Spatial and genotypic clustering of Salmonella over time in a swine production unit

Transmission patterns of Salmonella in a swine production unit were investigated by statistical analysis of the spatial distribution of isolates and the clustering of genotypes over a 12-week period. The study unit was a breeding-gestation building in a single-site farrow-to-finish swine production system. During the summer of 2003, 1746 pen floor samples were collected during 6 visits conducted at 2-week intervals. Genotyping was performed on the 107 Salmonella isolates obtained using repetitive sequence PCR (3 primers: REP, BOX, ERIC). Genetic similarity was evaluated by DNA fragment matching and hierarchical cluster analysis based on genetic similarities. For each visit, the distance at which spatial clustering of Salmonella isolates occurred was estimated using second order analyses. Significant spatial clustering of Salmonella up to a distance of 15.2 m was identified for 4 of the 6 farm visits, those for which the prevalence of Salmonella was the highest. Cluster analysis of genetic similarities identified 4 groups of Salmonella isolates at the level of at least 85% similarity in rep-PCR fragment matching patterns. Genetic clusters were relatively homogeneous for time of visit, with each genetic cluster consisting of isolates from the same or temporally adjacent visits. The correlation between genetic similarity and spatial proximity between pairs of Salmonella isolates, and the correlation between these measures and differences in time of sampling, were evaluated using Mantel's r. There was a strong positive correlation (r = 0.62, p < 0.0001) between genetic distance and time of sampling, indicating evolution of the Salmonella population over time. For 4 of the 6 visits, a pattern of decreasing genetic similarity between isolates with increasing distance between sampling locations was apparent. However, when viewed over all 6 visits, Salmonella was concentrated in one area of the building and did not move in any specific direction. These results suggest that a particular genotype of Salmonella, if introduced in the breeding-gestation unit of a swine farm would evolve slowly over short time intervals; its spatial distribution would be limited primarily to adjacent or nearby pens. In this study spatial analysis (e.g., Ripley's K-function) and matrix correlation methods (e.g., Mantel's r) expanded upon cluster analysis of genotypic similarities to provide additional interpretable information regarding the spatial distances to which Salmonella is transmitted over time in swine production facilities.