title: Identification of novel Salmonella enterica serovar Typhimurium DT104-specific prophage and nonprophage chromosomal sequences among serovar Typhimurium isolates by genomic subtractive hybridization.
abstract: Genomic subtractive hybridization was performed between Salmonella enterica serovar Typhimurium LT2 and DT104 to search for novel Salmonella serovar Typhimurium DT104-specific sequences. The subtraction resulted mainly in the isolation of DNA fragments with sequence similarity to phages. Two fragments identified were associated with possible virulence factors. One fragment was identical to irsA of Salmonella serovar Typhimurium ATCC 14028, which is suggested to be involved in macrophage survival. The other fragment was homologous to HldD, an Escherichia coli O157:H7 lipopolysaccharide assembly-related protein. Five selected DNA fragments-irsA, the HldD homologue, and three fragments with sequence similarity to prophages-were tested for their presence in 17 Salmonella serovar Typhimurium DT104 isolates and 27 non-DT104 isolates by PCR. All five selected DNA fragments were Salmonella serovar Typhimurium DT104 specific among the serovar Typhimurium isolates tested. These DNA fragments can be useful for better detection and typing of Salmonella serovar Typhimurium DT104.
authors.affiliation: RIKILT Institute of Food Safety, P.O. Box 230, 6700 AE Wageningen, The Netherlands. armand.hermans@wur.nl
authors.forename: Armand P H M
authors.initials: AP
authors.lastname: Hermans
authors.forename: Tjakko
authors.initials: T
authors.lastname: Abee
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Zwietering
authors.forename: Henk J M
authors.initials: HJ
authors.lastname: Aarts
mesh_terms: D001434:Bacteriophage Typing; D002876:Chromosomes, Bacterial / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods; D016133:Polymerase Chain Reaction; D039002:Prophages / Q000235:genetics*; D012483:Salmonella Phages / Q000235:genetics*; D012486:Salmonella typhimurium / Q000145:classification* / Q000235:genetics / Q000472:pathogenicity / Q000821:virology; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial