S1056: Enhancing Microbial Food Safety by Risk Analysis

(Multistate Research Project)

Status: Inactive/Terminating

S1056: Enhancing Microbial Food Safety by Risk Analysis

Duration: 03/01/2013 to 09/30/2018

Administrative Advisor(s):

NIFA Reps:

Statement of Issues and Justification

The long-term goal of this project is the establishment of a multi-disciplinary network of scientists that performs comprehensive and integrated risk-based research and outreach to improve the safety of food from farm to fork. Interested stakeholders, including food producers and/or processors, retailers and consumers, have identified the need for an approach that conducts applied research to determine the prevalence and ecology of foodborne pathogens (including antibiotic resistant bacteria) in fresh and processed foods coupling that to research aimed at establishing effective control methods to decrease pathogen contamination of foods. Several outreach objectives have also been developed in support of this project. These objectives include communication of risk-based management recommendations derived from the research aspects of this proposal to stakeholders as well as to those who interact with stakeholders. Communication strategies will be precisely tailored to the particular audience (processors, distributors, retailers, consumers). Message content will focus on risk-based strategies and microbial control opportunities deemed critical for each target audience to achieve the greatest strides in improving food safety in the U.S. Outreach to those who advise producers and consumers (e.g. educators, extension personnel) who are not part of the project will be achieved through ongoing symposia to disseminate key information concerning lessons learned during the course of this project.

This project has been specifically designed to address the critical needs of the fresh and processed food industries by developing a thorough understanding of how these foods become contaminated with foodborne microbial pathogens. It is well established that the heterogeneous distribution of pathogens in food makes studying the ecology of these pathogens difficult. The problems facing the food industry are also sufficiently complex such that solutions to these problems are beyond the scope of any single investigators programmatic outputs. This means they are most efficiently addressed through multidisciplinary efforts with expertise in risk analysis, microbial ecology, epidemiology of foodborne disease, and food safety microbiology.

The results of this project will directly impact industries that handle low moisture food sector (emphasis on 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 read-to-eat products subject to post-process contamination), as well as other multi-component and processed foods. The studies proposed here will be the first comprehensive attempt to develop risk-based strategies leading to effective control of pathogens from the farm through consumption across all food commodities in the U.S. Additional expected outcomes include the use of microbiological data to develop risk-based models that can be used to better predict microbial contamination and predict the reduction of pathogens in foods due to application of various control strategies. It is expected that the outcomes of this project will contribute to the long-term profitability and sustainability of the food industry as a whole by making accessible a suite of new tools with which the microbial safety of foods will be enhanced. This group will also work to standardize protocols among laboratories so that research results can be easily and directly compared. Many funding opportunities for food safety require collaboration by several universities. Having a mechanism in place prior to release of a formal Request for Proposal enables the scientists in this group to be more responsive and successful in acquiring external funding than if collaborations were formed ad hoc.

The Centers for Disease Control and Prevention (CDC) has recently reported new, more accurate estimates of foodborne illnesses that occur annually in the U.S. Approximately 48 million cases of foodborne illness, 128,000 hospitalizations, and 3,000 deaths occur each year from foodborne microorganisms (Scallan et al., 2011). The food safety surveillance system, FoodNet, documented in 2008 (the latest year for which data are available) that the Noroviridae were identified as the most common etiological agent of microbial foodborne disease, accounting for almost 50% of the outbreaks and 46% of illnesses. Salmonella spp. accounted for 23% of the outbreaks and 31% of illnesses. The commodities that led to the most outbreak-related illnesses were fruits and nuts (24%), vine-stalk vegetables (23%) and beef (13%) (Anonymous, 2011).

In addition to human suffering, foodborne illnesses also have a substantial economic impact in the United States. Based on data from Scallan et al. (2011) and Scharff (2010), the annual cost of foodborne illness in the U.S. is estimated at $89 billion for loss of productivity, other economic losses and medical expenditures. The most costly foodborne illnesses are caused by Vibrio vulnificus and Listeria monocytogenes (Scharff, 2010). The availability of improved microbiological methods will facilitate the goal of reducing the burden of current and emerging foodborne pathogens at all points of the food chain from farm to fork. Such methods will decrease foodborne related illnesses and deaths, and reduce economic losses to the food industry.

Finally, in addition to developing a better understanding of the microbial ecology of foodborne pathogens and methods to detect and control their presence in foods, this multi-state project will permit undergraduate and graduate students to gain experience in current and emerging methods used to identify, track, and control foodborne pathogens in the food production environment, as well as the use of modern molecular methods to identify and study emerging pathogens that may contribute to the burden of foodborne illnesses. The need for training programs to support the next generation of food safety specialists is clear, as is the need to increase the ethnic and cultural diversity among food safety researchers to reflect the ethnic and cultural composition representative of the U.S. population. Greater diversity is critical not only from the perspective of educational opportunity but also relative to food safety and public health. The prevalence of foodborne illnesses associated with culturally prepared foods and preparation practices associated with preparation of these foods is growing, making cultural competence among food safety professionals not simply attractive, but absolutely necessary.

Related, Current and Previous Work

Previous Work, S1033 10/2006 - 09/2012.

Since 2009, member of the previous S1033 group have authored over 450 peer-reviewed papers on the subject of food safety (see 2009 - 2012 Publications in the Additional Documents section). Notably, approximately 20% (85/450) of these papers were co-authored by more two or more members of the multi-state group, providing direct and tangible evidence of effective multi-member collaboration. Moreover, funding acquired among group members supported research described in many of these papers. The impact of this research is significant. The increased understanding of the ecology, biology, epidemiology, of foodborne pathogens in pre and post- harvest environments, foods and the environment has been used to populate risk models of disease transmission and develop a variety of intervention strategies to control risk. In addition, the data has been incorporated into systematic reviews and meta-analytical studies which are available to inform decision makers in industry and in government positions.

The participants of this project have a very productive history of collaboration and successful research. Interactions amongst researchers from the 28 universities participating in S1033 are outlined in Table 1 (see Table 1 in the Additional Documents Section). This table indicates collaborations (defined as funded projects, extension activities, or co-authored publications) between universities over the course of the previously active multistate project S1033 between 2006 and 2012. Outputs and deliverables among S1033 members is high, individually averaging more than 5 publications, 6 presentations, and $426,000 of research support each year. It should be noted that S1033 members have formed collaborations and developed multi-institutional, trans-disciplinary successful research programs funded by a variety of federal (USDA, FDA, NIH, USAID, and FAS), state, private, and stakeholder groups.

One of the most underrated benefits of participation in a project with so much collaboration is the opportunity to work with erudite researchers across the country. As a result, many of the grants received and goals achieved would not have been practical or possible if working alone. These relationships included, but are not limited to, obtaining samples or microbial cultures, performing analytical services and the sharing of technical guidance and advice. Although not always obvious from annual reports, meeting minutes or publications, these difficult-to-quantify benefits springing from the frequent collaborations is a key component of what has helped to make the past project so successful.

Current Work

Food safety is an important agricultural, public health, and economic concern in the U.S. and worldwide. As such, there is an emphasis regionally, domestically, and globally, to conduct research to better understand foodborne pathogens, disease transmission and prevention. For example, in 2012 alone, there were over 40,000 research papers published on the topic of the most common foodborne pathogens (10 bacterial, 3 parasitic, and 1 viral) occurring in the US (See Table 2 in the Additional Documents Section).

In the past few years, federal funding for agricultural research has not kept pace with increasing demands, but resources for food safety food safety research have been somewhat prioritized. The availability of resources for food safety research has attracted a large number of investigators not traditional trained in or previously involved in this field. This influx of new researchers brings exciting new ideas and approaches and the opportunity for novel interdisciplinary strategies to address some of the most pressing food safety challenges. However, the competition for available resources in 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 in laboratories 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 multi-state, regional, or other appropriate teams that build on the strengths of different individuals to develop innovative approaches to food safety that 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 extension and expansion of the work completed on S1033, and address current and emerging food safety concerns in 2012 and beyond. We have identified seven additional universities that have expressed interest in participating in this project (See Table 3 the Additional Documents Section). As is apparent by comparing collaborations from Table 1 between universities participating in S1033, and the rather limited collaborations obvious in Table 2, we see tremendous opportunity for future, previously uncultivated, collaborations. While these additional seven universities have already been contacted for future participation, we anticipate the efforts of the group will expand to invite participation of additional, historically underrepresented, institutions such as 1890s Universities.

Our previous objectives focused on control of foodborne pathogens in pre- and post-harvest environments, development and validation of mathematical modeling, and antimicrobial resistance in production and processing environments. As the importance placed on risk-based standards in food safety has evolved, we have modified our objective areas to integrate research, extension and teaching to cover the broad areas of Risk Assessment, Risk Management and Risk Communication. Risk Communication is an expansion of our former outreach component and is an attempt to highlight the diverse range of Extension activities at many of the participant universities. Our movement from targeted, isolated objectives to integrated, systems and risk based objectives is a logical evolution. Objective areas previously covered under S1033, will continue in this new project. For example, rather than a unique objective focusing specifically on antibiotic resistance amongst bacterial pathogens and its significance/mitigation, research and extension related to antibiotic resistance in foodborne bacteria will be covered under all three objective areas. The prevalence of and risk factors involved will be covered under 1) Risk Assessment; potential control strategies will be covered under Aim 2) Risk Management; and the knowledge obtained from objectives 1 and 2 will be transferred to stakeholders under Aim 3) Risk Communication. The adoption of this risk-based systems-type approach allows member 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, 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

A systematic search of electronic databases, including the USDA CRIS and NIMSS databases, yielded a larger number of past and active projects that address a wide variety of food safety topics. Of 243 active AFRI, Animal Health, NRI, and HATCH projects identified by the search term FOOD SAFETY, 72% are conducted by investigators at institutions involved in this project and are partially an outcome of previous involvement with this group. In addition, several ARS units are also involved in food safety research. The following seven other multi-state projects identified in the NIMSS search included some mention of food safety objectives:

NC1023: Engineering for Food Safety and Quality.

NC1041: Enteric Diseases of Swine and Cattle: Prevention, Control and Food Safety.

NE1028: Mastitis Resistance to Enhance Dairy Food Safety.

NC1183: Mycotoxins: Biosecurity, Food Safety and Biofuels Byproducts.

S_TEMP2882: Fly Management in Animal Agriculture Systems and Impacts on Animal Health and Food Safety.

S294: Quality and Safety of Fresh-cut Vegetables and Fruits.

W3122: Beneficial and Adverse Effects of Natural Chemicals on Human Health and Food Safety.

A detailed table (Table 4) of how each of the above projects compares to SDC346 is included in the Additional Documents Section.

Food systems are extremely complex and various aspects of production, quality, and animal and plant health may impact food safety. The major difference between the proposed multistate project, and other projects, that have in their title a reference to food safety, is the fact that these projects include the topic of food safety because it is often on the periphery of many non-food safety topics related to agriculture and production of food. In contrast, members of SDC346 conduct food safety research as a primary focus. Other differences include the fact that most other projects focus on a single class of food commodity (e.g. fresh/minimally processed produce, dairy), whereas SDC346 will conduct research related to the safety of multiple food commodities.


  1. Risk Assessment: Assess food safety risks in agriculture systems
  2. Risk Management: Develop science-based interventions to prevent and mitigate food safety threats
  3. Risk Communication: Communicate food safety messages to stakeholders


SEE ATTACHMENT S1033 resubmit_21513

Measurement of Progress and Results


  • Increased understanding of the contamination, ecology, and risk based prevention strategies for food safety
  • Validated decontamination methods that can be used by the food producers, processors, retailers and consumers to enhance the safety of their finished product
  • Outreach/extension education and training materials for stakeholders including regulatory personnel, extension agents
  • Engagement of minority food safety researchers and more students in 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 capacity to meet growing food safety intellectual capacity for the country


(2013): Ensure that at least one representative from each State Agricultural Experiment Station has been contacted and invited to participate in this project. Achieve a membership of at least 50 individuals with broad geographic, commodity and area of representation

(2014): Enhance diversity of membership through targeted recruitment of individuals working on food safety issues at 1890 Institutions, Hispanic Serving Institutions, and Tribal Colleges and Universities.

(2015): Establish a student mentoring program to recruit and mentor students into a variety of food safety related disciplines

(2016): Invite Participants from USDA ARS laboratories and other state and federal governmental laboratories and organizations with interest in food safety (FDA, EPA, etc.).

(2017): Publish a white paper highlighting advantages of and detailing how participant research has evolved into risk based standards targeted for publication in Trends in Food Protection.

Projected Participation

View Appendix E: Participation

Outreach Plan

Outreach activities and the evaluation/impact of this project are fully integrated into the methods of this proposal under objective 3.


The membership of the Regional Technical Committee includes: a. The regional administrative advisor (non-voting); b. A technical representative of each cooperative experiment station, appointed by the respective station director; c. A technical representative of each cooperative USDA research division or other Federal agency named by the director of the division or Head of the agency; An executive committee consisting of Chairman, Vice Chairman, and Secretary, elected by the Technical Committee members, is designated to conduct business of the Technical Committee between meetings and to perform other duties assigned by the Technical Committee. The term of office for each Executive Committee member is two years. The progression is Secretary, Vice Chairman, Chairman, for a total of six years.

The duties of the Technical Committee will be to coordinate planning and work of the project and make such recommendations as are necessary through the Administrative Advisor to the Southern Association of Agricultural Experiment Station Directors. The functions of the Chair will be to preside over meeting and edit the annual report. The recording secretary shall take minutes at the annual meeting and distribute these to members of the committee within a month of the meeting.

The Technical Committee will meet annually to review progress, develop research plans and coordinate research efforts in order to maintain the Committee's focus on the objectives identified in the project. During the annual meeting, the research coordinators from each of the lead states (Table 1) will summarize for the entire Regional Technical Committee the plan of work for the next year in the specified research areas in meeting the goals of each objective. In addition to the annual meeting, the coordinators are responsible for maintaining active communication with their cooperating stations principal investigator to maintain a current knowledge base of research accomplishment within the specified problem area. This linkage will enhance the research effectiveness and productivity, reduce duplication and unnecessary work, and strengthen the regionalism among cooperating stations. Copies of the Annual Progress Report, including major accomplishments of contributing project and minutes of the annual meeting will be distributed each year and available at the NIMSS website.

Literature Cited

Anonymous. 2011. Surveillance of Foodborne Disease Outbreaks - United States, 2008. Mobility and Mortality Weekly Report, 60:1197-1202.

Baranyi, J., P.J. McClure, J.P. Sutherland, and T.A. Roberts. 1993. Modeling bacterial growth responses. J. Ind. Microbiol. 12: 190-194.

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.

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

Montville, R.I., and D.W. Schaffner. 2005. Monte Carlo Simulation of Pathogen Behavior during the Sprout Production Process. Appl. Environ. Microbiol. 71: 746-753.

Ratkowsky, D.A., T. Ross, T.A. McMeekin, and J. Olley. 1991. Comparison of Arrhenius-type and Belehrádek-type models for prediction of bacterial growth in foods. J Appl. Bacteriol. 71: 452-459.

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.

Scharff, R.L. 2010. Health-Related Costs from Foodborne Illness in the United States. Washington: The Produce Safety Project at Georgetown University, An Initiative of the Pew Charitable Trusts. Available at: http://www.producesafetyproject.org/admin/assets/files/Health-Related-Foodborne-Illness-Costs-Report.pdf-1.pdf

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

LSU Agricultural Center, USDA ARS, Wayne State University
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