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

Guo-Chiuan Hung; Kenjiro Nagamine; Bingjie Li; Shyh-Ching Lo

doi:10.1128/JCM.01155-12

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

J Clin Microbiol. 2012 Aug;50(8):2770-3. doi: 10.1128/JCM.01155-12. Epub 2012 May 16.

Authors

Guo-Chiuan Hung¹, Kenjiro Nagamine, Bingjie Li, Shyh-Ching Lo

Affiliation

¹ 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.

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.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Bacteriological Techniques / methods*
Computational Biology
DNA Primers / genetics*
DNA, Bacterial / chemistry
DNA, Bacterial / genetics*
Genome, Bacterial
Humans
Molecular Diagnostic Techniques / methods*
Pilot Projects
Real-Time Polymerase Chain Reaction / methods*
Sensitivity and Specificity
Streptococcal Infections / diagnosis
Streptococcal Infections / microbiology
Streptococcus pyogenes / genetics*
Streptococcus pyogenes / isolation & purification*

Substances

DNA Primers
DNA, Bacterial