Evaluation of a nucleic acid amplification system, GENECUBE, for rapid detection of staphylococcal nuc and mecA in blood culture samples

This study determined whether the GENECUBE rapid nucleic acid amplification test could directly detect nuc and mecA genes in clinical blood culture samples of Staphylococcus and various other pathogens. Between September 2020 and December 2021, 537 blood culture samples from 192 patients with suspected bacteremia were tested using conventional assays (MicroScan WalkAway96 or VITEK 2 systems) and GENECUBE nuc and mecA assays. Isolates from samples with discrepant results between the conventional and GENECUBE assays were further evaluated using MALDI-TOF mass spectrometry, disk diffusion testing using cefoxitin, broth microdilution testing using oxacillin, and sequencing for mecA. Bacterial solutions containing a mixture of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus epidermidis (MRSE) were prepared to evaluate the limit of detection (LOD) of mecA. Using conventional assays as the reference, the sensitivity, specificity, and positive and negative predictive values (95 % confidence interval) of GENECUBE were 100 % (96.8–100 %), 100 % (99.1–100 %), 100 % (96.8–100 %), and 100 % (99.1–100 %), respectively, for nuc detection and 100 % (96.1–100 %), 98.9 % (97.4–99.6 %), 94.9 % (88.5–98.3 %), and 100 % (99.2–100 %), respectively, for mecA detection. Sequencing analysis of five samples identified as methicillin-sensitive staphylococci using conventional assays and methicillin-resistant staphylococci using GENECUBE revealed the presence of methicillin-resistant isolates in all samples. The estimated LOD of mecA was 104 colony-forming units (CFU)/mL of MRSE with GENECUBE, compared with 105 CFU/mL with conventional assays. The GENECUBE assay accurately detected mecA in positive blood culture samples and had higher sensitivity than conventional assays. •GENECUBE accurately detected nuc and mecA in various blood cultures within 35 min.•GENECUBE could detect mecA in cultures containing both MS- and MR- bacteria.•Limit of detection of mecA by GENECUBE was 10-fold lower than conventional assays.