Food Safety Research Priorities & Studies

The Food Safety and Inspection Service (FSIS) has developed a listing of the top food safety research areas of interest. FSIS has also identified key data gaps and laboratory methods that are needed to fulfill our mission.

While FSIS is not a research funding organization, it recognizes the importance of keeping abreast of the latest scientific endeavors as well as its role in promoting research in areas important to the FSIS mission. This listing supports the three goals of the FSIS Strategic Plan:

Prevent Foodborne Illness and Protect Public Health
Modernize Inspection Systems, Policies, and the Use of Scientific Approaches
Achieve Operational Excellence

These priorities are presented as suggestions for researchers interested in pursuing food safety objectives that are relevant to FSIS regulated products. This list of research areas of interest may be useful to researchers who are preparing grants for submission to agencies that fund food safety research (e.g., USDA National Institute of Food and Agriculture (http://www.nifa.usda.gov), National Institutes of Health (https://www.nih.gov/), Grants.gov (http://www.grants.gov), or researchers with resources to conduct such research.

While FSIS is extremely interested in these research areas, this interest does not imply that the data and/or technologies generated by this research will be endorsed by FSIS.

This list represents FSIS' current assessment of priority research that will help further its public health mission; the list will be updated biannually. We encourage researchers to contact Dr. Isabel Walls by e-mail (isabel.walls@usda.gov) or at (202) 924-1420 and Dr. John Hicks by e-mail (john.hicks@usda.gov) or at (301) 504-0840 with questions. We also welcome information about research on related topics not currently listed here.

Research Priorities

Chemicals of Potential Concern

Screening/Detection Methods
- Develop or improve rapid methods for screening chemical compounds in FSIS regulated products
- Develop models to estimate chemical residue concentrations in beef, pork, and chicken tissues
Chemical Characterization
- Determine the magnitude and significance of migration of chemicals (e.g., endocrine disruptors) from packaging into FSIS regulated products
Intervention Strategies
- Identify and/or develop and evaluate the effectiveness of pre- and post-harvest interventions to reduce levels of chemical hazards in FSIS regulated products

Biological Hazards

Screening/Detection/Enumeration Methods
- Identify and evaluate improved sampling methods to ensure statistically relevant samples are collected in the most appropriate manner
- Develop or refine technologies to reduce pathogen detection time, including improved sample preparation methods
- Develop or refine technologies to detect multiple pathogens from a single sample of an FSIS regulated product
- Develop or refine testing methods for quantifying pathogens in meat, poultry, and egg products
Pathogen Characterization
- Develop bioinformatic methods for identifying epidemiologically meaningful patterns in whole genome sequence data
- Develop or refine technologies for virulence/ pathogenicity characterization of pathogens
- Improve our understanding of antimicrobial resistance in pathogens in poultry and cattle
- Develop or refine cooking and cooling models for pathogens in foods
- Determine the contribution of endogenous extra-intestinal sources of pathogens (e.g., lymph nodes) to contamination of FSIS-regulated products
- Evolution and Ecology of Foodborne Pathogens
Intervention Strategies
- Identify and/or develop and evaluate the effectiveness of pre- and post-harvest interventions to reduce levels of pathogens in FSIS regulated products
- Evaluate the impact of regulatory initiatives on food contamination
- Identify consumer or retail practices which compromise the safety of FSIS regulated products
- Generate data to develop public education and outreach to improve food-handling practices

Animal Welfare

Identify or develop approaches to facilitate humane handling of FSIS regulated livestock

Label Verification

Develop improved techniques for species identity in raw and processed products

Data Gaps

FSIS has identified the following data gaps, where data are needed to inform FSIS policy and guidance documents. Collecting these data will benefit small and very small producers of meat, poultry, and egg products.

Study Title / Description	Additional Information
Determine procedures to control pathogen growth throughout slaughter, dressing, and carcass chilling processes (2021)	More research is needed to support industry best practices to control pathogen growth during and after the slaughter process. FSIS would like more information that addresses the time and conditions required to chill beef carcasses to 40-45ºF to control pathogen outgrowth and ensure food safety as well as the impact of the length of time from bleed out to the start of chilling. Further analysis of parameters that may affect the carcass chilling process, such as the use of carcass sprays in chillers, carcass moisture levels, temperatures of coolers, and humidity and airflow parameters require further study to define a supportable carcass chilling procedure. The resulting data will assist the industry in creating targeted procedures to chill beef carcasses and enhance food safety by more consistently limiting biological growth of pathogens on carcasses after the slaughter process. Additionally, the resulting data will assist FSIS in providing best practice guidance to industry.
Determine the critical operating parameters to address gaps in the cooling of scalded offal to control the growth of C. perfringens (2021)	FSIS permits establishments to treat scalded offal like carcasses and cool to 45°F within 24 hours. However, this has not been determined to limit growth of C. perfringens. These parameters do not take into account the amount of time product remains between 120°F to 80°F. If products take more than 1 hour to cool between 120°F to 80°F, excessive growth of C. perfringens may occur. In the event of a deviation, if product takes more than 1 hour to cool between 120°F to 80°F, it is unlikely that pathogen modeling will support product safety, and sampling may be needed. This study will improve food safety by providing FSIS with data to address the gap in the cooling of scalded offal, in the event of a deviation where scalded offal products may take more than 1 hour to cool between 120°F to 80°F. Further, the results of this study will allow establishments to validate their processes to prevent the excessive growth of C. perfringens and C. botulinum in the cooling of scalded offal
Identify acceptable methods for measuring moisture in high temperature/short time cooking processes in impingement, spiral, steam injected ovens. (2018)	Moisture during cooking is a critical factor to ensure adequate lethality for pathogens in meat and poultry products. The most common method to measure moisture during cooking, and one supported by Appendix A, is Relative Humidity. However, some experts believe that RH is not the best measurement with high temperature (> 212°F), short time (< 1hr) cooking methods such as those used with impingement, spiral, and steam-injected inline ovens. Recent studies have also indicated that other methods of measuring moisture may be effective for high temperature, short time cooking methods. In addition, reaching 90% RH during high temperature, short time cooking methods (above 212°F, < 1 hr., and at atmospheric pressure), is very difficult and not feasible for many cooking operations. Studies are needed regarding high temperature (> 212°F), short time (<1 hr) cooking methods such as impingement, spiral, or steam injected ovens to determine 1) what method are acceptable for measuring moisture in high temperatures (above 212°F) short time (<1 hr.) cooking methods; 2) the effects of dehydration during high temperature, short term cooking on Salmonella surface colonies; 3) scientific time/ temperature and humidity considerations including when to apply humidity in the cook cycle for adequate Salmonella lethality.
Develop or identify approaches to control human pathogens in dried and fermented products. (2014)	There has been an increased demand for ethnic/specialty sausages (e.g., basturma, soudjouk, and droëwors) in the U.S. in recent years. There is limited data demonstrating at least a 5-log reduction for Salmonella and a sufficient reduction for Lm and E. coli O157:H7 for the processes used to manufacture dried and fermented products. A study is needed to identify safe processes for the manufacture of dried and fermented products. This may assist small and very small establishments to develop safe processes without having to commission expensive studies.
Develop or identify approaches to control human pathogens in dry cured ham. (2014)	Currently, there is insufficient data available for the reduction of Salmonella, L. monocytogenes, E. coli O157:H7, or S. aureus during the dry curing process for hams. Validation of the procedures currently used and required in 9 CFR 318.10(c)(3)(iv)(G) in the dry curing process of hams have been validated for the treatment of Trichinae but have not been validated for the effectiveness in controlling other pathogens. Validation may facilitate the effectiveness of dry cured ham procedures in controlling for human pathogens and will likely have a positive public health impact.
Determine the effect of low levels of relative humidity on survival of E. coli O157:H7 and Salmonella in beef jerky. (2011)	Elucidating the impact of humidity on pathogen survival in FSIS-regulated products may lead to improved processing guidelines and reduced risk for these products.

Laboratory Detection Methods

FSIS has identified studies that pertain to validating and optimizing new laboratory methods, that may be adopted in the FSIS laboratory system after the basic research has been completed.

Study Title / Description	Additional Information
Use MALDI mass spectrometry coupled with a detection system for the rapid serological classification of Salmonella sp. and/or Shiga toxin-producing Escherichia coli (E. coli) from solid agar matrices (2022)	FSIS wishes to establish a new rapid method to distinguish serotypes of both Salmonella spp. and E. coli isolates. FSIS has recently adopted the MALDI Biotyper to quickly confirm bacterial isolates. This platform may also be used to screen presumptive isolates at any stage in which isolated organisms are grown on a solid matrix. Combining MALDI Biotyper with a rapid serotyping procedure would allow analysts to identify a target pathogen and a serotype in approximately one hour. To do this, an appropriate database of specific Salmonella serotypes would need to be developed and validated before adoption by FSIS. If successful, the ability to rapidly identify serotypes would allow the Agency to better detect diversity in all regulated sample types.
Identify and characterize Salmonella virulence markers to detect Salmonella strains most likely to cause illness. (2021)¹	Salmonella virulence and pathogenicity vary extensively across 2000+ serotypes. Salmonella Cerro and Salmonella Kentucky are frequently found in meat and poultry, but rarely cause illness, while Salmonella Typhimurium, Dublin and Enteritidis, which are also found in meat and poultry, cause very severe illness. A laboratory method is needed to identify and characterize Salmonella virulence markers, for example, using genetic sequencing technologies combined with machine learning techniques. Distinguishing Salmonella based on virulence properties rather than serotypes would enable FSIS to focus risk management strategies on the strains most likely to cause illness.
Develop a method to detect Shiga toxin-producing Escherichia coli (STEC) based on virulence factors. (2021)¹	FSIS is interested in a laboratory method to detect STEC based on virulence factors. The current gold standard method for detection and recovery of STEC uses a multiplex PCR method to detect the presence of virulence genes, Shiga toxin (stx), intimin (eae), and O-antigen (serogroup) genes in enrichment broths, followed by plating on counter-selective chromogenic agar. This method is not designed to detect or recover STEC carrying novel adherence factors or O-antigens outside of the top 7 serogroups (O157, O26, O103, O111, O121, O145, O45). To support a public health criterion based on virulence factors, laboratories need to be able to identify biomarkers (including virulence genes) that discriminate STEC pathogens from other pathogenic and non-pathogenic E. coli. Ideally, the new method should be sensitive enough to detect the presence of STEC pathogens without an enrichment step. Failure to recover emerging STEC pathotypes which may be present at low quantities in food products may pose a public health risk because many STEC strains only need a very low infectious dose to cause illness.
Develop and evaluate Assays for In-Plant Residue Screening (2021)¹	FSIS is seeking improved in-plant screening technique(s) for multiple classes of National Residue Program veterinary drugs (e.g., NSAIDs, beta agonists, and growth promotors). The technique should ideally be cost effective, easily applied and more rapid than the current Kidney Inhibition Swap (KIS test) (< 3 hours). One approach is to use Lateral Flow Assays for detection of veterinary drugs in bovine and porcine samples, ideally, in multiple matrices (e.g., blood, urine, kidney, and/or liver).
Develop an improved method for enumerating bacterial populations, including specific pathogens, in meat, poultry and egg products. (2020)¹	FSIS needs improved methods for enumerating bacteria in foods. Current FSIS testing utilizes an MPN approach to determine the total load of a targeted pathogen, such as Salmonella spp., in meat and poultry samples. FSIS is seeking alternatives, for example, one approach could be to use Liquid Chromatography-Mass Spectrometry (LC-MS). A confident correlation can likely be established between the abundance of high copy number proteins (as measured by LC-MS) and bacterial populations in liquid matrices. Accomplishing this would establish an entirely new paradigm for quantifying bacterial populations in liquid matrices and could be leveraged in both research and regulatory environments. Alternatively, an image-based automated cell counting technique could be developed for the enumeration of food borne pathogens in meat and poultry. A simple image-based automated cell counter system works with easy-to-use fluorescent stains and an automated optical system that quickly counts individual bacterial cells. This approach is more direct than the current MPN analysis and could reduce empirical/statistical errors which are currently biases inherent to the MPN process.

^1. A study is underway at USDA's Agriculture Research Service in support of this project.

Research Studies

The Food Safety and Inspection Service (FSIS) has developed a list of the top food safety research areas of interest. Below are a list of specific research studies associated with our food safety research priorities.

Screening/ Detection Methods

Study Title / Description	Additional Information
Priority: Develop or improve rapid methods for screening chemical compounds in FSIS regulated products
Develop rapid screening methods for contaminants in ante-mortem (live) food animals (2020)	Development and application of methods suitable for screening ante-mortem food animals for contaminants could potentially identify animals that would likely be violative post-mortem. Such methods would be especially valuable for suspect herds, by offering a means to minimize violative carcasses and the associated waste of resources. Ante-mortem identification of animals/herds that would likely be violative could be followed by risk management strategies aimed at producing acceptable animals for eventual slaughter.
Develop practical in-field screening techniques to identify samples containing no detectable chemical contaminants and requiring no additional laboratory analyses (2015)	The majority of samples analyzed by FSIS laboratories contain no detectable chemical residue hazards. A field-suitable (in the establishment) technique to permit FSIS to differentiate between samples that do/do not require additional analyses would permit the Agency to triage samples in the field; only samples requiring confirmatory analyses would be shipped to the labs. These screening techniques could encompass pesticides, veterinary drugs, and/or environmental contaminants. A triage method could significantly increase the efficiency of FSIS hazard monitoring programs. Ideally, the sensitivity of the field techniques would be at least equivalent to those of FSIS laboratory methods and the probability of false negatives would be zero.

Intervention Strategies

Study Title / Description

Additional Information

Priority: Develop and evaluate the effectiveness of pre- and post-harvest interventions to reduce levels of chemical hazards in FSIS regulated products

Determine whether rework processes can effectively reduce curing agent levels in cured and cooked meat and poultry products. (2024)

FSIS requires that meat and poultry products are formulated with curing agents at levels safe for human consumption. Research is needed to determine whether rework processes can effectively reduce curing agent levels in cured and cooked products (e.g., bacon, sausage) so that reformulated products meet regulatory requirements.

This research will determine whether pathogen inhibition is achieved during rework processes when the amount of curing agent added to fresh raw product is reduced, to account for higher levels of curing agent in a previously cured and cooked product, with which the fresh raw product is combined.

Determine whether interventions such as chemical treatments or thermal processing alter the allergenicity of or inactivate food allergens in finished products or on food processing equipment. (2017)

More than 170 foods have been reported to cause allergic reactions in the United States. There are eight major allergens that cause 90 percent of food-based allergic reactions. These eight allergens, the "Big 8 Allergens," are: peanuts; tree nuts (almonds, pecans, walnuts, etc.); egg; milk; soy; wheat; fish; and shellfish. Food allergies affect 3-4% of the population, and there is no effective treatment. Analytical detection methods are limited for most allergens, which challenges FSIS to monitor producers’ requirements to declare all ingredients on the label.

Allergen recalls commonly occur due to omission of allergens on food labels. Cross-contact or the inadvertent transfer of allergens to a food product from other food products, food contact surfaces, equipment, utensils, etc. can also occur if ingredients or allergen-containing products are not handled properly. Limited studies have been done on whether chemical treatments or thermal processing can reduce the allergenicity of or inactivate food allergens in foods or on food processing equipment.

Screening/ Detection/ Enumeration Methods

Study Title / Description	Additional Information
Priority: Develop or refine technologies to reduce pathogen detection time, including improved sample preparation methods
Develop practical in-field screening techniques to identify samples with no detectable pathogens and requiring no additional laboratory analyses. (2017)	For many sampling programs, most samples analyzed by FSIS laboratories contain no detectable hazards. A field-suitable (in the establishment) technique to permit FSIS to differentiate between samples that do/do not require additional analyses would permit the Agency to triage samples in the field; only samples requiring confirmatory analyses would be shipped to the labs. These screening techniques could encompass microbiological pathogens, indicator organisms, and/or organoleptic laboratory evaluations. A triage method could significantly increase the efficiency of FSIS hazard monitoring programs. Ideally, the sensitivity of the field techniques would be at least equivalent to those of FSIS laboratory methods and the probability of false negatives would be zero.
Identify biomarkers that are correlated to metabolic changes, disease severity and/or microbial phenotypic traits of interest to food safety and public health. (2015)	Rapid screening for biological markers may provide an efficient and pro-active approach to identify foodborne pathogens. Biological markers could include resistance to antimicrobials and other interventions, and/or pathogenicity. Detection methods that incorporate important biological markers may help refine the definition of adulterants by FSIS. Development of these markers may be facilitated by whole genome sequencing.
Validation of Clostridium botulinum toxin detection assay in FSIS-regulated meat products (2012)	Rapid response to Clostridium botulinum toxin contamination incidents requires the availability of reagents, methods, equipment, and expertise. The mouse bioassay is still the gold standard. An improved method is desirable.
Develop and evaluate a systematic mechanism to sample cattle pre-harvest to determine prevalence of Shiga toxin producing E. coli (STEC). (2011)	If pathogenic E. coli status of animals could be determined prior to slaughter, ante mortem slaughter procedures could be developed to minimize cross contamination. These data could be used to develop management strategies to minimize cross contamination of carcasses (e.g., positives could be slaughtered last or have specific interventions).

Pathogen Characterization

Study Title / Description

Additional Information

Priority: Develop bioinformatic methods for identifying epidemiologically meaningful patterns in whole genome sequence data

Develop a user-friendly, scalable and flexible bioinformatic pipeline for analyzing bacterial genome populations at different scales of resolution, and for incorporating features from the accessory genome (2022)

Analysis of bacterial genome populations can be used to detect outbreaks and emerging subtypes (e.g., Salmonella Infantis), and to study the evolutionary and ecological processes driving emergence and spread of pathogens. This research would encourage development of methods that allow analysis at different levels of resolution and the inclusion of accessory genes which are not shared by all members of the population. Such analyses have been shown to distinguish otherwise hidden (cryptic) subpopulations. This can be helpful in real time to detect outbreaks among some Salmonella serotypes (e.g., serotypes Enteritidis, Typhimurium and Infantis) that have very minor differences using existing methods. These methods would also be useful for detecting emerging pathogens and understanding factors driving emergence and spread of pathogens.

Study Title / Description	Additional Information
Priority: Evolution and Ecology of Foodborne Pathogens
Exploratory sampling for Salmonella in Raw Poultry Products After Release from the Establishment (2022)	FSIS is interested in whether the microbial load in raw poultry products increases along the supply chain after leaving the establishment and prior to the product reaching consumers. The research project should enumerate Salmonella on raw poultry products at the point of shipment from establishments and compare that data to the microbial load of the same type of product at retail. Retail samples are currently collected through the National Antimicrobial Resistance Monitoring System (NARMS) for enteric bacteria; however, positive results are not enumerated. Information on how a product's microbial characteristics change in the time between shipment and purchase could help inform the Agency's efforts to reduce Salmonella illnesses linked to poultry.
Determine pre-harvest sources of Salmonella strains that cause recurrent or widespread outbreaks (2021)	Several Salmonella strains have emerged recently that are now widespread in an animal industry (e.g., Salmonella Reading associated with turkey and Salmonella Infantis associated with chicken) or have caused multiple, recurrent outbreaks (e.g., pan-susceptible Salmonella Newport associated with beef). Research is needed to elucidate the sources of these strains and production/ harvesting practices that may have contributed to their emergence. These studies could further our understanding of Salmonella ecology during preharvest and identify interventions to help prevent future illnesses.
Determine the presence and/or levels of human pathogens that FSIS does not currently test for, e.g., Shigella, Yersinia enterocolitica, Toxoplasma (2021)	FSIS recognizes the need to expand its sampling projects to detect and quantify other foodborne human pathogens which it does not currently test for in raw or ready-to-eat (RTE) meat, poultry, siluriformes, and egg products. FSIS currently executes robust regulatory testing for Shiga toxin- producing Escherichia coli (STEC) in raw beef products. The Agency monitors, through a vigorous sampling program, Salmonella in beef, poultry, pork, siluriformes, eggs, and RTE products. Listeria monocytogenes is recognized as a public health threat in RTE and egg products. In addition, poultry products are tested for Campylobacter. Some pathogens which cause significant foodborne illnesses and high economic impact of interest to the Agency include, but are not limited to, Shigella spp., Clostridium perfringens, Yersinia enterocolitica, and Toxoplasma gondii. The goal would be to determine if these pathogens (or their toxins) occur in the food products that FSIS regulates, and if they are a threat to public health through consumption of these products.
Identify factors critical for persistence of STEC in multiple biotic niches such as animals and vegetation (2019)	Identification of key novel genetic characteristics, and unique biotic niches that support survival of STEC will increase understanding of these important human pathogens and/or facilitate the development of improved control strategies. Such research could include identification of the following: Agricultural and/or non-agricultural environments that provide a source of STEC ultimately linked to infection of livestock. Pathways that facilitate transmission of STEC from the environment to livestock including the following: Elucidation of the biphasic lifestyle (inside and outside the host) of STEC identifying key factors that lead to successful survival inside and outside the animal host Identification of any cross-feeding scenarios within the context of the microbiota crucial for STEC survival within the bovine gastrointestinal niche of cattle versus veal food animals. Genetic characteristics of STEC and its environment that enhance its environmental fitness, including: Delineation of the structure of the microbiome of animal hosts or reservoirs that provide a competitive edge to STEC allowing it to persist. Identification of key novel genetic markers that support the biphasic lifestyle of STEC; this should include genetic markers required for plant, animal, and environmental survival.

Study Title / Description	Additional Information
Priority: Develop or refine technologies for enhanced virulence/ pathogenicity characterization of pathogens
Assess the occurrence of Escherichia albertii in poultry to assist in determining the public health significance of E. albertii in FSIS regulated products. (2018)	E. albertii has been observed in approximately two percent of broiler chicken carcass rinsates. Research could include comparisons of different poultry classes to distinguish species or product types that are likely to harbor this microorganism, and to learn more about its virulence and pathogenicity.
Assess the occurrence of hepatitis E virus (HEV) in FSIS regulated products, primarily swine products, to assist in determining the public health significance of HEV in FSIS regulated products. (2018)	Zoonotic HEV genotype 3 has been detected in swine in the U.S. and in retail pork products. Additionally, HEV has been a cause of transplantation failures. Occupational exposure to HEV via contact with pigs has been documented in several countries. In Europe, reported cases of hepatitis E increased from 514 in 2005 to 5,617 in 2015. A recent publication in the U.K. linked human hepatitis E illnesses in England and Wales with consumption of sausages and ham at a major supermarket chain. More research is needed to understand the virulence and pathogenicity of HEV.
Develop analytical methods and assess occurrence of Campylobacter ureolyticus and other Campylobacter species in FSIS regulated products to assist in determining the public health significance of these Campylobacter species in FSIS regulated products. (2018)	Campylobacter ureolyticus, a more fastidious species than the traditional foodborne pathogens of the Campylobacter genus, is responsible for febrile gastroenteritis and may be linked to other cases and/or outbreaks. The extreme difficulty in culturing and isolation of this organism implies that improved methodology may be required prior to assessing prevalence in FSIS-regulated products. One study in Ireland indicated that nearly one quarter of all cases of human campylobacteriosis over a twelve-month period demonstrated the presence of C. ureolyticus, when tested with species-specific PCR primers. These cases also demonstrated a seasonal pattern where the peak occurred earlier in spring than the historical C. coli/C. jejuni seasonal peak. Researchers interested in pursuing this study topic should develop and/or identify acceptable laboratory methods and carry out a program of targeted surveillance for the emerging non-jejuni/non-coli Campylobacter. Research to understand its virulence and pathogenicity would also be of value.
Evaluate biocide resistance of outbreak vs. non-outbreak pathogen strains. (2014)	Increased resistance to biocide interventions could significantly increase the ability of pathogens to survive biocide processing techniques and cause foodborne illnesses. Identification of biocide resistant outbreak strains may lead to the identification of strains for subsequent studies aimed at elucidating the molecular mechanisms that result in increased biocide resistance, virulence, and risk to consumers.

Study Title / Description	Additional Information
Priority: Improve our understanding of antimicrobial resistance in pathogens in poultry and cattle
Investigate acquired antibiotic resistance in microorganisms in poultry and cattle. (2020)	Research is needed to learn more about acquired antibiotic resistance from ceca derived microbial flora. One approach is to investigate potential selective pressures at the pre-harvest stages which may lead to horizontal gene transfer in microorganisms from poultry and cattle.
Study the survival characteristics for Salmonella and STEC serotypes to identify serotypes which are resistant to pre- and/or post-harvest antimicrobial interventions. (2011)	Identification of intervention-resistant serotypes provides important data for developing effective intervention procedures.
Improve detection methodology to determine the prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) and C. difficile prevalence in FSIS-regulated products. (2011)	Increased understanding of S. aureus and C. difficile in FSIS-regulated products (especially pork and beef RTE products) may facilitate the development of improved pathogen management strategies.

Study Title / Description	Additional Information
Priority: Develop or refine predictive models for pathogens in foods.
Determine Clostridium perfringens levels in raw products prior to cooking and cooling (2023)	Clostridium perfringens spores and vegetative cells may contaminate raw meat and poultry products during the slaughter process. C. perfringens spores can survive cooking, germinate, and grow to unsafe levels during cooling, particularly if the products are improperly cooled. Baseline data are needed to determine the levels of C. perfringens vegetative cells and spores in a variety of different product types including raw poultry, pork, and beef products that will be cooked and cooled. Information is needed for non-intact products (e.g., injected or needle tenderized and comminuted products), and those with added ingredients (e.g., spices) that may contribute to the contamination of the product. The Agency would also like additional data on the survival of C. perfringens in the finished products during normal storage, shipping, and distribution to retail. The data from different product types and processes can be compared to determine the risk from raw products that are cooked and cooled before consumption. The results of these studies could be used, along with risk assessments, to determine the public health impact from these products and if changes are needed to the performance standards (9 CFR 318.17(a)(2), 9 CFR 318.23(c)(1), and 9 CFR 381.150(a)(2)).
Improve our understanding of the cumulative growth of C. perfringens during production of products that involve multiple heating and cooling steps (2023)	Research is needed to develop and validate a tool to assess the cumulative growth of Clostridia in FSIS regulated products during multiple heating and cooling steps. Such a tool could help provide establishments with alternative scientific support to validate processes that include cooking and cooling followed by a partial heat-treatment, such as surface pasteurization or oil-browning, and a second cooling step. These are common processes used in industry and yet research on the outgrowth of C. perfringens during these processes is lacking. Research could include processes in which a partial heat-treatment precedes a lethality treatment (non-continuous cook process). Such processes are performed under inspection, such as when a meat or poultry product is seared before sous vide cooking. This research could also be used to help establishments evaluate storage temperature deviations associated with fully cooked product that is temperature abused and held at temperatures potentially conducive to C. perfringens growth (i.e., above 50F).
Develop validated predictive microbial models that predict the growth of Clostridium botulinum during cooling. (2011)	Cooling models may be used by FSIS to estimate the impact of deviations in product handling procedures on pathogen populations and/or to develop processing criteria for a variety of FSIS-regulated products. The models should be based on dynamic (changing) temperature experiments addressing variable product temperature profiles (e.g., single, dual and multiple cooling rates) for cooked, uncured ground meat and poultry products (e.g., ground beef, ground pork, ground chicken and ground turkey) containing no food additives (e.g., salt, phosphates, nitrite, sodium and potassium lactate, sodium and potassium diacetate) that would impact on the growth of the pathogen during cooling.
Develop validated dynamic growth models for S. aureus, C. perfringens, and B. cereus to evaluate heating deviations (e.g., product with slow heating come-up times, products held at elevated sub-lethal temperatures for an extended period of time, and products that achieve incomplete lethality during the heating or cooking step) in cooked/heat-treated, cured and uncured meat and poultry products. (2011)	The proposed growth models would assist FSIS in estimating the public health impact of process deviations of FSIS-regulated products. These dynamic growth models should take into consideration the potential growth-affecting interactions between the bacterial pathogens and low levels of non-pathogenic bacteria indigenous to commercial products.

Study Title / Description	Additional Information
Priority: Determine the contribution of endogenous extra-intestinal sources of pathogens (e.g., lymph nodes) to contamination of FSIS-regulated products
Determine the contribution of Salmonella from lymph nodes of slaughtered swine to the Salmonella contamination of ground pork (2019)	The major peripheral lymph nodes of cattle carcasses have been identified as a probable source of Salmonella contamination in ground beef. The peripheral lymph nodes in pork carcasses could play a similar role in the contamination of ground product. Preliminary results from FSIS testing of ground pork suggest that ground pork is more likely to be Salmonella-positive when compared to ground beef. To ascertain the potential importance of lymph nodes to the contribution of Salmonella in ground pork, the initial step is to determine the occurrence of Salmonella in the lymph nodes of pigs slaughtered for consumption.
Determine interventions that will reduce Campylobacter and Salmonella in raw chicken livers. (2016)	The Agency continues to investigate outbreaks attributable to chicken liver. One factor that appears to largely account for this risk is pathogen contamination within the parenchymal tissue of raw chicken liver. Additional research is needed to identify and develop process intervention technologies to reduce levels of human pathogens in raw chicken livers. This will likely have a positive public health impact by reducing exposure of these pathogens to consumers.

Intervention Strategies

1. Preharvest Interventions

Study Title / Description	Additional Information
Priority: Develop and evaluate the effectiveness of pre-harvest interventions to reduce levels of pathogens in FSIS regulated products
Determine whether differences in poultry-rearing practices influence the microbiological profile and pathological disease conditions of poultry carcasses. (2017)	Large-scale commercial poultry husbandry practices typically rear birds in confinement in large houses that control environmental conditions, minimize disease exposure, and maximize stocking density. Cramped spaces limit the birds’ mobility and can induce stress, leading to leg problems, injuries, and increased mortality. Alternative rearing practices (including but not limited to pasture or free-range husbandry) may provide conditions that could impact the pathogen profile, reduce the incidence of certain poultry diseases. FSIS would like to better understand the impact of traditional versus alternative (e.g. free-range or pasture) rearing of poultry on the prevalence of poultry diseases and human pathogens at post-harvest. This research may also support changes to FSIS policies, and allow for post-harvest innovation in food safety technologies by industry.
Develop or identify effective pre-harvest interventions to reduce levels of human pathogens in poultry. (2014)	Research is needed on the efficacies of practical and applicable technologies that could be employed by poultry producers and industry to better protect public health. Pre-harvest intervention technologies (including but not limited to vaccines, competitive exclusion products and probiotics, organic acids, and prebiotics) can be used to reduce the incidence of human pathogen colonization in birds and to reduce pathogen levels in colonized birds. Using such pre-harvest interventions to reduce pathogens (e.g., Salmonella and Campylobacter) in poultry may minimize pathogens on poultry presented for slaughter and ultimately consumer exposure to pathogens.
Develop a model to estimate the effect of pre-harvest practices and interventions on pathogen contamination of ground beef. (2011)	Pre-harvest interventions have the potential to minimize pathogen concentrations in meat. Potential interventions include manipulation of feeding strategies, transportation, vaccine, source (feedlot), time of year of slaughter.
Determine the impact of climate and weather conditions on microbial pathogens in FSIS regulated products. (2011)	As environmental conditions (e.g., temperature, humidity) may influence pathogen concentrations, tailoring sampling and intervention strategies to environmental conditions may provide increased efficiency and public health benefit.

2. POSTHARVEST

Study Title / Description	Additional Information
Priority: Develop and evaluate the effectiveness of post-harvest interventions to reduce levels of pathogens in FSIS regulated products
Validate endpoint temperatures in cooking of not-ready-to-eat (NRTE) fermented, salt-cured, and dried meat and poultry products (2024).	FSIS cooking guidance for consumers is based on the temperature and, if applicable, dwell time needed to achieve reductions in pathogens in raw meat or poultry that have not been dried first. Once a product is dried, any Salmonella surviving the drying process will have increased thermal tolerance and additional heat is needed to destroy any remaining bacteria. Some NRTE products that are salt-cured and then dried, like country cured ham, are rehydrated during cooking by consumers (e.g., by boiling in a soup or stew) which would address this concern. However, other NRTE dried products are cooked under conditions that do not rehydrate the surface (i.e., grilling or pan frying using direct heat) and additional heat is needed for these products. Research is needed to validate temperatures/dwell times for achieving a 5-log reduction in Salmonella in NRTE fermented, salt-cured, or dried products cooked under dry conditions. This may include products such as chorizo, Chinese-style dried sausage, and pancetta products that are often grilled or fried by consumers. Dried products may need to be cooked to higher temperatures to kill Salmonella since Salmonella becomes much more tolerant to heat in a dried product.
Determine the effect of dry slaughter and/or delayed evisceration on the microbiological contamination of poultry carcasses. (2017)	The typical commercial poultry slaughter operation uses large volumes of water throughout the process. Consequently, cross-contamination at various steps, such as scalding, de-feathering, evisceration and chilling, can result in microbial contamination of carcasses. Establishments typically use antimicrobial interventions at various points in the process to reduce microbial contamination of carcasses with enteric pathogens. Using a dry slaughter process greatly reduces water usage and conditions that may enhance microbial outgrowth. Using a dry slaughter process can reduce cross-contamination, reduce the need for water reuse processes, and reduce the negative environmental impact from poultry wastewater. Dry poultry slaughter processing can also address restrictions that some foreign countries place on the application of certain chemical interventions to poultry products accepted for import from the United States. The dry slaughter process, alone or in combination with a delayed evisceration step, may be a feasible alternative to the traditional poultry slaughter process, especially for smaller-scale poultry slaughter establishments.
Determine prevalence, load and strains of Salmonella in roaster swine carcasses. (2017)	There have been at least two Salmonella outbreaks over the last two years attributed to cooking roaster swine. This has led to two Class I Recalls and two public health alerts. The outbreaks involved Salmonella I,4,5,12:i:-. FSIS would like to better understand interventions to effectively reduce/eliminate Salmonella on roaster swine carcasses that address the novel slaughter of this class of swine. Specifically, are there interventions that would be more effective for roaster swine since they are sold as a whole carcass, with the head still attached? FSIS would also like to better understand the factors that contribute to survival of Salmonella on roaster swine carcasses cooked on rotisseries. For example, do consumer storage practices prior to cooking result in excessive growth of Salmonella, rendering the cooking process less effective? What is the thermal profile of the entire carcass of roaster swine during cooking on rotisseries and how does that impact survival of Salmonella during roasting? Are there areas of the roaster swine such as the lymph nodes where Salmonella is more likely to survive during roasting over a heat source? In addition, FSIS would value information on livestock carcass sampling schemes to compare pathogen prevalence on the inside of the carcass and head to the outside of the carcass. This might be accomplished by conducting comparison testing of carcasses utilizing sampling techniques on the outside of the carcass compared to the inside of the carcass, and specifically the area inside the head around the tonsils and lymph nodes.
Determine whether there are unique husbandry, physiological, transportation, or processing factors that may lead to higher farm-to-table incidence and/or concentrations of STECs and Salmonella in the different classes of veal (bob veal, non- formula-fed, formula-fed, and heavy calves), and under what conditions are these pathogens more likely to occur, persist, and facilitate transmission. (2013)	Research is needed to determine for each class of veal, what is the relationship between contamination and interaction among the infected animals, farm/pen environment, STEC and Salmonella pathogens, and animal husbandry practices.
Determine the susceptibility of Salmonella enterica (Hadar and Heidelberg) ground turkey associated outbreak strains to heat, hydrostatic pressure and acid. (2012)	FSIS investigations suggest that Salmonella strains were able to survive poultry slaughter processing interventions and consumer preparation to ultimately cause illness. FSIS would like to determine if these outbreaks associated strains show unique characteristics (e.g., resistance to heat, pressure pasteurization and/or acid) which may contribute to virulence and the breadth of the outbreaks.
Identify and quantify the transfer of pathogenic hide and/or surface contaminants and gastrointestinal contents to carcasses during sanitary dressing. (2012)	Identification and quantification of sources of contamination during processing of carcasses provide the basis for the development of (1) processing procedures that minimize contamination of meat and (2) effective and efficient HACCP plans.
Determine the translocation and thermal inactivation of Salmonella and Campylobacter in tenderized and/or injected poultry products. (2011)	Campylobacter-Poultry and Salmonella-Poultry have been cited as the first and fourth highest Pathogen-Product combination with respect to annual foodborne disease burden. (UF Emerging Pathogens Institute, 2011)

3. Consumer/Retail

Study Title / Description	Additional Information
Priority: Generate data to develop public education and outreach to improve food-handling practices.
Consumer Attitudes and Safe Food-Handling Behaviors (2022)	FSIS is interested in understanding what factors influence whether consumers follow specific food safety practices (e.g., handwashing, food thermometer use, etc.). For example, caring for someone considered at high-risk for foodborne illness or having experienced severe foodborne illness in the past could potentially encourage someone to engage in safe food-handling practices. Circumstances or experiences that might serve to discourage someone from consistently practicing safe food-handling and cooking techniques could include lack of time, lack of perceived personal risk, unreliable sources of information or cultural/familial beliefs. FSIS could benefit from consumer research that addresses questions such as: Do respondents wash hands prior to preparing a meal? If not, why not? Is there anything that would compel them to change their behavior? Do respondents use a food thermometer? If not, why not? Is there any person or entity who could convince them to do so? Other useful information would include: Household data used to examine whether specific circumstances are tied to attitudes, beliefs and/or behaviors, such as: Household member age 65+ Children in the household under age 5 Household member whose immunity is compromised English is not the primary household language This research would be used to help craft consumer messaging that would make positive changes in consumer knowledge, attitudes and beliefs around safe food-handling practices.
Consumer Interpretation of Raw Product Safety-based Food Labels (2022)	A key part of FSIS' public health mission is educating consumers on safe food-handling behaviors. Labels and markings on food packaging, such as the Safe Handling Instructions (SHI) and manufacturer's cooking instructions (MCI), represent opportunities to educate consumers on how to safely handle, prepare and store meat and poultry products at the point of consumption. FSIS is interested in data to better understand what people pay attention to on raw beef, pork and poultry labels, including specific items such as the USDA mark of inspection, the sell-by and/or use-by dates, Safe Handling Instructions (SHIs) and Manufacturer's Cooking Instructions (MCIs). FSIS also wants to understand what label modifications might be most impactful in driving the desired safe food handling practices. Specifically, FSIS seeks data in the following categories: Part 1: data that captures the amount of visual attention consumers pay to various label elements; this could be used to learn which label elements hold the most promise for consumer education Part 2: data that identifies what sorts of modifications would be most impactful in making changes to the label elements identified in part 1, e.g., larger font, images, color, etc. Part 3: Whether consumers prefer embedding information about thermometer use and end-point temperatures in MCIs or keeping it in the SHI. This research will be used to help inform potential revisions to raw beef, pork and poultry labels.
Investigate common preparation practices used by consumers and restaurants that can result in undercooking of chicken livers and investigate alternative preparation options that reduce the public health risk while maintaining the desired organoleptic and sensory properties of the prepared chicken livers. (2016)	In recent years, the Agency has investigated several outbreaks attributable to chicken livers. The continued occurrence of these outbreaks indicates that chicken liver consumption is associated with elevated risk. One factor that appears to largely account for this risk is consumer bias towards consuming chicken liver that may have been undercooked by other preparers, such as restaurant cooks. Research is needed to investigate common preparation practices used by consumers and restaurants that result in undercooking of raw chicken livers and investigate alternative preparation options that reduce the public health risk while maintaining the desired organoleptic and sensory properties of the prepared chicken livers.
Develop effective risk communications for subpopulations who choose to consume raw or undercooked FSIS-regulated products. (2016)	FSIS investigations have revealed several foodborne outbreaks attributable to consumption of raw or undercooked FSIS-regulated products (for example, raw beef, chicken livers). Consumption of these products is often associated with ethnic traditions and certain niche communities. Improving identification and awareness of cultural or traditional situations, and subsequent development of effective risk communication methods will help FSIS tailor specific messaging on safe food handling and preparation practices for various at risk, vulnerable, and under-served populations, particularly those that knowingly consume raw or undercooked FSIS-regulated products. Research into different communication techniques, presentation of information, and expression of risk will help FSIS shape and deliver appropriately sensitive, effective, food safety messages.
Review and evaluation of FSIS’ cooking recommendations as applied to thin cuts of meat. (2013)	Food safety recommendations for cooking meat often assume that the temperature of the meat is constant or increases for several minutes after the meat is removed from the heat source. This may not be true for thin cuts of meat.
Determine how retail-to-table practices affect the quality and supply of fresh whole turkeys. (2013)	Differences in retail vs. consumer refrigerated storage conditions may result in spoiled product that is prepared prior to the "sell by" date. Research is needed to determine the food safety implications of this discrepancy and possibly improve communication to consumers regarding home storage of fresh whole turkeys.
Review and evaluation of FSIS' Safe Lunch Packing Recommendations. (2012)	Preliminary findings indicate that a significant portion of home packed lunches deviate from the Agency's safe temperature handling recommendations, suggesting increased risk of foodborne illness to school children and other sub-populations which bring their lunches from home. Further research is needed to substantiate these preliminary findings and, if warranted, to develop means to assure the safety of home packed meals.
Determine the correlation between ground turkey consumer preferences and undercooked/increased risk products. (2012)	Consumers' preferences for moist ground turkey may result in products that are not fully cooked. FSIS is interested in determining whether consumer preference for finished ground poultry products corresponds with a product not receiving adequate lethality for microbial contaminants. Such a correlation could indicate increased risk of human illness.

Study Title / Description	Additional Information
Priority: Identify consumer or retail practices which compromise the safety of FSIS regulated products
Identify critical operational parameters and determine pathogen control strategies for rotisserie chicken cooked at retail. (2017)	There have been Salmonella illness clusters involving rotisserie chicken in the past several years (2013-present). Recent outbreaks involved Salmonella I,4,5,12:i:-. FSIS would like to better understand the critical operational parameters during preparation, cooking and holding of retail rotisserie cooked chicken to inform guidance regarding best practices. Such parameters could include rotisserie oven design, oven cold spots and temperature measurement. FSIS would also like to better understand the potential for Salmonella biofilm formation to contribute to these outbreaks.
Determine the potential for spices and/or non-FSIS-regulated ingredients to contribute pathogens to FSIS-regulated products. (2012)	When FSIS-regulated products are combined with chemical and/or microbial contaminated spices or other ingredients, the products may become contaminated, thereby increasing the risk of foodborne illness for consumers. There is need to determine (1) the magnitude of risk for FSIS-regulated products which contain potentially contaminated ingredients and (2) develop risk management approaches where warranted.

Study Title / Description

Additional Information

Priority: Develop approaches to facilitate humane handling of FSIS regulated livestock

Determine the effectiveness of humane practices and timely corrective measures for stunning FSIS regulated livestock. (2017)

While a variety of animal handling practices are available to producers, the appropriateness and success rate of these practices may be influenced by factors such as species, product class, age, weight, plant design, transport and lairage conditions, temperature, precipitation, etc. Research is needed to identify the success rate and humanness of livestock stunning, including but not limited to corrective measures (e.g. follow-up/adaptive procedures for livestock animals that are ineffectively stunned) for the breadth of FSIS regulated product classes and establishments.

Study Title / Description	Additional Information
Priority: Develop improved techniques for species identity in raw and processed products
Development of a single technology for species testing of FSIS-regulated products.	FSIS is responsible for ensuring accuracy and compliance to species labeling requirements. Greater efficiencies could be achieved if a cost-effective alternative could be identified to consolidate current testing methods for animal species identification into one method.