title: Influence of primer sequences and DNA extraction method on detection of non-O157 Shiga toxin-producing Escherichia coli in ground beef by real-time PCR targeting the eae, stx, and serogroup-specific genes.
abstract: Non-O157 Shiga toxin-producing Escherichia coli (STEC) infections, particularly those caused by the "big six" or "top six" non-O157 serogroups (O26, O45, O103, O111, O121, and O145) can result in severe illness and complications. Because of their  significant public health impact and the notable prevalence of STEC in cattle, methods for detection of the big six non-O157 STEC in ground beef have been established. Currently, the U.S. Department of Agriculture, Food Safety and Inspection Service detection methods for screening beef samples  for non-O157 STEC target the stx(1), stx(2), and eae virulence genes, with the 16S rRNA gene as an internal control, in a real-time PCR multiplex assay. Further, the serogroup is determined by PCR targeting genes in the E. coli O-antigen gene clusters  of the big six non-O157 serogroups. The method that we previously reported was improved so that additional stx variants, stx(1d), stx(2e), and stx(2g), are detected. Additionally, alignments of the primers targeting the eae gene  were used to improve the detection assay so that eae subtypes that could potentially be of clinical significance would also be detected. Therefore, evaluation of alternative real-time PCR assay primers and probes for the stx and eae reactions was carried out in order to  increase the stx and eae subtypes detected. Furthermore, a Tris-EDTA DNA extraction method was compared with a previously used procedure that was based on a commercially available reagent. The Tris-EDTA DNA extraction method significantly decreased the cycle threshold values  for the stx assay (P < 0.0001) and eae assay (P < 0.0001), thereby increasing the ability to detect the targets. The use of different stx primers and probes increased the subtypes detected to include stx(1d), stx(2e),  and stx(2g), and sequence data showed that modification of the eae primer should allow the known eae subtypes to be detected.
authors.affiliation: U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA 19038, USA.
authors.forename: Jamie L
authors.initials: JL
authors.lastname: Wasilenko
authors.forename: Pina M
authors.initials: PM
authors.lastname: Fratamico
authors.forename: Neelam
authors.initials: N
authors.lastname: Narang
authors.forename: Glenn E
authors.initials: GE
authors.lastname: Tillman
authors.forename: Scott
authors.initials: S
authors.lastname: Ladely
authors.forename: Mustafa
authors.initials: M
authors.lastname: Simmons
authors.forename: William C
authors.initials: WC
authors.lastname: Cray
mesh_terms: D018829:Adhesins, Bacterial / Q000235:genetics; D000818:Animals; D015373:Bacterial Typing Techniques; D002417:Cattle; D003257:Consumer Product Safety; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis*; D029968:Escherichia coli Proteins / Q000235:genetics*; D005506:Food Contamination / Q000032:analysis*; D005516:Food Microbiology; D006801:Humans; D008461:Meat Products / Q000382:microbiology*; D019081:O Antigens / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D012703:Serotyping; D022621:Shiga Toxin / Q000235:genetics; D054323:Shiga-Toxigenic Escherichia coli / Q000145:classification / Q000302:isolation & purification*
chemical_list: D018829:Adhesins, Bacterial; D017931:DNA Primers; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D019081:O Antigens; C073819:eaeA protein, E coli; D022621:Shiga Toxin