In the United States, the N60 excision sampling method for beef trim products used by FSIS collects 60 thin slices of raw meat which are then analyzed for bacteria. This destructive sampling method is time-consuming, results in inconsistent sample mass, and has a risk of worker injury. To address these limitations, FSIS conducted a series of laboratory and field studies to determine if a surface sampling method could achieve equal or better bacterial recovery compared to N60 excision for sampling beef trim products. The first study compared, under laboratory conditions, sponge and cloth surface sampling methods against N60 excision using Salmonella and three strains of Shiga toxin-producing Escherichia coli (STEC), which led to the selection of the cloth-based method. An extensive field trial comparing the cloth and N60 excision sampling methods found that the dry cloth method was inferior for the detection of Salmonella and aerobic bacteria counts (p = 0.05). FSIS hypothesized bacterial die-off during sample shipping to the laboratory may have reduced dry cloth recovery. FSIS completed two additional laboratory studies to compare cloth with the addition of two types of Buffered Peptone Water to the dry cloth and found statistically significant improvements (p=0.012 and 0.039) in all measures of bacterial recovery with added buffer. The final study repeated the original field trial, except that sample collectors added 25 mL of neutralizing Buffered Peptone Water (nBPW) to the cloth prior to shipping. This study found that the cloth, with buffer recovered significantly higher counts of aerobic bacteria compared to the N60 excision sampling method and there was no significant difference in the recovery of Salmonella (p = 0.41). FSIS concluded that the cloth sampling method is the regulatory equivalent to the N60 excision sampling method and replaced N60 excision sampling with the cloth sampling method with nBPW for domestic raw beef trim products on February 1, 2023.

There are more than 2500 serotypes of Salmonella enterica. One interesting feature of this bacterium is that regardless of whether samples are collected from food commodities, a single animal species, humans, or a specific environmental setting, only about 5 serotypes constitute 50% or more of all positive samples. Another interesting feature of Salmonella is that the most common serotypes are not consistent across time or broad geographic region. Examples of this phenomenon are that Salmonella Heidelberg was the third most common serotype found in United States human illness cases in 1996, but the 53rd most common serotype in 2022. An example of serotype-specific spatial clustering is the occurrence of Salmonella Weltevreden predominantly in continental Southeast Asia. Clustering in space and time presents opportunities to control more pathogenic serotypes. In this study, data from a seven-month survey of broiler chicken carcass production in the United States are used to assess how the occurrence of the dominant serotypes changes as carcasses move through the production process. Samples were collected at rehang and postchill, with the number of positive samples at each location being 2909 and 233, respectively. Different intervention strategies may impact specific serotypes differently. Additional analyses demonstrate how serotypes are clustered (or not) as a function of production volume and corporate ownership. Understanding how the occurrence of serotypes varies across the industry can provide insights into factors that lead to the clustering of specific serotypes and has the potential to help identify intervention strategies that effectively reduce the risk of human salmonellosis.

In the United States, the Food Safety and Inspection Service (FSIS), which is part of the U.S. Department of Agriculture, oversees multiple sampling programs that focus on detecting microbial contamination of meat and poultry in slaughter and processing establishments. There have been efforts across scientific disciplines to describe data collection methods and estimation strategies for large scale surveys to allow for the integration of data from multiple sources. The FSIS sample selection methods can be described as a close approximation of either a stratified or two-stage cluster sampling design. These surveys therefore support estimates of pathogen occurrence that are derived under both design- and model-based inferential paradigms. This retrospective study will describe population-level estimation strategies and how changes in pathogen contamination can be monitored across time using a trend analysis. An example based on Campylobacter on broiler chicken carcasses is provided. The example demonstrates that changes in the apparent prevalence during the study period are predominantly the result of changes in laboratory methods.

A blood-based screening method was developed to facilitate ante-mortem screening of dairy cattle suspected of containing elevated concentrations of perfluorooctanesulfonic acid (PFOS) in their muscle tissue. The collection and subsequent laboratory analyses of 28 paired blood plasma and muscle samples from PFOS-exposed dairy cattle provided the PFOS plasma and muscle data to develop a model to estimate muscle PFOS concentrations based on plasma PFOS concentrations. The blood-based ante-mortem screening approach could be applied to predict whether beef (skeletal bovine muscle) from suspect cattle populations (or subpopulations) exceeds a particular level of concern. The data analyses indicated that the relationship between muscle and plasma PFOS concentrations differed by the class of dairy cattle (heifer, lactating, and dry) and the duration of removal (withdrawal time) from exposure to PFOS. A plasma depletion model was also developed to evaluate the estimated withdrawal time required to reduce PFOS in dairy cattle muscle to below an identified level of concern. The model indicated complex PFOS plasma depletion dynamics with a nonconstant rate of depletion. The required withdrawal time also depends on the initial concentration distribution (which differed between heifers and lactating/dry cows) and the identified level of concern.

In order for the United States Department of Agriculture's (USDA) Food Safety and Inspection Service (FSIS) to make an equivalence determination for a foreign meat, poultry or egg products inspection procedure that differs from FSIS inspection procedures (an Individual Sanitary Measure or ISM), a country must demonstrate objectively that its food safety inspection system provides the same level of public health protection as the FSIS inspection system. To evaluate microbiological testing data that such countries may submit to this end, we present a possible risk metric to inform FSIS's assessment of whether products produced under an alternative inspection system in another country pose no greater consumer risk of foodborne illness than products produced under FSIS inspection. This metric requires evaluation of prevalence estimates of pathogen occurrence in products for the foreign country and the U.S. and determining what constitutes an unacceptable deviance of another country's prevalence from the U.S. prevalence, i.e., the margin of equivalence. We define the margin of equivalence as a multiple of the standard error of the U.S. prevalence estimate. Minimizing the margin of equivalence ensures the maximum public health protection for U.S. consumers, but an optimum choice must also avoid undue burden for quantitative data from alternative inspection systems in the foreign country. Across a wide range of U.S. prevalence levels and sample sizes, we determine margin of equivalence values that provide high confidence in conclusions as to whether or not the country's product poses no greater risk of foodborne illness from microbiological pathogens. These margins of equivalence can be used to inform FSIS's equivalence determination for an ISM request from a foreign country. Illustrative examples are used to support this definition of margin of equivalence. This approach is consistent with the World Trade Organization's concept of risk equivalence and is transparent and practical to apply in situations when FSIS makes an equivalence determination for an ISM requested by a foreign country.

The United States Department of Agriculture's Food Safety and Inspection Service implemented Salmonella performance standards for establishments producing chicken parts in 2016. The standards were chosen based on the assumption that a 30 % reduction in the occurrence of Salmonella-contaminated chicken parts samples (i.e., legs, breasts or wings) would result following implementation of the performance standard program. The deri-vation of the performance standards was based on data collected prior to the implementation of the standards and in the intervening years, so overall changes in the Salmonella contamination of this product can be assessed. This study presents a historical review of changes in Salmonella contamination on chicken parts as these changes relate to the performance standard. The analysis demonstrates that the reduction in Salmonella contaminated chicken parts samples was more than 75 %, so the FSIS risk assessment significantly underestimated the actual reduction in Salmonella contamination. An analysis of chicken parts samples collected at retail demonstrates reductions of a similar magnitude. Changes in the characteristics of Salmonella contamination that are potentially relevant to the occurrence or severity of human illness, such as seasonal changes in contamination, the composition of serotypes and changes in antimicrobial resistance, are also assessed. Small but significant sea-sonal increases in contamination were observed, with the peaks occurring in late winter rather than the more traditional late summer peak. Rapid changes in both the five most common serotypes and antimicrobial resis-tance patterns were also observed.

Using data from 20 years of Salmonella foodborne outbreaks, this study investigates significant trends in the proportion of outbreaks associated with 12 broad commodity groups. Outbreak counts are demonstrated to have a stronger trend signal than outbreak illness counts. The number of outbreaks with an identified food vehicle increased significantly between 1998 and 2000. This was followed by a 10-year period when the number of outbreaks decreased. The number of outbreaks increased significantly between 2010 and 2014 and then remained unchanged for the remainder of the study period. During the period of 1998 through 2017, the proportion of outbreaks for three commodities groups, consisting of eggs, pork and seeded vegetables, changed significantly. No significant changes were observed in the remaining nine commodity groups. Simple approximations are derived to highlight the effect of dependencies between outbreak proportions and a consumption analysis for meat and poultry is used to enhance the limited interpretability of the changes in these proportions. Given commodity-specific approaches to verifying food safety and promoting pathogen reduction, regulatory agencies benefit from analyses that elucidate illness trends attributable to the products under their jurisdiction. Results from this trend analysis can be used to inform the development and assessment of new pathogen reduction programmes in the United States.

In many countries campylobacteriosis ranks as one of the most frequently reported foodborne illnesses and poultry is the commodity that is most often associated with these illnesses. Nevertheless, efforts to reduce the occurrence of pathogen contamination on poultry are often more focused on Salmonella. While some control measures are pathogen specific, such as pre-harvest vaccination for Salmonella, improvements in sanitary dressing and interventions applied during the slaughter process can be effective against all forms of microbial contamination. To investigate the potential effectiveness of these non-specific pathogen reduction strategies in the United States, it is helpful to assess if, and by how much, Campylobacter contamination of chicken meat has changed across time. This study assesses change considering data collected in both slaughter and retail establishments and comparing observed trends in contamination with trends in human surveillance data. The results support the assertion that substantial reductions in Campylobacter contamination of chicken meat in the late 1990s and early 2000s contributed to a reduction in the human case rate of campylobacteriosis. Further reductions in chicken meat contamination between 2013 and 2018 are more difficult to associate with trends in human illnesses, with one contributing factor being the inclusion of culture independent diagnostic test results in the official case counts during that time. Other contributing factors are discussed.

Revised Salmonella performance standards for ground chicken and turkey were chosen based on a risk assessment model that predicted a 25% reduction in occurrence of human exposures to Salmonella-contaminated comminuted products following implementation of the standards. To assess the validity of the risk assessment model and its predictions, this study uses a Bayesian framework to compare prior and posterior distributions for model parameters. Prior distributions are informed by 24 months of data collected before the performance standards were implemented. The posterior distributions are generated using a sampling-importance resampling algorithm based on 36 months of data collected after implementing the standards. For the comminuted turkey model parameters, prior and posterior distribution comparisons suggest that the 25% reduction target was accomplished. In contrast, the results for comminuted chicken suggest that the actual reduction in Salmonella was somewhat less than the 25% target. For both commodities, the analysis does not invalidate the risk assessment model, although it does suggest areas for modification in the future.

In 1996, the Food Safety and Inspection Service (FSIS) published its pathogen reduction and hazard analysis and critical control point (PR-HACCP) rule. The intention of this program was to reduce microbial contamination on meat, poultry, and egg products. The program was implemented in stages between January 1998 and January 2000, with sampling for Escherichia coli O157:H7 and/or Salmonella in large production establishments beginning in 1998. As the PR-HACCP program begins its third decade, it is reasonable to question whether there have been reductions in the frequency of pathogen-contaminated meat and poultry products reaching consumers. This study summarizes the results for over 650,000 samples collected by FSIS between 2000 and 2018 in slaughter and processing establishments across the United States and compares these results to the roughly 100,000 retail samples collected by the U.S. Food and Drug Administration between 2002 and 2017. The data demonstrate that there has been an overall reduction in the occurrence of Salmonella on meat and poultry products, but the direction and magnitude of change has not been consistent over time or across commodities. Although the available data do not support the identification of causal factors for the observed changes, a historical review of the timing of various factors and policy decisions generates potential hypotheses for the observed changes.

When interpreting the status of poultry processing establishments subject to performance standards testing, USDA-FSIS employs a round-up rule when fewer than the standard 52 samples per establishment per year are collected. This rule is to ensure that an establishment with fewer than 52 samples is held to a performance standard with a threshold that is not less than that based on the full 52 samples.By estimating population-based sensitivities and specificities for six pathogen reduction performance standards implemented in 2016 (i.e., comminuted chicken, comminuted turkey, and chicken parts standards for both Salmonella and Campylobacter), this study assesses the effect of the round-up rule on correctly classifying commercial poultry establishments as not meeting or meeting the performance standards. Population specificity is greater than 80% for all the performance standards and only modestly affected by reduced sample sizes. Therefore, the round-up rule mitigates against increased misclassification of establishments with low prevalence when sample size is reduced.Population sensitivity is greater than 80% for four of the performance standards but is lower for both comminuted poultry-Campylobacter standards. This sensitivity decreases with reduced sample size and changes sharply as the round up rule is applied.These sensitivity and specificity estimates can serve as benchmarks for future pathogen reduction performance standards, as well as explaining differences with past performance standards.

The Food Safety and Inspection Service (FSIS) implemented a 2-class attributes sampling plan for Campylobacter (i.e., a performance standard) for comminuted chicken based on a 1 mL direct plating assay. The performance standard specified only one allowable positive out of 52 samples. This paper explores an alternative performance standard that is based on an assay with a lower limit of detection (i.e., 30 mL instead of 1 mL) but that continues to meet the same objectives as the original standard. A multi-objective optimization algorithm is applied to determine a new number of allowable Campylobacter positives based on a 30 mL enrichment assay, such that the new performance standard would meet the public health and regulatory cost objectives of the original direct plating standard. Two scenarios are considered. Scenario one assumes there was no change in pathogen occurrence since the original 1 mL performance standard was implemented. For Scenario one, the new number of allowable positives (five) that minimizes the objective function also reflects a naïve expectation based on the ratio of the mean prevalence levels from 30 mL and 1 mL data. Scenario two considers the implications of a change in pathogen occurrence since the original 1 mL performance standard was implemented. This latter approach demonstrates the complications of reconciling the dynamics of industry distributions while referencing performance standards derived from past data.

Foodborne disease outbreaks are rare events that can be extremely costly in terms of public health as well as monetary losses for industry and government. These events can overwhelm the local public healthcare network and exceed the capacity of epidemiologists and local public health officials to investigate and manage the outbreak. Planning and allocation of sufficient resources requires an understanding of both the frequency and magnitude of large foodborne outbreaks. Describing these two characteristics is difficult because most statistical methods describe central tendencies of the phenomena under study. An exception is extreme value theory (EVT), which intends to estimate the size and frequency of adverse events as large as, or larger than, those previously observed. This study applies extreme value theory methods to foodborne disease outbreak data collected in the United States between 1973 and 2016. A brief summary of the data, including changes in the surveillance system and their effect on the outbreak data, is provided. Estimates of the outbreak size expected to be exceeded within time periods of 10, 20, 40 and 100 years, referred to as the return level, ranged from 2500 to 10,400. The estimated time period time between outbreaks (i.e., the return period) of at least 500, 5,000, 10,000 and 20,000 cases ranged from 1 to greater than 400 years.

Buffered peptone water is the rinsate commonly used for chicken rinse sampling. A new formulation of buffered peptone water was developed to address concerns about the transfer of antimicrobials, used during poultry slaughter and processing, into the rinsate. This new formulation contains additives to neutralize the antimicrobials, and this neutralizing buffered peptone water replaced the original formulation for all chicken carcass and chicken part sampling programs run by the Food Safety and Inspection Service beginning in July 2016. Our goal was to determine whether the change in rinsate resulted in significant differences in the observed proportion of positive chicken rinse samples for both Salmonella and Campylobacter. This assessment compared sampling results for the 12-month periods before and after implementation. The proportion of carcass samples that tested positive for Salmonella increased from approximately 0.02 to almost 0.06. Concurrently, the proportion of chicken part samples that tested for Campylobacter decreased from 0.15 to 0.04. There were no significant differences associated with neutralizing buffered peptone water for the other two product-pathogen pairs. Further analysis of the effect of the new rinsate on corporations that operate multiple establishments demonstrated that changes in the percent positive rates differed across the corporations, with some corporations being unaffected, while others saw all of the establishments operated by the corporation move from passing to failing the performance standard and vice versa. The results validated earlier concerns that antimicrobial contamination of rinse samples was causing false-negative Salmonella testing results for chicken carcasses. The results also indicate that additional development work may still be required before the rinsate is sufficiently robust for its use in Campylobacter testing.

Understanding how changes in the prevalence of Salmonella-positive chicken carcasses affects the prevalence of Salmonella-positive chicken parts samples across slaughter establishments is necessary to model the risk of foodborne illness. When developing new Salmonella performance standards for chicken parts—that were implemented following existing chicken carcass performance standards—FSIS made assumptions regarding the correlation between these two forms of chicken products marketed to consumers. These assumptions were necessary because data were not available at the time to measure this correlation. Using recent FSIS sampling data and covariate information concerning antimicrobials applied during chicken processing, regression analysis suggests a slight negative relationship between the prevalence of Salmonella-positive chicken parts in slaughter establishment and the use of peracetic acid on carcasses, as well as a large positive relationship between prevalence of Salmonella-positive chicken parts and carcasses. Nevertheless, using a repeated random sub-sampling cross-validation approach, the regression model has very limited predictive value. In lieu of a predictive model, estimation of the correlation between prevalence of Salmonella-positive chicken carcass and parts samples is useful for understanding the public health value of performance standards and other interventions applied to these chicken products. After adjusting the observed correlation of the sampling evidence to account for the underlying beta and binomial distribution errors inherent in observed results, the estimated correlation of prevalence of Salmonella-positive chicken carcass and parts is 0.54. This implies a moderate degree of relatedness but may still understate the true correlation because of limitations in the available data.

Advances in microbiological testing methods have led to faster and less expensive assays. Given these advances, it is logical to employ these assays for use in the sampling plan of an existing microbiological criterion. A change in the performance characteristics of the assay can affect the intended effect of the microbiological criterion. This study describes a method for updating a 2-class attributes sampling plan to account for the different test sensitivity and specificity of a new assay and provides an example based on the replacement of a culture-based assay with a real-time polymerase chain reaction assay.

The presence or absence of contaminants in food samples changes as a commodity moves along the farm-to-table continuum. Interest lies in the degree to which the prevalence (i.e., infected animals or contaminated sample units) at one location in the continuum, as measured by the proportion of test-positive samples, is correlated with the prevalence at a location later in the continuum. If prevalence of a contaminant at one location in the continuum is strongly correlated with the prevalence of the contaminant later in the continuum, then the effect of changes in contamination on overall food safety can be better understood. Pearson's correlation coefficient is one of the simplest metrics of association between two measurements of prevalence but it is biased when data consisting of presence/absence testing results are used to directly estimate the correlation. This study demonstrates the potential magnitude of this bias and explores the utility of three methods for unbiased estimation of the degree of correlation in prevalence. An example, based on testing broiler chicken carcasses for Salmonella at re-hang and post-chill, is used to demonstrate the methods.

Improvements in food hygienic production practices and intervention technologies have reduced the prevalence of pathogen-contaminated carcasses during slaughter. While this unequivocally reduces the risk of foodborne illness, the selection of microbiologic standards based on pathogens for application to raw meat and poultry commodities becomes more burdensome because of the large number of samples required to distinguish between good and poorly performing establishments. This study examines the feasibility of two alternative performance standards based on levels of APC contamination at different locations in the beef slaughter process. An example, based on the Salmonella and E. coli O157:H7 contamination on beef carcasses in the United States provides a case study for the potential effectiveness of the indicator organism-based performance standards. In the example, a performance standard based on the reduction in log 10 aerobic plate counts was shown to be superior to a performance standard based on setting a maximum log 10 aerobic plate count on finished carcasses. Published by Elsevier B.V.

Many countries operate public health surveillance systems to monitor foodborne disease occurrence. The illness counts for pathogens of interest are monitored across time to assess if changes have occurred in case rates or the overall illness burden. Common to all of these systems is that only a fraction of all foodborne illnesses are reported and the relationship between observed and the total number of illnesses is uncertain. Food-safety policies intend to affect both the total and observed number of illnesses. Ideally, the surveillance system would be sufficiently sensitive to detect these changes, but the statistical power of these systems is generally not well understood. This study proposes two approaches for estimating the power of a foodborne illness surveillance system. These methods are then applied to assess the power of detecting specified changes in the total number of illnesses in an existing surveillance system. The findings suggest that the power of a national foodborne disease surveillance system to detect modest annual reductions in Salmonella illnesses may be limited. For example, a naive presumptive model that assumes observed illnesses are reduced directly by 10% predicts that the power to discern this difference, from one year to the next, is 0.21. A Bayesian model, that accounts for uncertainty in projecting changes in total illnesses to the number of observed illnesses, predicts that the power to detect a true 10% reduction is 0.04 (i.e., 4% confidence of detecting this magnitude of reduction or 96% chance of a Type II error) one year after the change has taken effect. Although the power of a national surveillance system increases as the magnitude of reductions increases or as the number of years the reduction is maintained increases - the Bayesian model demonstrates that power is less than 0.5 for reductions up to 50% for one year and is less than 0.53 for reductions of 30% that are maintained for four years. The limited power to detect intended changes in total annual illnesses of national public health surveillance systems may highlight the need for regulators to also monitor food contamination evidence to gauge progress towards achieving intended policy effects.