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

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.