Prophage Sequences Defining Hot Spots of Genome Variation inSalmonella entericaSerovar Typhimurium Can Be Used To Discriminate between Field Isolates

Abstract

Sixty-oneSalmonella entericaserovar Typhimurium isolates of animal and human origin, matched by phage type, antimicrobial resistance pattern, and place of isolation, were analyzed by microbiological and molecular techniques, including pulsed-field gel electrophoresis (PFGE) and plasmid profiling. PFGE identified 10 profiles that clustered by phage type and antibiotic resistance pattern with human and animal isolates distributed among different PFGE profiles. Genomic DNA was purified from 23 representative strains and hybridized to the compositeSalmonellaDNA microarray, and specific genomic regions that exhibited significant variation between isolates were identified. Bioinformatic analysis showed that variable regions of DNA were associated with prophage-like elements. Subsequently, simple multiplex PCR assays were designed on the basis of these variable regions that could be used to discriminate betweenS. entericaserovar Typhimurium isolates from the same geographical region. These multiplex PCR assays, based on prophage-like elements andSalmonellagenomic island 1, provide a simple method for identifying new variants ofS. entericaserovar Typhimurium in the field.