The invention relates to the quality control of Staphylococcus aureus testing using nucleic acid amplification-based detection assays. A Staphylococcus aureus control containing a quantified amount of the microorganism with high reproducibility across vials and which is used to calibrate, validate, or verify the performance of an MRSA detection assay and methods to test patient samples together with a control. Disclosed are specific Staphylococcus aureus strains that have a phenotype demonstrating reduced aggregation and increased consistency by Real-Time PCR compared to current Staphylococcus aureus strains used as external controls. Also disclosed is a process for increasing the reproducibility of Staphylococcus aureus strains that do not exhibit a non-aggregating phenotype.