Case report: false-negative Xpert MRSA/SA BC result due to spa gene deletion in a patient with methicillin-resistant Staphylococcus aureus bacteremia

Rapid diagnostic tests like the Xpert MRSA/SA BC assay are valuable for the early detection of Staphylococcus aureus (SA) and methicillin-resistant S. aureus (MRSA) in positive blood cultures. However, genetic variations in target regions can lead to false-negative results. We report a case of an 80's male with MRSA bacteremia where the Xpert MRSA/SA BC assay initially yielded false-negative results for both SA and MRSA. Subsequent culture confirmed MRSA, and whole-genome sequencing identified deletions within the spa gene, the target used for SA identification in the assay. This case highlights the importance of integrating molecular results with traditional culture methods, especially in cases of discordance, as genetic variants can impact the accuracy of rapid molecular assays.