Objectives.To assess the impact of real‐time polymerase chain reaction (PCR) detection of methicillin‐resistant Staphylococcus aureus (MRSA) on nosocomial transmission and costs.

Design.Monthly MRSA detection rates were measured from April 1, 2000, through December 31, 2005. Time series analysis was used to identify changes in MRSA detection rates, and decision analysis was used to compare the costs of detection by PCR and by culture.

Setting.A 1,200‐bed, tertiary care hospital in Canada.

Patients.Admitted patients at high risk for MRSA colonization. MRSA detection using culture‐based screening was compared with a commercial PCR assay.

Results.The mean monthly incidence of nosocomial MRSA colonization or infection was 0.37 cases per 1,000 patient‐days. The time‐series model indicated an insignificant decrease of 0.14 cases per 1,000 patient‐days per month (95% confidence interval, −0.18 to 0.46) after the introduction of PCR detection ( ). The mean interval from a reported positive result until contact precautions were initiated decreased from 3.8 to 1.6 days ( ). However, the cost of MRSA control increased from Can$605,034 to Can$771,609. Of 290 PCR‐positive patients, 120 (41.4%) were placed under contact precautions unnecessarily because of low specificity of the PCR assay used in the study; these patients contributed 37% of the increased cost. The modeling study predicted that the cost per patient would be higher with detection by PCR (Can$96) than by culture (Can$67).

Conclusion.Detection of MRSA by the PCR assay evaluated in this study was more costly than detection by culture for reducing MRSA transmission in our hospital. The cost benefit of screening by PCR varies according to incidences of MRSA colonization and infection, the predictive values of the assay used, and rates of compliance with infection control measures.