Salmonella species are one of the major causes of foodborne diseases in the US and worldwide. The objectives of this dissertation were to describe the shedding pattern of Salmonella in feces of naturally infected finishing pigs, to compare direct q-PCR detection of Salmonella in swine feces to the microbiological culture, to quantify the fecal concentration of Salmonella in naturally infected pigs, to evaluate the association between the environmental thermal parameters in the barn and Salmonella shedding in finishing pigs, and to estimate the proportion of total model variance attributable to cohort, pig and individual sample level effects when predicting Salmonella shedding in swine. A 3 year longitudinal study was conducted on 3 sites of a multi-site farrowtofinish production system. Individual fecal samples from 900 finishing pigs (8 collections per pig) were repeatedly collected from 18 cohorts (50 pigs per cohort). Fecal samples were collected every 2 weeks for 16 weeks. Salmonella was cultured from 453 (6.6%) of 6836 fecal samples. Individual fecal samples (positive (n=443), negative (n=1225) determined by microbiological culture) were submitted for q – PCR. Pen temperature and humidity were measured every 2 minutes during the study period. The thermal parameters of interest were: hourly average, minimum and maximum lagged temperatures, hourly temperature variation, temperature humidity index (THI) and cumulative number of hours/degree above and below the thermal of neutral zone at the pen level prior to fecal sampling for 6 time periods (12h, 24h, 48h, 72h, 1 week and 1 month). The pig &ndash level incidence of Salmonella was 20.8% (187/899 pigs). Salmonella prevalence varied between both sites and cohorts within sites. The proportion of positive samples decreased over the finishing period from 12.9% to 2.8%. Intermittent detection of Salmonella was found in more than 50% of pigs that were positive at more than one collection. The finding that the majority of pigs shed intermittently has implications for surveillance and research study design when determining Salmonella status. For culture positive samples, 15.4% (68/443) were detected by qPCR, but only 3.4% (15/443) were within the q– PCR quantifiable range (≥ 10 3 CFU/g of feces). Of these latter samples, the concentration range was 1.06x10 3 – 1.73x10 6 CFU/g feces. When high shedding was detected it was clustered within a single pig and its pen – mates. Direct q – PCR may be an alternative to traditional culturedependent methods for detection of pigs with high fecal concentrations of Salmonella, but not for detection of pigs shedding low concentrations. Multilevel logistic models using generalized linear models, with random intercepts at pig, pen and cohort levels to account for clustering were constructed. The outcome variable was Salmonella fecal status of the individual sample. Cold exposure (temperatures below the thermal neutral zone) and exposure to a THI >72 were both associated with risk of Salmonella shedding. Nursery Salmonella status, site, pig age and cohort mortality rate were also associated with Salmonella shedding. The largest proportion of model variance was associated with the individual fecal sample (44.7%) followed by cohort (24.1%) and pen (20.7%). Interventions that target the thermal environment may have an effect on reducing Salmonella shedding in swine and also improve pig wellbeing and production efficiency. Alternatively, thermal parameters may be used to identify groups of pigs at high risk for Salmonella shedding.
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