Abstract
The Cepheid Xpert® MRSA/SA Blood Culture test is widely used for rapid molecular identification of Staphylococcus aureus directly from positive blood cultures with suggestive microscopy, and for upfront characterisation of methicillin susceptibility (MSSA) or resistance (MRSA). The assay targets proprietary sequences of the spa gene, a highly conserved genetic element present in virtually all S. aureus. It also incorporates targets for the mecA and staphylococcal cassette chromosome mec (SCCmec) genes, to differentiate MSSA and MRSA.
We describe a false-negative Xpert MRSA/SA blood culture interpreted as neither S. aureus nor MRSA (negative spa, mecA and SCCmec), but S. aureus was ultimately identified by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry, 16s-rRNA sequencing, and Illumina sequencing. Whole genome sequencing identified a ∼7000 base pair deletion of the spa gene region, and absent key SCCmec elements and mecA gene. In silico multi-locus sequence typing assigned sequence type 45, a common MRSA lineage, however our isolate was phenotypically penicillin-susceptible and tested negative for blaZ beta-lactamase, and repeated susceptibility testing attempts with the Vitek 2 system failed from termination.
This clinically significant S. aureus demonstrated large-scale spa gene deletions and uncharacteristic susceptibilities for sequence type, highlighting the necessity for continued multimodal identification and susceptibility testing methods given unpredictable species mutability.