensively during the project duration, we have identified one sector for which future collaborative efforts and project involvement would be beneficial. By actively recruiting food safety researchers within different sectors of the federal government, such as USDA-ARS, FDA, and CDC during the next project we hope to successfully once more expand collaborative efforts and better understand current food safety research focuses across the United States.

The objective areas of S1056 were shifted to focus on Risk Assessment, Risk Management and Risk Communication. While specific objectives of the project have evolved, members feel that these areas of focus are appropriate and very timely to capture the logical progression of research inputs from many different facets of food safety research. The prevalence of foodborne pathogens and risk factors involved will be covered under 1) Risk Assessment; potential control strategies will be covered under 2) Risk Management; and the knowledge obtained from objectives 1 and 2 will be transferred to stakeholders under 3) Risk Communication. The adoption of this risk-based systems approach allows researchers to: (i) continue to be engaged along the entire farm-to-fork continuum on a variety of food products including dairy products, meat, poultry, seafood, fruits, spices, dried fruits and nuts, and vegetables; (ii) work on a number of bacterial, parasitic, and viral pathogens; (iii) to evaluate emerging detection and decontamination technologies and processing methods; (iv) to input data into more complex and all-inclusive mathematical models; and (v) to transfer this information through innovative and evolving methodologies to stakeholders along the continuum. 

Related Work. It is important to establish the unique nature of any multistate project upon renewal. The following five other multi-state projects identified in the NIMSS search included some mention of food safety objectives:

Project Number Title Duration 18335 Enteric Diseases of Food Animals: Enhanced Prevention, Control and Food Safety 10/01/2017 - 09/30/2022 NECC1701 Luminescence Techniques for Food Quality, Stability & Safety 10/01/2017 - 09/30/2022 S294 Quality and Safety of Fresh-cut Vegetables and Fruits 10/01/2017 - 09/30/2022 NC1023 Engineering for Food Safety and Quality 10/01/2015 - 09/30/2020 W4122 Beneficial and Adverse Effects of Natural Chemicals on Human Health and Food Safety 10/01/2017 - 09/30/2022
Amongst these active projects, there are none which overlap significantly with the proposed objectives described for this project. Projects 18335 and S294 are both commodity-specific. NC1023 has a focus on food engineering rather than food safety. NECC1701 focuses strictly on methods development, and W4122 focuses on chemical rather than microbiological aspects of food safety as well as health.


  1. Risk Assessment: Characterize food safety risks in food systems
  2. Risk Management: Develop, validate, and apply science-based interventions to prevent and mitigate food safety threats
  3. Risk Communication: Convey science-based messages to stakeholders to improve food safety behaviors and practices


This proposal describes a collaborative effort between researchers at multiple institutions in the US and includes basic and applied research over a wide range of food commodities with a goal of risk-based research and outreach to address the safety of food from farm to fork. The principal investigators (PIs) meet annually to foster and cement collaborations, and expand their many regional and national connections in food commodity production, processing, distribution and retailing across the US. The PIs have, and continue, to work to standardize microbiological methods among laboratories so that results may be directly comparable and reproducible. Whenever appropriate, standard methods such as those from the Compendium of Methods for the Microbiological Examination of Foods, the U.S. Food and Drug Administration’s Bacteriological Analytical Manual (BAM), or other applicable sources (AOAC, USDA, etc.) are used for the enumeration or identification of foodborne pathogens. Additionally, records of the specific source of materials and reagents used will also be compared in cases where notable differences are identified, as inconsistencies or differences in the production practices of different suppliers can affect the observed results. The use of standardized, validated methodologies—and the materials used to perform them—are often overlooked but critically important aspects of collaborative studies. PIs of this group have already previously developed and validated many of the methods that we propose to use here. However, additional cross- laboratory validations of new and emerging methods are continually evolving and include: evaluation of strain, inoculum preparation and concentration method, impact of laboratory humidity, and recovery methods.

Feedback from the food production and processing industries on a notable amount of food safety research has suggested that concentrations of microorganisms used in the laboratory are often too unrealistically high to be of practical value. Indeed, the experience of PIs confirms that concentration and inoculation-preparation methods often have significant impact on pathogen behavior (Flessa et al., 2005; Uesugi et al., 2006; Montville and Schaffner, 2003) and thus interpretation and external validity of results. However, in other cases, inoculum level or culture preparation plays a minor role. The ability of researchers to meet to discuss, compare, and evaluate influence of these factors is a vital component of this project.

The proposed research reflects the diversity of the member scientists, and will cover food commodities including aquaculture (fish and shellfish); meat (beef, pork sheep, goat, and other); poultry and eggs; dairy; fruits; vegetables; low moisture foods (primarily nuts and dried fruits); dry, raw, ready-to-eat and processed foods; and animal feeds. In addition to multiple commodities, numerous conventional and emerging pathogens, including bacterial (Salmonella spp., Campylobacter spp., Vibrio spp., shiga toxin producing Escherichia coli (STEC), Listeria spp., Clostridium spp., Yersinia spp., Shigella spp., Staphylococcus spp., Enterococcus spp., Mycobacterium spp.), viruses (hepatitis A/E, norovirus, FRNA phages), and parasites (Cryptosporidium spp., Cyclospora spp., Toxoplasmosis spp. and Giardia spp.) are investigated by members of this group. The project also includes PIs that do research on these pathogens and their interactions with each other and other members of the host microbiota.

General Methods Applicable to Objectives 1 and 2.
A combination of basic and applied science questions will be addressed using laboratory experiments, field trials, and epidemiological investigations.

Food Commodities. Food commodities will be obtained from producers or processors, or purchased from local retailers or distributors. Occasionally, specific animals may be utilized. Samples will be stored at appropriate temperatures prior to use. Time between obtaining the foods/samples and experimental use will be minimized. Commercially relevant varieties will be utilized.

Pathogens. Strains that have been associated with outbreaks from the commodities of interest will be used whenever possible. If not possible, other significant pathogenic strains will be selected. These strains are often available in the PIs’ laboratories and their availability amongst participating researchers will be facilitated in part as a result of this project. As appropriate, antibiotic-resistant variants of these strains have been isolated, and several have been modified (i.e. addition of fluorescent proteins) to further facilitate their study. Validated non-pathogenic surrogate species of various microorganisms are also available for those situations where the use of such organisms may be appropriate. Effort to screen and evaluate additional surrogate species will also be a part of this project. Strains of different genera can be engineered to contain traits noted above as required. The modifications will allow, when necessary, easy identification of the inoculated strains in the presence of high levels of background microflora. Additionally, any animal tissue samples or animal models used to cultivate or study some of these pathogens will also be made available. This is especially relevant in the case of viruses, as two recent tissue culture methods for human noroviruses have been reported (Ettayebi et al., 2016; Jones et al., 2014). One goal of the project is to recruit a member who has access to and can utilize one of these systems.

Inoculation. Frozen stock cultures of bacterial strains are typically stored in glycerol stock solutions at -80°C. Prior to use strains are streaked onto non-selective media supplemented with selective agents as appropriate. Inocula may be prepared from plate or broth cultures, and may or may not be washed (i.e. 1×PBS wash is commonly utilized to remove nutrients from media and microbial waste products) prior to use. Appropriate carrier media will be used for inoculations at volumes, levels and methods typical for the commodity being evaluated or assay conducted. Standard methods will also be used for viral or parasitic inocula. Methods for inoculation of food commodities will vary, as required, to best mimic standard commodity-specific criteria and the specific hypothesis-based research questions being addressed.

Recovery of Pathogens from Inoculated Samples. Sample sizes, buffering solutions, and maceration methods will vary depending upon commodity- and experiment-specific requirements. Enumeration of bacterial pathogens following serial dilution using standard plating techniques onto selective and non-selective media, Most Probable Number techniques, or by more sophisticated molecular techniques are commonly used by project PIs. When samples fall below the limit of detection, standard enrichment protocols (FDA BAM or others) will be followed. The collection of quantitative data will be encouraged whenever possible and can be used to populate risk models. Standard methods will also be used for the recovery of viral or parasitic organisms from relevant food commodities. With respect to the viruses, the European Committee for Standardization has developed a standard method for the recovery, concentration, and detection of noroviruses and Hepatitis A virus from select food commodities (vegetables, soft fruits, and oysters) which will be used until the US develops its own standard or adopts the EU standard EN ISO 15216-1:2017.

Recovery of Pathogens from Environmental and Uninoculated Food Sources. Sampling methods to recover pathogens from the environment and foods will vary depending upon the sampling scheme and source based on experimental design. All attempts will be made by project PIs to not only determine frequency of pathogen isolation, but also investigate concentration of identified pathogens, as concentration is a critical variable required in Objective 2. When appropriate, concentration techniques may be used to evaluate larger than typical sample volumes/weights, and enrichment techniques used to evaluate samples when low numbers of cells are present.

Objective 1: Risk Assessment: Characterizing food safety risks in food systems

The long-term goals of this objective include (i) evaluating and modeling environmental parameters and indicator organisms as related to the presence of pathogenic microorganisms; (ii) understanding prevalence of pathogens and antimicrobial resistance within the environment, food products, food production, food processing, food distribution, and consumer systems; and (iii) understanding persistence, dissemination and traceability of microorganisms within the environment, food products, food production, food processing, food distribution and consumer systems.

Evaluate and model environmental parameters and indicator organisms as related to the presence of pathogenic microorganisms. Critical to the development of risk-based approaches to food safety is the understanding of how the presence and populations of pathogenic microorganisms relate to measurable physicochemical and microbial indicators. Currently employed standards throughout the food production and manufacturing sectors involve the frequent sampling for various indicator or index organisms. However, while dogma dictates that changes in indicators or indexes result in an increased risk for a product, very little published literature on this topic is available. One of the drawbacks of testing for pathogens or microbial indicators is the interval between testing and the time of result. In many instances, this time delay can range anywhere from 12 h to five or more days depending on target organism(s) that are being detected. Long detection times preclude testing from being used in real time. To address these issues, we propose to evaluate and model these relationships using available, classical methods combined with emerging detection technologies.
One specific novel approach to investigating the relationship between indicators and pathogens will be to apply some of the emerging “omics” technologies to identify better indicators or predictors of pathogen presence under varying environmental conditions—patterns that remain undetected by classical methods. For instance, one could apply metagenomics for enhanced characterization of the microbial communities in food and food manufacturing environment and determine how these communities may change over time in relation to the environmental conditions associated with processing, preservation, sanitation, and storage. There has already been some progress in identifying markers that can allow for qualitative or even quantitative relationships to be drawn between specific processes and/or formulation conditions and strain level microbial responses. The use of strain level response data will introduce added value to quantitative microbial risk assessment (QMRA) and associated modeling tools. As outlined by den Besten et al. (2018), instead of relying on phenotypic data such as a minimal temperature where growth is expected, the model inputs could look at strain level response intensity (i.e. a biomarker identified via metagenomics) over a continuous variable (i.e. temperature range). To further enhance and address some of the shortcomings of metagenomics (i.e. poor sensitivity for low level contamination, amplification bias, and inability to distinguish between genetic material originating from viable and non-viable cells), metatranscriptomic sequencing may be used as a complimentary tool. Basically, metatranscriptomic sequencing detects cDNA created from RNA extracted from a given microbial community and thus identifying genes in a population that are being transcribed and maybe even translated.

Understanding prevalence of pathogens and antimicrobial resistance within the environment, food products, food production, food processing, food distribution and consumer systems. The success of any risk assessment hinges on a comprehensive understanding of both concentration and distribution of risk factors, including foodborne pathogens and presence of antimicrobial resistance genes. Much of the currently available prevalence data is lacking critical concentration data (i.e. how much of a given pathogens is anticipated in a specified amount of food product?), which while difficult to determine, is an essential piece of any risk assessment. Also commonly overlooked are the potential spatial-temporal population differences that may exist across the US, and offer a unique niche for PIs collaborating on this multistate project to evaluate. These spatial patterns that exist along the farm-to-fork continuum provide insight into current relative risk of food products and production environments and are a critical starting point against which all risk reduction attempts can be benchmarked. Statistically-sound sampling methods and sample sizes are of fundamental importance to all studies. These issues will be addressed by our plan to 1) evaluate frequencies and concentrations of pathogens and antimicrobial-resistance genes and 2) identify production, manufacturing, distribution or consumer management practices that improve public health by reducing these risks. The approaches used to address our plan will use both classical bench-science as well as surveys based in the social sciences. The aforementioned emerging “omics” technologies can help address these questions as well.


Understanding persistence, dissemination, and traceability of microorganisms within the environment, food products, food production, food processing, food distribution, and consumer systems. In addition to understanding relationships between indicator organisms/pathogens as well as concentration/frequencies of risk factors during food production, of crucial importance is an understanding of how risk factors can vary from the time a food product is conceived to consumption by a consumer, and how typical industry or consumer practices and handling can influence these risks. While a significant amount of data exists for some commodities, others remain relatively understudied, and handling practices are continually evolving within the industry. For data that do exist, a systematic review to identify critical data gaps and extraction of data for meta-analyses and inclusion into comprehensive risk assessments is an opportunity for PIs of this project. While the term “cross-contamination” is often used and training and education on the principles of prevention of cross-contamination is employed across all facets of the industry, data to model and understand the fundamental mechanism of cross-contamination and elucidate novel prevention strategies are lacking. Our strategy to tackle this concern rests in our multidisciplinary, systems approach of critical data gap identification, data generation, and modeling of multiple commodity, production, process, distribution and consumption patterns.

Objective 2: Develop, validate, and apply science-based interventions to prevent and mitigate food safety threats

This section describes the current and planned activities and methods under the risk management component of the project. Risk management is the process of applying the results of risk assessments for the control and mitigation of foodborne pathogens, including regulatory action. This project is designed as a systems approach to food safety. More specifically, this is the process of studying discrete but interrelated sections of the farm-to-table continuum to provide comprehensive and integrative solutions to complex food protection issues. Along with source and food attribution data, the recently published scheme for categorizing foods implicated in foodborne disease outbreaks (Richardson et al., 2017) will be used to prioritize the food commodities for which science-based interventions will be designed and validated. This will in turn reduce the risk of foodborne illness to the consumer.

To accomplish the tasks associated with Objective 2, a risk management framework based on commodity-specific flow diagrams and inputs from Objective 1 will be developed. A key component of this activity will be the use of risk modeling techniques to relate the levels of microbial contamination in food to the likelihood of a foodborne illness or outbreak occurring. The information developed using this approach will then be used to development of specific interventions for risk mitigation at specific points along the farm-to-fork continuum. The results of the risk modeling approaches will also help identify critical data gaps, which will feed back into new projects under Objective 1.

Models and risk management. Predictive microbiology and QMRA are rapidly developing scientific disciplines that use mathematical equations, numerical data, outbreak data, and expert elicitation to estimate the presence, survival, growth, and death of microbes in foods. These models allow for the prediction of the safety of a product based on the entire sequence of events up to consumption, including worst-case food handling scenarios. They provide a framework for evaluating the effectiveness of risk-reduction strategies.

Under this objective, predictive models will be built and validated for appropriate food/pathogen combinations. Multiple extrinsic factors affect microbial growth and survival in foods. For example, many antimicrobial interventions rely on thermal destruction of microbial cells for product safety. Because temperature may change drastically during processing, storage, and distribution, pathogen predictive models will be developed to describe microbial behavior in various food commodities, especially those subjected to novel thermal interventions (e.g., radio frequency, microwave, or ohmic heating). These models will be validated using real-life scenarios whenever possible. Microbial predictive models will be developed using kinetics derived from microbial growth experiments under different conditions, including not only temperature but the interaction with other intrinsic and extrinsic factors. The models generated for one commodity can be used to guide a series of experiments to validate the model for different, closely related commodities. Following the development of temperature and other models, expert opinion, industry, experimentally-derived and published, peer-reviewed data for processing and handling conditions to the point of consumption can be integrated into risk assessment models to estimate changes in microbial population dynamics. Alternatively, established models such as the USDA Pathogen Modeling Program or ComBase can be used. This will also be a critical point to integrate microbial community data as well as strain-level data using metagenomics and metatranscriptomics as discussed in Objective 1.

Examples of approaches to QMRA can be found in Membré and Boué (2018). Briefly, published data are collected during a thorough search of medical and biological databases for documents related to the food commodity. A “flow diagram” documenting the specific food commodity (including its ingredients) from production through retail should also be developed with expert opinion. Data from this objective and Objective 1 as well as the peer-reviewed literature will be translated into appropriate discrete or probability distribution functions and assigned to processes in the commodity flow diagram. The QMRA model can be created using a variety of constantly evolving software tools. Results for simulated input distributions as well as final results will be obtained by running from 1,000 to 1,000,000+ iterations of the simulation. Tornado analysis can then be used to determine the relative significance of the input variables. In addition, there are emerging statistical and probabilistic techniques that have been developed to support the inclusion of “omics” data within QMRA. As highlighted by Membré and Guillou (2016), partial least square regression is being optimized for interpretation of omic data to aid in subsequent quantification of the probability of exposure to a given pathogen in food. Another useful technique is the use of Bayesian networks and inference to build gene regulatory networks that could help, for example, 1) predict the duration of lag growth phase of a given foodborne pathogen or 2) overcome lack of biological data which drives the uncertainty in the most QMRA models. By integrating these new techniques into QMRA, the data generated in these emerging “omics” technologies will become more applicable.
Risk Mitigation. Food safety mitigation strategies include, but are not limited to, those related to high pressure processing (HHP), ultraviolet (UV) radiation, radio frequency, cold plasma, ozone, electrolyzed water, bacteriophages, peroxyacetic acid, essential oils, and value-added packaging, alone or in combination, as methods to control food safety risks on various food commodities. Aside from continued investigation and evaluation of known mitigation strategies, we will also seek out novel approaches for the prevention and control of foodborne pathogens including 1) the optimization or development of transformative technologies and 2) the discovery or synthesis of new antimicrobial compounds with potential GRAS status. Emerging technologies may include high-intensity ultrasound, microwave heating, and pulsed electric fields for the inactivation of primarily vegetative bacteria, yeast, and molds with potential to also inactive viruses (Jermann et al. 2015). With respect to new antimicrobial compounds, there is the possibility to continue optimizing the application of biologically-derived antimicrobials including peptides and essential oils via integration of nanotechnologies. Moreover, novel delivery systems for established and newly discovered antimicrobials will be explored further to increase applicability. The response of various food/pathogen combinations to one or more of these interventions will be assessed to determine synergistic effects and the emergence of cross resistance among different microbiological stress sources. All microbiological interventions will be accompanied by sensory and quality evaluations to determine the potential impact of those interventions on consumer acceptance of the product.

Maintaining proper temperature during transportation is essential to ensure the safety of foods. In order to develop effective interventions, it is first necessary to understand the effects that cold chain temperature abuse have on the ability of bacterial foodborne pathogens to grow during transportation and viral and parasitic pathogens to persist and remain infective. The ecology of foodborne pathogens during transportation between unit operations within the food continuum is grossly understudied and misrepresented in current risk modeling simulations. To address these issues, we will employ wireless temperature sensors to monitor fluctuations in temperature that occur during commercial transportation of food products (pre-, post-, and during harvest and processing), as well as transportation from retail to domestic kitchens. Data from these studies will be used in risk assessment models to predict the growth of foodborne bacterial pathogens during various stages of transport, especially during temperature abuse.

A major area of concern with respect to contamination of food is the domestic kitchen, where multiple opportunities arise for mishandling. Similar to temperature control during various phases of transportation, consumer behaviors and actions may increase food safety risks. Because of the unpredictable nature of consumer practices at home, inclusion of behavioral responses in risk assessment models becomes extremely challenging. One method to determine food safety practices is by observational studies in kitchens and food service operations. For example, the FDA 2016 Food Safety Report found that consumer compliance with handwashing and thermometer use is quite low—only 10% report using a thermometer to check the doneness of hamburgers (FDA, 2016). Moreover, even with the “Don’t Wash Your Chicken” campaign from 2013, 67% of consumers still wash their chicken prior to cooking it. Therefore, the risk assessment component of the project will also simulate consumer practices in laboratory kitchens so that the safety of those practices can be assessed and improved.

Finally, education and outreach activities outlined in Objective 3 will be based on the results of these experiments targeting specific populations. The risk assessment activities of this program will be designed with small and very small food industry in mind. This will help small producers comply with current food safety regulations under the Food Safety Modernization Act.

Objective 3: Risk Communication: Convey science-based messages to stakeholders to improve food safety behaviors and practices

Effective communication is critical to incite behavior and management changes towards a safer food supply. Instead of relying solely on passive diffusion of information through the publication of fact sheets, peer-reviewed journal articles, and presentations, herein we propose to use two-way exchanges of information between stakeholders and researchers to tailor risk management messages for each specific audience. Multiple criteria will be used to evaluate and assess message content and media. The efficacy of these messages to result in measurable changes in behavior and tangible impacts on improving food safety within the food production continuum will be evaluated. Based on stakeholder feedback and the assessed success or limitations of various communication strategies, changes will be made in approaches to outreach to meet specific audience needs.

Risk avoidance messages should be based on data. Some of the data to support the risk message content will be derived from the research of this multi-state project (See Objectives 1 and 2). However, it is equally important that information from other multi-state groups and individuals, both nationally and internationally, be included in crafting appropriate messages and determining the best route for message delivery. We anticipate that each stakeholder will require unique combinations of specific information and route of delivery (print, electronic, presentations, video animation, interactive games, etc.). PIs of this group have partnerships and collaborations with a wide variety of stakeholder groups situated at all levels of the farm to table continuum. Targeted stakeholders include producers, processors, retailers, food service employees, and consumers. However, to enhance the capacity of this group to communicate food safety information to stakeholders, we will expand our communication efforts in to the following groups:

a) Seafood industry
b) Juice and beverage industry
c) Fresh produce, dried fruit, and nut industries
d) Dairy industry
e) Meat industries
f) Poultry and egg industries
g) Ingredient manufacturers
h) Consumers
i) Food service and retail organizations
j) Public health agencies
k) Regulatory agencies

In addition, Technical Committee members (See Organization and Governance) working directly with the abovementioned groups will enhance Objective 3 by expanding the breadth and diversity of the multi-state team. Invitations to join this group will be sent to professional contacts of current Technical Committee members, especially other academics who are already working with stakeholders. This multi-state group offers the unique advantage to form regional working groups to coordinate targeted information and outreach activities. Conversely, when geographically based regions are inappropriate for maximizing impact to stakeholder groups. For example, juice safety efforts are ongoing in Florida and New Jersey which are not geographically similar areas; thus regional-based groups would be beneficial. Additional examples oyster safety efforts in the Pacific Northwest, Louisiana/Gulf Coast, and Maryland, and or cantaloupe safety in California, Arizona, Texas, Colorado, Indiana and Florida. Therefore, the diverse geographic representation and backgrounds of participating institutions and individuals allows for maximum impact and uniform messages across a single food commodity to be communicated.

The following approaches will be exploited:

1) Increase communication by recruiting additional university personnel with research and extension appointments, including 1890’s land-grant schools and Hispanic-serving institutions. Several of our current members have ongoing collaborations with researchers at these institutions so we will capitalize on those existing relationships.

2) Strengthen collaborative networks and exchange of information about integrated food safety issues, fostering communication with food industry/target audiences and other stakeholders (e.g., USDA, FDA, State Departments of Agriculture and Health, etc.) on a regional and national scale. This will specifically be achieved by inviting key persons from the aforementioned groups to participate in our annual meetings and present in the proposed pre-meeting short courses (see Milestones) when applicable. Personal invitations will be the primary method to engage these stakeholders as our group is both diverse and well-connected.

3) Increase USDA-ARS scientist participation in group meetings and research collaborations on a regional and national scale. Research centers participating in USDA-ARS National Programs in Food Safety (NP-108), Animal Health (NP-103), Aquaculture (NP-106), and Food Animal Production (NP-101) will specifically be targeted. These may include the U.S. National Poultry Research Center, the Food Science Research Unit, the Eastern Regional Research Center, and the Feed and Food Safety Research Unit as well as others across the U.S. As indicated, collaborations already exist among many in this group and USDA-ARS scientists; thus, recruitment of these scientists for participation in this multi-state project will again be primarily by personal invitation.

4) Through stakeholder participation in meetings, conduct needs assessment/survey of stakeholders to determine current trends and food safety issues at annual meetings of International Association for Food Protection, American Meat Science Association, Produce Marketing Association, North American Meat Institute, National Cattlemen’s Beef Association, National Restaurant Association, Grocery Manufacturers Association, Poultry Science Association, United Egg Producers, organic producers/processors, etc. Other venues for conducting risk communication-based research will also be explored outside of scientific and trade association meetings.

5) Transfer food safety knowledge to undergraduate and graduate students via training opportunities at collaborating institutions, resident education, extension and/or outreach activities nationwide.

6) Facilitate national networking and coordination amongst the users of food safety information from production to consumption (farmers, producers, processors, inspectors, researchers, consumers, etc.), to explore regional specific and national barriers and opportunities. One example of how to accomplish this will be to engage with the four Regional Centers for Food Safety Training, Outreach, and Technical Assistance. Another example of how our group has already established this type of networking is through the engagement of specific, local food industries during each annual meeting. For example, in 2015, we toured an aquaculture operation in Rhode Island, and the following year, in New Mexico, we visited a start-up salsa factory to learn about the challenges they may have faced with respect to implementation of food safety regulations. Food industry visits have been a staple during the past five years of this project, and fully plan to continue this type of engagement at our annual meetings.

7) Identify and disseminate information about databases of food safety information and interactive software to support decision-making amongst food safety professionals, on a regional or national scale as necessary.

8) Disseminate (share among partners) food safety trainings, multi-user distance education programs, satellite communication, webinars, etc., to deliver food safety training on topics such as:
a) Produce Safety Alliance curriculum
b) Preventive Controls for Human Foods curriculum
c) Preventive Controls for Animal Foods curriculum
d) Foreign Supplier Verification Program curriculum
e) Supplemental curricula for adherence to various regulations associated with the Food Safety Modernization Act
f) Validation for meat and poultry industries
g) HACCP (seafood, juice)
h) Food defense
i) Traceability
j) ServSafe

9) Encourage our multi-state project Technical Committee members to participate actively in professional food safety venues and acknowledge the multi-state contributions of their activities publically in programs such as:

a) International Association for Food Protection (Professional Development Groups and Regional Affiliates)
b) Institute for Food Technologists (Food Microbiology and Extension Divisions etc.)
c) Conference for Food Protection
d) Other professional societies including the American Society for Microbiology and the Society for Risk Analysis
e) Commodity-based organizations (meat, poultry, fruit, vegetable, confectionary, ingredient, dairy, etc.)
f) National Advisory Committee on the Microbiological Criteria for Foods

10) Conduct evaluations to determine impact of educational and/or outreach activities on student and/or workshop participants’ food safety knowledge, attitude, behavior change, and/or skills.

In addition to the research activities performed by the group’s members, the extent to which team members participate in the aforementioned outreach activities (outputs), and outcomes and impacts associated with the fulfillment of these objectives will be documented annually, and national and regional efforts and collaborations will also be identified. Collectively, this emphasis on two-way exchange of information and participatory decision-making will foster an increased understanding of stakeholders’ goals and needs, and strengthen the relationships between all partners in the food system. As an expected outcome, we anticipate a decrease in redundancy in regional efforts and a more efficient use of financial resources in food safety research and outreach, with more directed focus on current and emerging problems. Because of the increased availability of information and knowledge transfer among stakeholders, the opportunity will exist for decision-makers in industry, academia and government to make better, risk-informed, choices related to regulations and the allocation of resources.

Measurement of Progress and Results


  • Increased understanding of contamination, ecology, and risk-based prevention strategies for food safety
  • Validated decontamination methods that can be used by food producers, processors, retailers and consumers to enhance the safety of food products
  • Outreach/extension education and training materials for stakeholders including regulatory personnel, extension agents, producers, processors, and consumers
  • Increased engagement of food safety researchers at minority-serving institutions and diverse students in the discipline

Outcomes or Projected Impacts

  • Enhanced safety of fruit, vegetable, dried fruit and nut, seafood, meat, and poultry products
  • Increased understanding of food safety measures by regulatory personnel, producers, processors, consumers, extension agents
  • Overall enhanced food safety and health for consumers
  • Increased opportunities for trade of food products
  • Increased ability to meet growing food safety intellectual capacity for the country


(2018):Increase participation of USDA Agricultural Research Service scientists through active recruitment (See Objective 3 for specific approach)

(2019):Expand knowledge and application of risk assessment by hosting a 1-day short course in conjunction with the annual meeting

(2020):Invite representatives of NC 1023, Engineering for Food Safety and Quality, to share outcomes from their multistate project with project members and foster collaboration for developing more robust risk management tools o Risk management focus on novel interventions: low aw foods, non-thermal interventions as well as discoveries/obstacles when implementing these technologies

(2021):Expand knowledge and application of risk communication by hosting a one-day short course in conjunction with the annual meeting: innovative approaches, how to design messaging for your audience, and media training.

(2022):Members of the multistate project will write an opinion tied to one or more of the objectives of the project which will be published in a food safety journal/publication.

Projected Participation

View Appendix E: Participation

Outreach Plan


Literature Cited

Batz, M.B., S. Hoffmann, and J.G. Morris Jr. 2012. Ranking the disease burden of 14 pathogens in food sources in the United States using attribution data from outbreak investigations and expert elicitation. J. Food Prot. 75:1278-91.


den Besten, H.M., A. Amézquita, S. Bover-Cid, S. Dagnas, M. Ellouze, S. Guillou, G, Nychas, C. O'Mahony, F. Pérez-Rodriguez, and J.M. Membré. 2018. Next generation of microbiological risk assessment: Potential of omics data for exposure assessment. Int. J. Food Microbiol. In press.


Ettayebi, K., S.E. Crawford, K. Murakami, J.R. Broughman, U. Karandikar, V.R. Tenge, et al. 2016. Replication of human noroviruses in stem cell-derived human enteroids. Science 353:1387-1393.


FDA. 2017. 2016 Food Safety Survey. Accessed on 28 February 2018. Available online at https://www.fda.gov/Food/FoodScienceResearch/ConsumerBehaviorResearch/ucm529431.htm


Flessa, S., D.M. Lusk, and L. J. Harris. 2005. Survival of Listeria monocytogenes on fresh and frozen strawberries. Int. J. Food Microbiol. 101:255-262.


Hoffmann, S., B. Maculloch, and M. Batz. 2015. Economic Burden of Major Foodborne Illnesses Acquired in the United States. United States Department of Agriculture Economic Research Service. Accessed on 19 December 2017. Available online at https://www.ers.usda.gov/webdocs/publications/43984/52807_eib140.pdf?v=42136   


Jermann, C., T. Koutchma, E. Margas, C. Leadley, and V. Ros-Polski. 2015. Mapping trends in novel and emerging food processing technologies around the world. Innov. Food Sci. Emerg. Technol. 31:14-27.


Jones, M.K., M. Watanabe, S. Zhu, C.L. Graves, L.R. Keyes, K.R. Grau, et al. 2014. Enteric bacteria promote human and mouse norovirus infection in B cells. Science 346:755-759.


Membré J-M and Boué G. 2018. Quantitative microbiological risk assessment in food industry: Theory and practical application. Food Res. Int. 106:1132–1139.


Membré J-M and Guillou S. 2016. Latest developments in foodborne pathogen risk assessment. Curr. Op. Food Sci. 8:120–126.


Montville, R.I. and D.W. Schaffner. 2003. Inoculum size influences bacterial cross contamination rates between surfaces. Appl. Environ. Microbiol. 69: 7188-7193.


Richardson, C.L., M.C. Bazaco, C. Chen Parker, D. Dewey-Mattia, K. Jones, K. Klontz, C. Travis, J. Zablotsky Kufel, and D. Cole. 2017. An updated scheme for categorizing foods implicated in foodborne disease outbreaks: A tri-agency collaboration. Foodborne Pathog. Dis. 14:701-709.


Scallan, E., R.M. Hoekstra, F.J. Angulo, R.V. Tauxe, M.A. Widdowson, S.L. Roy, J.L. Jones, and P.M. Griffin. 2011.  Foodborne illness acquired in the United States-major pathogens. Emerg. Infect. Dis. 17: 7-15.


Uesugi, A.R., M.D. Danyluk, and L.J. Harris. 2006. Survival of Salmonella Enteritidis phage type 30 on inoculated almonds stored at -20, 4, 23 and 35°C. J. Food Prot. 69:1851




Land Grant Participating States/Institutions


Non Land Grant Participating States/Institutions

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