Universal surveillance upon patient admission is important in reducing the 
transmission of methicillin-resistant Staphylococcus aureus (MRSA) and 
associated disease in hospitals. High costs for the health care system in 
conjunction with MRSA have promoted the development of rapid screening methods 
to detect MRSA carriers. This study compared two real-time PCR methods, the BD 
GeneOhm MRSA assay (BDGO) and the Xpert MRSA assay, with broth-enriched culture 
to define their performance characteristics and rapidity in an area with low 
MRSA prevalence. In total, 414 swabs from the nose and 389 swabs from the groin 
from 425 patients were tested. Of those 425 patients, 378 had swabs from both 
the nose and groin in parallel. Two hundred thirty-one and 194 patients were 
randomly assigned to the BDGO group and the Xpert MRSA group, respectively. In 
general, sensitivity, specificity, and negative predictive value (NPV) were high 
for the BDGO (100%, 98.5%, and 100%, respectively) and the Xpert MRSA (100%, 
98.2%, and 100%, respectively), irrespective of whether or not nasal and 
inguinal specimens were considered alone or combined. In contrast, the positive 
predictive value (PPV) was lower: before the resolution of discrepant results, 
the PPVs for nasal and inguinal specimens alone and combined were 87.5%, 86.7%, 
and 82.4% for the BDGO and 91.7%, 66.7%, and 92.9% for the Xpert MRSA, 
respectively. After the resolution of discrepant results, PPVs were 93.8%, 93.3% 
and 94.1% for the BDGO and 91.7%, 88.9% and 92.9% for the Xpert MRSA, 
respectively. With the BDGO, 4 of 16 carriers were each identified by nasal or 
inguinal swabs alone, whereas in the Xpert MRSA group, 4 of 13 carriers were 
exclusively identified by nasal swabs and 2 of 13 were identified by inguinal 
swabs alone. Both PCR methods showed no significant difference in the number of 
discrepant results (odds ratio, 0.70 [P = 0.789]), but specimens from wounds and 
other body sites (axilla, vagina, and throat) produced discrepancies more often 
than nasal and groin specimens (odds ratios, 4.724 [P = 0.058] and 12.163 [P < 
0.001], respectively). The facts that no false-negative PCR results were 
detected and increased PPVs were found after the resolution of discrepant 
results point to PCR as the actual gold standard. Since both sensitivity and NPV 
were exceptionally high for PCR, backup cultures may, therefore, be unnecessary 
in an area with low prevalence and with a preemptive isolation strategy but may 
still be useful for PCR-positive specimens because of the lower PPV for both 
methods and the possibility of susceptibility testing. The median time for 
analysis, including extraction, hands-on time, and actual PCR was 2 h 20 min for 
the Xpert MRSA versus 5 h 40 min for the BDGO. Concerning reporting time, 
including administration and specimen collection, the Xpert MRSA was faster than 
the BDGO (7 h 50 min versus 17 h).