title: Identification of DNA signatures suitable for use in development of real-time PCR assays by whole-genome sequence approaches: use of Streptococcus pyogenes in a pilot study.
abstract: A stepwise computational approach using three layers of publicly available software was found to effectively identify DNA signatures for Streptococcus pyogenes. PCR testing validated that 9 out of 15 signature-derived primer sets could detect as low as 5 fg of target DNA with high specificity. The selected signature-derived primer sets were successfully evaluated against all 23 clinical isolates. The approach is readily applicable for designing molecular assays for rapid detection and characterization of various pathogenic bacteria.
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA.
authors.forename: Guo-Chiuan
authors.initials: GC
authors.lastname: Hung
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Nagamine
authors.forename: Bingjie
authors.initials: B
authors.lastname: Li
authors.forename: Shyh-Ching
authors.initials: SC
authors.lastname: Lo
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D010865:Pilot Projects; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D013290:Streptococcal Infections / Q000175:diagnosis / Q000382:microbiology; D013297:Streptococcus pyogenes / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial