A simple STAR Element Repetitive-PCR (SER-PCR) typing method for the rapid characterization of Staphylococcus aureus

Abstract

Introduction: Staphylococcus aureus repeat (STAR) elements are abundant repeat sequences that are highly variable in numbers and locations within the genome of S. aureus. The evolutionary variation of these repeats occurs rapidly over time and may correlate with their evolutionary lineage. Therefore, the aim of this study is to analyze STAR elements to develop a simple PCR-based typing technique that can be used routinely in clinical laboratories.

Methodology: The genomes of 10 reference strains of S. aureus were analyzed to identify the number and location of STAR elements. One pair of PCR primers was designed to target the variable region of these elements. The designed primers were first evaluated against 13 well-known reference strains of S. aureus and eventually evaluated against 40 well-characterized clinical isolates.

Results: STAR element repetitive-PCR (SER-PCR) showed good typeability with acceptable discriminatory power against the reference and clinical strains. The new method clearly differentiated between community-associated methicillin-resistant S. aureus (CA-MRSA) and hospital-associated (HA-MRSA) strains. Phylogenetic analysis of the SER-PCR patterns and multilocus sequence typing (MLST) data showed good correlation between the two methods.

Conclusions: This study provides a simple genotyping method for S. aureus based on the variation of the amplicon size of a single set of primers and rapidly extracted DNA. The method is rapid with acceptable discriminatory power and does not require a sophisticated apparatus or special expertise. The results suggest that SER-PCR could be routinely useful in any clinical microbiology laboratory, particularly in developing countries.