1. To increase the accuracy for WGS-based attribution, these models ideally have sufficient numbers of sequences from a variety of reservoir sources and not just FSIS-regulated foods.
2. An imbalance of isolates from any one particular reservoir could bias the predictive outcome

Determine procedures to control pathogen growth throughout slaughter, dressing, and carcass chilling processes (2021)

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)

Develop or identify approaches to control human pathogens in dry cured ham. (2014)

Determine the effect of low levels of relative humidity on survival of E. coli O157:H7 and Salmonella in beef jerky. (2011)

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

Develop a method to detect Shiga toxin-producing Escherichia coli (STEC) based on virulence factors. (2021)¹

Develop and evaluate Assays for In-Plant Residue Screening (2021)¹

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.

Develop rapid screening methods for contaminants in ante-mortem (live) food animals (2020)

Develop practical in-field screening techniques to identify samples containing no detectable chemical contaminants and requiring no additional laboratory analyses (2015)

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.

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.

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.

Develop/improve foodborne Illness source attribution models to evaluate predictions and assess uncertainty for limited datasets. (2025)

1) Develop/improve WGS-based models for foodborne Illness source attribution that evaluate prediction precision and account for uncertainty when trained on imbalanced or limited source datasets.
2) Develop models to improve food source specificity by comparing specialist and generalist strains to better predict the strain source when isolated from humans.

1. Specialist strains are more restricted to a host/reservoir and therefore have more specific genetic markers. Generalist strains have less host restriction and therefore contain markers that are less useful. The key is to find markers in specialist strains that are missing from generalist strains.

1. Reflex culture refers to the process of attempting to grow the identified pathogen in a laboratory culture medium after a Culture Independent Diagnostic Test positive result.

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.

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.

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.

• 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.

Assess the occurrence of Escherichia albertii in poultry to assist in determining the public health significance of E. albertii in FSIS regulated products. (2018)

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)

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)

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.

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. 

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.

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.

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.

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.