title: A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella enterica serotype Typhimurium.
abstract: BACKGROUND
  Typhimurium is the main serotype of Salmonella enterica subsp. enterica implicated in food-borne diseases worldwide. This study aimed to detect the prevalence of ten markers combined in a macro-array based on multiplex real-time PCR. We targeted characteristic determinants located on pathogenicity islands (SPI-2 to -5, virulence plasmid pSLT and Salmonella genomic island 1 (SGI1)) as well as a specific 16S-23S rRNA intergenic spacer sequence of definitive type 104 (DT104). To investigate antimicrobial resistance, the study also targeted the presence of genes involved in sulfonamide (sul1) and beta-lactam (blaTEM) resistance. Finally, the intI1 determinant encoding integrase from class 1 integron was also investigated.
  
  
  RESULTS
  A total of 538 unrelated S. Typhimurium strains isolated between 1999 and 2009 from various sources, including food animals, food products, human and environmental samples were studied. Based on the combined presence or absence of these markers, we distinguished 34 different genotypes, including three major genotypes encountered in 75% of the studied strains, Although SPI determinants were almost always detected, SGI1, intI1, sul1 and blaTEM determinants were found 47%, 52%, 54% and 12% of the time respectively, varying according to isolation source. Low-marker patterns were most often detected in poultry sources whereas full-marker patterns were observed in pig, cattle and human sources.
  
  
  CONCLUSIONS
  The GeneDisc® assay developed in this study madeit easier to explore variability within serotype Typhimurium by analyzing ten relevant gene determinants in a large collection of strains. This real-time multiplex method constitutes a valuable tool for strains characterization on epidemiological purposes.
authors.affiliation: French Agency for Food, Environmental and Occupational Health Safety (ANSES) Laboratory for Food Safety, Maisons-Alfort Cedex, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Bugarel
authors.forename: Sophie A
authors.initials: SA
authors.lastname: Granier
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
authors.forename: Patrick
authors.initials: P
authors.lastname: Fach
authors.forename: Anne
authors.initials: A
authors.lastname: Brisabois
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D024881:Drug Resistance, Bacterial; D004783:Environmental Microbiology; D005516:Food Microbiology; D005838:Genotype; D006801:Humans; D058889:Molecular Typing / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods*; D012480:Salmonella Infections / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000382:microbiology; D012486:Salmonella typhimurium / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D014774:Virulence; D037521:Virulence Factors / Q000235:genetics*; D001618:beta-Lactamases / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D021903:DNA, Ribosomal Spacer; C562100:Sul1 protein, Salmonella typhimurium; D037521:Virulence Factors; D001618:beta-Lactamases