Assess serotype-specific and dose-response risks associated with Salmonella in poultry (2022)¹

FSIS needs an improved understanding of risks associated with consumption of poultry contaminated with Salmonella, including serotype-specific risks and those associated with higher numbers of Salmonella in poultry. One approach is to use data modeling tools that incorporate epidemiological factors and other analytical measures to characterize these risks.

Data are needed to address the risk management question, “What are the most effective strategies for reducing Salmonella foodborne illness associated with poultry?” These data and potential tools are needed to advance the science and develop available controls to further reduce Salmonella in poultry. A key data gap is which strategy will be most effective to reduce human illness attributed to poultry:

1. reducing the quantity of Salmonella in poultry,
2. reducing specific Salmonella serotypes that are more likely to cause illness,
3. or both.

Over the past 25 years, there have been significant reductions in the proportion of poultry contaminated with Salmonella but there has not been a reduction in the estimate of human Salmonella infections attributed to poultry, based on recent attribution estimates that used Salmonella outbreak data. This may be because consumption of poultry has increased over time, therefore the likelihood of illness from poultry has increased.  Another reason is that certain Salmonella serotypes are more likely to cause severe illness than others. As establishments implement controls for a particular serotype, such as pre-harvest flock vaccination, another serotype may gain prominence and cause illness. FSIS needs additional serotype-specific data and tools to inform risk assessments that are underway, to help determine the most appropriate approach for reducing Salmonella illnesses attributed to poultry consumption.

Develop a predictive model for Bacillus cereus in Egg Products (2021)²

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

Determine Clostridium perfringens Levels in Large Mass Ready-to-eat (RTE) Products. (2020)

Estimate drying times needed for different diameter dry and semi-dry fermented sausages. (2020)³

Determine whether sufficient lethality of Listeria monocytogenes and Salmonella is achieved for low water activity cured meat products such as country cured hams cooked using Appendix A time/temperature recommendations under high humidity conditions (2019)²

Identification of acceptable lethality treatments for baked goods cooked with raw meat and poultry components. (2018)²

FSIS provides guidance for lethality treatments for cooked meat and poultry products. For meat products, this guidance includes recommended time-temperature combinations that achieve a 5 to 7-log reduction in Salmonella. For poultry products, this guidance includes recommended time-temperature combinations that achieve a 7-log reduction in Salmonella. In addition to time and temperature, FSIS guidance incudes relative humidity targets to ensure acceptable lethality during cooking of meat and poultry products.

Baked goods (pastry) type products are typically heated to higher temperatures than FSIS "safe harbor" guidance. However, for quality and practical reasons, it is not desirable to maintain relative humidity during the lethality treatment of baked goods.

FSIS has received several individual askFSIS questions from establishments that produce various pastry type products in which a raw meat or poultry filling is wrapped in raw dough requesting feedback as to whether FSIS lethality guidance can be used when the relative humidity options cannot be met. FSIS has indicated that FSIS guidance was not designed to support lethality of raw meat or poultry filling wrapped in raw dough. This has created a gap in scientific support. To address this gap establishments may choose to fully cook the filling before wrapping in dough or may choose to conduct a challenge study which can be costly.

Therefore, the key question is do these bakery types of meat and poultry products achieve sufficient lethality of the bacterial pathogens of concern (e.g., Salmonella) throughout the product, especially on the surface of the product based on the use of dry heat. Other questions include whether fats within the dough can migrate to the meat or poultry filling creating a protective effect or whether coatings between the dough and filling designed to prevent migration could also protect pathogens within the filling by reducing heat transfer. The proposed study would validate lethality treatments for these types of baked goods cooked with raw meat and poultry components as well as raw dough and addressing the questions above.

Validate heat treatment and cooling processes used for partially heat-treated large and small mass smoked meat products and identify the constituents in smoke that provide antimicrobial activity during smoking of meat products. (2018)

Determine if natural casings maintain sufficient moisture to ensure product lethality using Appendix A time and temperature tables. (2018)

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 turkey carcass sampling shows very low positive rates for Salmonella and Campylobacter, while much higher rates are found in comminuted and mechanically separated turkey. One potential reason for the difference may be the different methods of collection. The current FSIS sample collection method for carcasses uses a handheld cellulose sponge and a 5x10 cm template to swab the back and thigh (FSIS Directive 10250.1), while finished product is collected for comminuted and mechanically separated turkey testing.

Studies are needed to evaluate improved methods for sampling turkey carcasses to optimize detection of Salmonella and Campylobacter. Anon-destructive sampling method is preferred, which will result in an increased recovery and improved detection of pathogens in turkeys.

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)⁴

Develop a method to detect Shiga toxin-producing Escherichia coli (STEC) based on virulence factors. (2021)⁴

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

Develop an improved method for enumerating bacterial populations, including specific pathogens, in meat, poultry and egg products. (2020)

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.

Improve Salmonella detection methods when multiple serotypes are present, to reduce Salmonella serotype bias in enrichment media (2020)⁴

Develop methodology to identify illegal use of Nitrofurazone. (2019)⁴

Develop analytical methods beyond what is currently available in the FSIS laboratories to improve the Agency’s ability to monitor allergens. (2017)

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)

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 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.

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.

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.