Whole-herd risk factors associated with wean-to-finish mortality under the conditions of a Midwestern USA swine production system.

Swine wean-to-finish (W2F) mortality is a multifactorial, dynamic process and a key performance indicator of commercial swine production. Although swine producers typically capture the relevant data, analysis of W2F mortality risk factors is often hindered by the fact that, even if data is available, they are typically in different formats, non-uniform, and dispersed among multiple unconnected databases. In this study, an automated framework was created to link multiple data streams to specific cohorts of market animals, including sow farm productivity parameters, sow farm and growing pig health factors, facilities, management factors, and closeout data from a Midwestern USA production system. The final dataset (master-table) contained breeding-to-market data for 1,316 cohorts of pigs marketed between July 2018 and June 2019. Following integration into a master-table, continuous explanatory variables were categorized into quartiles averages, and the W2F mortality was log-transformed, reporting geometric mean mortality of 8.69 % for the study population. Further, univariate analyses were performed to identify individual variables associated with W2F mortality (p < 0.10) for further inclusion in a multivariable model, where model selection was applied. The final multivariable model consisted of 13 risk factors and accounted for 68.2 % (R2) of the variability of the W2F mortality, demonstrating that sow farm health and performance are closely linked to downstream W2F mortality. Higher sow farm productivity was associated with lower subsequent W2F mortality and, conversely, lower sow farm productivity with higher W2F mortality e.g., groups weaned in the highest quartiles for pre-weaning mortality and abortion rate had 13.5 %, and 12.5 %, respectively, which was statistically lower than the lowest quartiles for the same variables (10.5 %, and 10.6 %). Moreover, better sow farm health status was also associated with lower subsequent W2F mortality. A significant difference was detected in W2F mortality between epidemic versus negative groups for porcine reproductive and respiratory syndrome virus (15.4 % vs 8.7 %), and Mycoplasma hyopneumoniae epidemic versus negative groups (13.7 % vs 9.9 %). Overall, this study demonstrated the application of a whole-herd analysis by aggregating information of the pre-weaning phase with the post-weaning phase (breeding-to-market) to identify and measure the major risk factors of W2F mortality.