Genotypic diversity and antimicrobial resistance in asymptomatic Salmonella enterica serotype Typhimurium DT104

The recent emergence of multidrug-resistant Salmonella enterica subspecies enterica serotype Typhimurium phage-type DT104 represents a challenge to health workers from both human and veterinary medicine. In an effort to develop effective control strategies, it is vital to characterize accurately the extent of genetic and phenotypic variation present in the pathogen population. While previous studies have focused on disease-associated populations, we report the genetic diversity and the diversity in antimicrobial resistance associated with asymptomatic Salmonella Typhimurium DT104 isolates found in pigs. Using pulsed-field gel electrophoresis (XbaI and SpeI), we identified 62 different genotypes associated to 13 different antimicrobial resistant phenotypes among 80 asymptomatic DT104 isolates collected from the Canadian swine industry. When rarefaction curves of a subsample the asymptomatic isolates were compared to that of disease-associated isolates from a similar spatial and temporal scale, we identified significantly more genotypes among the asymptomatic populations with 27 PFGE patterns against 23.0 ± 1.4 (95% confidence intervals) in the latter. Also, using Simpson's diversity index, we observed considerably higher genetic and phenotypic diversity in the asymptomatic isolates within herds and detected possible patterns of periodic selection within the disease-associated population. We thus concluded that an important aspect of Salmonella population structure and ecology is overlooked in investigations of disease-associated isolates.