Key Farm-to-Fork Factors Influencing E. coli Levels in Pastured Poultry Production

Pastured poultry farms offer a unique model for investigating microbial ecology in less controlled environments, presenting challenges and opportunities for food safety management. This study aims to identify the key factors that influence <i>Escherichia coli</i> levels with two complementary modeling approaches: a linear mixed-effect model (LMM) and a random forest (RF) model. Data were collected from 11 pastured poultry farms in the southeastern United States from 2014 to 2017. Five sample types were analyzed: soil (<i>n</i> = 812), feces (<i>n</i> = 817), ceca (<i>n</i> = 206), postprocessing whole carcass rinse (WCR-P; <i>n</i> = 235), and final product whole carcass rinse (WCR-F; <i>n</i> = 230). Two different sets of predictor variables were used separately: 1) 32 farming practices and 26 physicochemical properties and 2) 80 meteorological factors. The model performance was compared with the randomized mean squared error (RMSE) with a test dataset. LMM was not used for meteorological factors because of the multicollinearity. Significant differences (α = 0.05) in <i>E. coli</i> levels were observed between all sample types, with feces samples showing the highest level. Compared to LMMs, RF models generally showed higher predictive accuracy (lower RMSE) on the test dataset. For soil samples, higher pH and sodium levels were linked to higher <i>E. coli</i> levels. The same trend with pH was observed in fecal samples. WCR-P samples showed that the organic acid treatment in the rinse water led to lower <i>E. coli</i> levels than other treatments. In WCR-F samples, longer storage time led to lower <i>E. coli</i> levels. Meteorological factors showed a weaker relationship with <i>E. coli</i> levels compared to farming practices and physicochemical properties, but in soil samples, mild and stable temperature played an important role in <i>E. coli</i> survival. This study can help stakeholders develop data-driven management strategies targeting key factors to aid in the reduction of food safety and animal health risk.