Identification of patterns of transmission of Salmonella within swine production systems using pulsed field gel electrophoresis (PFGE) and repetitivesequence polymerase chain reaction (REP-PCR): a quantitative analysis

Pulsed field gel electrophoresis (PFGE) using 3 enzymes (Spe I, Xba I, Avr II) and repetitive sequence polymerase chain reaction (REP-PCR) with 3 prim ers (BOX, ERIC, REP) were compared with respect to their validity as a meth od for identifying transmission of Salmonella on swine farms. Sixty-eight i solates of Salmonella were obtained from feces of swine, cats, mice, and bi rds, insect body parts, water and floor samples, and boot scrapings collect ed on 9 swine farms in Illinois USA. Genetic distances between isolates wer e calculated using the Dice matching coefficient. Cluster analysis of dista nce matrices was conducted using the UPGMA algorithm. There was no signific ant difference between PFGE and REP-PCR in the genetic diversity detected; however, REP-PCR differentiated between 14 pairs of isolates which PFGE ide ntified as identical. There were no significant differences between PFGE an d REP-PCR in identifying all or most close genetic links as isolates from t he same farm, the same building, and from the same sampling visit, suggesti ng ecological validity for both methods. Thus, REP-PCR should be considered as an acceptable and perhaps preferable alternative to PFGE as a genotypin g method for studies of Salmonella transmission.