| This project was designed to understand Salmonella transmission and its antibiotic resistance in swine production systems. Floor samples (12,227) were collected systematically over space and time from gestation and finisher pens. Salmonella was isolated using enrichment bacteriological culture techniques and identified using PCR analysis with the invA primer. Genotyping of 722 isolates was performed using repetitive sequence PCR (REP, BOX, ERIC primers). Antibiotic resistance was determined using MIC panels. Class 1 integrons were detected using PCR method ( Int 1 primer). Hierarchical cluster analysis was performed to classify isolates based on genotypic similarity. Spatial analysis (Ripley's k-function) was performed to evaluate clustering of Salmonella by spatial distance. To evaluate the association between the spatial and genetic distance, Mantel's r was used.;Genotypic analysis of Salmonella isolates indicated spatial and temporal clustering of similar genotypes in 2 farrow-to-finish farms. The other 2 farms showed site-specific spatial clustering, one was farrow-to-finish, another all-in/all-out production system. Spatial analysis was performed only on a breeding gestation building of the single-site farm. Genetically similar isolates were significantly clustered to the second nearest neighboring pen during mid-June to the beginning of August, and to a few pens more distant during July. Genetic distances varied significantly over the spatial distances during six sampling time points.;Detection of antibiotic resistance of 730 Salmonella isolates and class 1 integrons types revealed 3 integron groups---1000 bp only, 1600 bp only, both 1000 and 1200 bp. Presence of any of the three integrons was associated with 4-drug resistance (Streptomycin, Spectinomycin, Sulfizoxazole, Tetracycline. In addition, presence of both 1000 and 1200 bp added resistance to Ampicillin and Chloramphenicol; 1600 bp integron added resistance to Gentamicin and Kanamycin. Int-PCR had high diagnostic accuracy (> 95% sensitivity and specificity) in detecting multi-drug resistance. The Int-PCR can be valuable in epidemiologic surveys as a screening tool to detect multi-drug resistant Salmonella . The integrons in this study were indicative of both horizontal as well as transmission of antibiotic resistant genes through clonal proliferation. Hence, integrons can be used to predict and monitor new genotypes of Salmonella entering the swine farms.;In conclusion, advanced molecular genotyping and spatial statistical methods used in the study of Salmonella transmission and its antibiotic resistance have contributed to an expanded understanding of the epidemiology of Salmonella. |
