Analysis of Salmonella control performance in U.S. young chicken slaughter and pork slaughter establishments

Comparison of Statistical Methods for Identifying Risk Factors for Salmonella Contamination of Whole Chicken Carcasses

ABSTRACT

The complexity of the food system makes analyzing microbiological data from food studies challenging because many of the assumptions (e.g., linear relationship between independent and dependent variable and independence of observations) associated with common analytical approaches (e.g., analysis of variance) are violated. Repeated sampling within an establishment introduces longitudinal correlation that must be accounted for during analyses. In this study, statistical methods for clustered or correlated data were used to determine how correlation impacts conclusions and to compare how assumptions associated with statistical methods impact the appropriateness of these methods within the context of food safety. Risk factor analyses for Salmonella contamination of whole chicken carcasses were conducted as a case study with regulatory data collected by the U.S. Department of Agriculture Food Safety and Inspection Service between May 2015 and December 2019 from 203 regulated establishments. Three models, generalized estimating equation, random effects, and logistic, were fit to Salmonella presence or absence data with establishment demographics and inspection history included as potential covariates. Beta parameter estimates and their standard errors and odds ratios and their 95% confidence intervals were compared across models. Conclusions drawn from the three models differed with respect to geographic region, whether the chicken establishment also slaughters turkeys, and establishment noncompliance with 9 CFR §417.4 (hazard analysis critical control point system validation, verification, and reassessment) in the 84 days leading up to sample collection. The results of this study reveal the need to consider clustering and correlation when analyzing food microbiological data, provide context for selecting a statistical method, and suggest that generalized estimating equation and random effects models are preferrable over logistic regression when analyzing correlated food data. These results support a renewed focus on statistical methodology in food safety.

HIGHLIGHTS

Risk Factors for Salmonella Contamination of Whole Chicken Carcasses following Changes in U.S. Regulatory Oversight

ABSTRACT

Salmonella is a common cause of foodborne illness in the United States and often is linked to chicken products. Salmonella contamination has been associated with meat processing facility characteristics, such as the number of employees (i.e., hazard analysis critical control point [HACCP]-based definition of size). The risk factors for Salmonella contamination in U.S. poultry have not been evaluated since implementation of the New Poultry Inspection System (NPIS) in 2014. The goal of this study was to determine whether risk factors for Salmonella contamination changed after implementation of the NPIS. Presence or absence of Salmonella in whole chicken carcasses was modeled using microbiological testing data collected from 203 poultry processing establishments by the U.S. Department of Agriculture Food Safety and Inspection Service between May 2015 and December 2019. A model was fit using generalized estimating equations for weekly presence or absence of Salmonella, and production volume, geographic location, and season were included as potential covariates among other establishment demographics. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated from the marginal model. Of the 40,497 analyzable samples, 1,725 (4.26%) were positive for Salmonella. Odds of contamination was lower among establishments slaughtering ≥10,000,000 birds per year (OR = 0.466; 95% CI, [0.307, 0.710]) and establishments producing ready-to-eat finished products (OR = 0.498; 95% CI, [0.298, 0.833]) and higher among establishments historically (previous 84 days) noncompliant with HACCP regulations (OR = 1.249; 95% CI, [1.071, 1.456]). Contamination also significantly varied by season and geographic region, with higher odds of contamination during summer and outside the MidEast Central region. These results support continuation of targeted food safety policies and initiatives promoting pathogen reduction by establishments with smaller volumes and those noncompliant with HACCP regulations.

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Analysis of the relationship between economic measures and Salmonella testing results in young chicken slaughter establishments

Food processing establishments incur costs to install, maintain, and operate equipment and implement specific food safety practices. During times of economic recession, establishments might reduce their food safety efforts to conserve resources and reduce costs of operation. This study was conducted to determine whether financial performance measures are systematically associated with Salmonella test results. The association between Salmonella test results from 182 federally inspected young chicken slaughter establishments from 2007 to 2009 and financial performance was examined while controlling for other establishment characteristics. Results indicated that the smallest establishments, which slaughtered fewer than 0.2 million chickens per year, had three times as many positive test results as did the largest establishments, which slaughtered more than 86.0 million chickens per year (P < 0.01). Establishments that slaughtered more than 0.2 million but fewer than 18.5 million chickens had 1.5 times as many positive test results (P = 0.02). Two statistically significant financial performance measures were identified, but the effects were limited. Establishments in bankruptcy had 1.4 times as many positive test results as did those not in bankruptcy (P = 0.02); however, only five establishments were in bankruptcy. Establishments with better payment performance generally had better Salmonella test results, but the effect was significant only in the winter season.