Open Access Highly Accessed Research article

A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella enterica serotype Typhimurium

Marie Bugarel1, Sophie A Granier1, François-Xavier Weill2, Patrick Fach1 and Anne Brisabois1*

Author Affiliations

1 French Agency for Food, Environmental and Occupational Health Safety (ANSES) Laboratory for Food Safety, 23 Avenue du Général de Gaulle, F-94706 Maisons-Alfort Cedex, France

2 Laboratoire des Bactéries Pathogènes Entériques, Centre National de Référence des Salmonella, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France

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BMC Microbiology 2011, 11:151  doi:10.1186/1471-2180-11-151

Published: 27 June 2011



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.


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.


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.