Computational protocol: Screening and Detecting Salmonella in Different Food Matrices in Southern Tunisia Using a Combined Enrichment/Real-Time PCR Method: Correlation with Conventional Culture Method

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Protocol publication

[…] Primers (F:5′-ACAGTGCTCGTTTACGACCTGAAT-3′,R:5′-AGACGGCTGGTACTGATT ATAAT-3′) and TaqMan probe (5′-Fam-CGA-CCC-CAT-AAACACCAATATCGCC-BHQ1b-3′) sequences were designed using Primer3 software () to amplify 243 bp of Salmonella spp. invA gene. They were examined to exhibit optimal biophysical properties, no dimer formation with Oligoanalyzer 3.1. They were blasted against the nucleotide database of the NCBI website to ensure identity among reported BLAST sequences for the target gene and the absence of significant homology with other microorganism sequences. The probe and primers were purchased from Integrated DNA Technologies (IDT, Coralville, IA, United States). The probe was labeled with a fluorescent reporter dye, 6-carboxyfluorescein (FAM), on the 5′-end and with Black Hole Quencher® (BHQ) at the 3′ end of the probe. […]

Pipeline specifications

Software tools Primer3, OligoAnalyzer
Application qPCR
Organisms Danio rerio, Salmonella enterica subsp. enterica serovar Kentucky
Diseases Salmonella Infections, Sprains and Strains
Chemicals Guanidine