title: A PCR-based assay for the detection of Escherichia coli Shiga-like toxin genes in ground beef.
abstract: A detection system based on the PCR has been developed for Escherichia coli strains which harbor the Shiga-like toxin genes. This quantitative detection system involves the 5'-->3' nuclease activity of Thermus aquaticus DNA polymerase, which cleaves an internal oligonucleotide probe that has been labeled with both a fluorescent reporter dye (6-carboxy-fluorescein [FAM]) and a quencher dye (6-carboxytetramethyl-rhodamine [TAMRA]). Parameters which affected the performance of the assay included primer probe distance, probe concentration, and probe target sequence homology. The optimized assay format includes two PCR primers that generate a 497-bp amplicon specific for the sltI gene with the fluorogenic probe located 19 bp from the upstream PCR primer. When the distance between the upstream PCR primer and the probe was reduced from 190 to 19 bp, delta RQ values increased from approximately 1.5 to 3.0. The delta RQ for Shiga-like toxin I probe 102 reached a maximum of 4.15 at concentrations between 25 and 50 nM. The assay is sensitive and can detect approximately 10 +/- 5 CFU per PCR. As few as 0.5 CFU of Shiga-like toxin I-producing E. coli per g could be detected in ground beef with only 12 h of enrichment in modified E. coli broth.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York 14853, USA.
authors.forename: P K
authors.initials: PK
authors.lastname: Witham
authors.forename: C T
authors.initials: CT
authors.lastname: Yamashiro
authors.forename: K J
authors.initials: KJ
authors.lastname: Livak
authors.forename: C A
authors.initials: CA
authors.lastname: Batt
mesh_terms: D000818:Animals; D001427:Bacterial Toxins / Q000235:genetics*; D001483:Base Sequence; D002417:Cattle; D015169:Colony Count, Microbial; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004926:Escherichia coli / Q000235:genetics* / Q000302:isolation & purification* / Q000472:pathogenicity; D005069:Evaluation Studies as Topic; D005456:Fluorescent Dyes; D005798:Genes, Bacterial; D015636:Magnesium Chloride; D008460:Meat / Q000382:microbiology*; D015336:Molecular Probe Techniques / Q000706:statistics & numerical data; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000706:statistics & numerical data; D012680:Sensitivity and Specificity; D022622:Shiga Toxin 1
chemical_list: D001427:Bacterial Toxins; D017931:DNA Primers; D004269:DNA, Bacterial; D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D022622:Shiga Toxin 1; D015636:Magnesium Chloride