We compared two walk-away molecular diagnostic assays, the GeneXpert MRSA Gen 3 assay and the BD-Max MRSA XT assay. A total of 119 prospective swabs and 36 culture-positive samples were tested. Xpert MRSA Gen 3 had sensitivity of 95.7% and specificity of 100% versus 87.5% and 97.1% for BD-Max. The difference in agreement with the enriched culture results was significantly in favor of the Xpert assay (P < 0.02, McNemar nonparametric text).T he transmission of methicillin-resistant Staphylococcus aureus (MRSA) from patient to patient in health care settings is a major concern due to a poorer prognosis associated with severe MRSA infections, such as bacteremia (1, 2). The rise in the incidence of methicillin-resistant Staphylococcus aureus infections was initially restricted to a few health care-associated clones and confined to a limited set of patients in high-risk groups. The molecular detection of MRSA directly from clinical samples is complicated by the frequent association of methicillin-susceptible S. aureus with methicillin-resistant coagulase-negative staphylococci. Distinguishing between this association and true MRSA requires the specific detection of the junction of the staphylococcal cassette chromosome in the orfX locus as well as positive detection of the mec gene encoding methicillin resistance (3). With the onset of community-acquired MRSA (4), outpatients and emergency room patients became at risk for MRSA carriage, further increasing the need for determination of carriage of MRSA. More recently, livestock-associated MRSA carrying variant mecC genes further complicated the epidemiology of MRSA by increasing its molecular diversity (5). Microbiology laboratories usually define MRSA phenotypically, but the underlying genetic structures responsible for this phenotype are constantly changing (6-8), and the molecular assays designed several years back are not necessarily relevant to the epidemiology observed today (9-11). A recent comparison of culture and a commercial molecular assay performed in a high-prevalence environment showed the molecular assay to be slightly less sensitive than enriched culture using ChromID MRSA agar but also showed that the results were not significantly different, although the molecular assay yielded results in hours instead of days (12).Two fully automated walk-away platforms offer molecular detection of MRSA in nasal swabs: the BD-Max (Becton Dickinson, Le Pont de Claix, France) and the GeneXpert (Cepheid, Maurens Scopont, France) platforms. Both tests rely on the same principle (3) and detect the presence of the mecA gene and the mecC gene (mecA/C) as well as the presence of the junction between the staphylococcal cassette chromosome mec element (SCCmec) and the chromosome. However, the sequences of the primers and probes in the two assays are likely distinct, and the extraction processes rely on different principles. The performances of the assays of the previous generations have recently been found to be similar (13), but the release of updated versions warrants a ren...