title: Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates.
abstract: Sixty-one Salmonella enterica serovar 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 composite Salmonella DNA 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 between S. enterica serovar Typhimurium isolates from the same geographical region. These multiplex PCR assays, based on prophage-like elements and Salmonella genomic island 1, provide a simple method for identifying new variants of S. enterica serovar Typhimurium in the field.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. fiona@sanger.ac.uk
authors.forename: Fiona J
authors.initials: FJ
authors.lastname: Cooke
authors.forename: John
authors.initials: J
authors.lastname: Wain
authors.forename: Maria
authors.initials: M
authors.lastname: Fookes
authors.forename: Alasdair
authors.initials: A
authors.lastname: Ivens
authors.forename: Nicholas
authors.initials: N
authors.lastname: Thomson
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Brown
authors.forename: E John
authors.initials: EJ
authors.lastname: Threlfall
authors.forename: George
authors.initials: G
authors.lastname: Gunn
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Foster
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D002417:Cattle; D016000:Cluster Analysis; D046368:Crows; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic; D039002:Prophages / Q000235:genetics; D011995:Recombination, Genetic; D012480:Salmonella Infections / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000382:microbiology; D012483:Salmonella Phages / Q000235:genetics*; D012486:Salmonella typhimurium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000821:virology; D013552:Swine
chemical_list: D004269:DNA, Bacterial