Longitudinal study to evaluate the association between thermal environment and Salmonella shedding in a midwestern US swine farm

Explanation and Elaboration Document for the STROBE-Vet Statement: Strengthening the Reporting of Observational Studies in Epidemiology-Veterinary Extension

The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) statement was first published in 2007 and again in 2014. The purpose of the original STROBE was to provide guidance for authors, reviewers, and editors to improve the comprehensiveness of reporting; however, STROBE has a unique focus on observational studies. Although much of the guidance provided by the original STROBE document is directly applicable, it was deemed useful to map those statements to veterinary concepts, provide veterinary examples, and highlight unique aspects of reporting in veterinary observational studies. Here, we present the examples and explanations for the checklist items included in the STROBE-Vet statement. Thus, this is a companion document to the STROBE-Vet statement methods and process document (JVIM_14575 "Methods and Processes of Developing the Strengthening the Reporting of Observational Studies in Epidemiology-Veterinary (STROBE-Vet) Statement" undergoing proofing), which describes the checklist and how it was developed.

Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine

Salmonella enterica (nontyphoidal) is one of the major causes of foodborne diseases in the United States and worldwide. Molecular typing methods are significant tools used to better understand the transmission and ecology of Salmonella in order to implement pre-harvest control measures. The objectives of this study were to describe the Salmonella genotypes, the distribution of isolate subtypes from different ecological niches (i.e., barn environment, nursery, and individual pigs) and their evolution over time in a longitudinal study conducted in three finishing sites (housing pigs from 10 weeks of age until slaughter at 24-26 weeks of age). Among the 107 Salmonella isolates submitted for pulsed-field gel electrophoresis (PFGE) analysis, there were 25 distinct subtypes. PFGE genotyping results were consistent with the serotype findings. A large number of distinguishable PFGE patterns (i.e., within the same serovar) were observed and different combinations of subtypes were identified within and across sites and cohorts. New subtypes may result of the introduction of new strains, genetic changes, or ongoing transmission of evolved strains within the production system. The same subtypes were detected intermittently during the study period, which suggests the persistence of indistinguishable subtypes in this production system. In addition, this study suggests persistence of the same subtype over several cohorts of pigs and potential residual contamination from the barn. Factors affecting adaptation and transmission of Salmonella within and among ecological systems (e.g., finishing pigs, nursery, and environment) should be further investigated. Understanding genotypic diversity of Salmonella in different ecological niches during pre-harvest may contribute to the development of more targeted and cost effective control programs during nursery and finishing phases.

Risk factors associated with persistence of Salmonella shedding in finishing pigs

The objective of this study was to identify risk factors associated with persistence of Salmonella shedding in finishing swine. A longitudinal study was conducted in 18 cohorts of pigs from three finishing sites of one swine production company. Among the 446 Salmonella isolates (isolated from 187 pigs), there were 18 distinct serovars. The six most common serovars were S. enterica serovar Derby (47.3%), S. Agona (27.4%), S. Johannesburg (10.5%), S. Schwarzengrund (2.7%), S. Litchfield (2.5%) and S. Mbandaka (2.2%). Survival analysis techniques, Kaplan-Meier methods and Log-rank test were used to estimate the duration of Salmonella shedding in days and to evaluate differences in shedding associated with risk factors at different organizational levels: isolate (serovar), pig, cohort and site. The risk factors at the pig-level were: sex, age and individual health status; and the risk factors at the cohort-level were: health risk, treatment and "at risk pigs" proportions, nursery and barn environment Salmonella status and prior exposure to the same serovar in the nursery or barn environment. Survival analysis using acceleration failure time models, with a log-normal distribution, was applied to investigate risk factors associated with Salmonella persistence (175 pigs) and serovar-specific persistence (151 pigs) during the study period. Pigs detected Salmonella positive for the first time at 10 weeks of age had a longer duration of shedding, than pigs first detected at an older age. The duration of shedding was shorter among pigs infected with S. Derby, S. Johannesburg and other serovars as compared to pigs infected with S. Agona. A significant difference was observed among sites. Cohorts with pig treatment proportions greater than the median were more likely to have a shorter duration of Salmonella shedding. Pigs from cohorts with nursery positive pools greater than the overall mean had a longer duration of Salmonella shedding as compared to pigs from cohorts with nursery pools less than or equal to the mean. These results suggest that the duration of Salmonella shedding may depend on Salmonella serovar, pig age at the time of infection, farm site and cohort-level risk factors. Identification of risk factors associated with the duration of shedding may allow more targeted interventions for the control Salmonella by evaluation of control measures not only for prevalence reduction, but also to decrease the duration of shedding. Such measures may decrease the risk of contamination of pork and subsequent risk of foodborne illness.