The lack of specificity of <i>sodC</i> -based PCR for the detection of <i>Neisseria meningitidis</i> carriage in pharyngeal swabs from adolescents

The utility of the superoxide dismutase C (<i>sodC</i>) gene for detecting <i>Neisseria meningitidis</i> carriage in pharyngeal swab samples is unclear. While it has been explored as an alternative to the capsule transport A gene for detecting invasive strains, its potential as the sole target for real-time PCR in meningococcal carriage screening remains unexplored. This study aimed to assess the utility of using <i>sodC</i> as a target for detecting invasive and non-invasive strains of <i>Neisseria meningitidis</i> in pharyngeal swabs. Oropharyngeal swab samples collected from adolescents (approximately 15-18 years of age) enrolled in the "B-Part-of-It" cluster-randomized controlled trial (NCT03089086) were selected for this study. Samples were initially screened for the presence of specific <i>N meningitidis</i> porin A gene (<i>porA</i>) using PCR and then preserved by freezing at -80°C. An assay targeting the <i>sodC</i> gene was developed using the locked nucleic acid probe-based method. Upon optimization of the <i>sodC</i> assay, 1,092 samples were retested using this assay and compared against the results from the <i>porA</i> assays to determine concordance. Out of 1,092 samples tested, 965 (88.4%) were <i>sodC</i> positive, with 100% sensitivity and 13% specificity compared to <i>porA</i>. The positive predictive values and negative predictive values for the <i>sod</i>C assay were 12% and 100%, respectively. When compared to <i>porA</i> PCR as the gold standard, the <i>sodC</i> assay lacks sufficient specificity to serve as a stand-alone screening assay for the detection of <i>Neisseria meningitidis</i> carriage in pharyngeal samples from adolescents.IMPORTANCEWhile the <i>sodC</i> assay successfully detects <i>N. meningitidis</i>, we identified a limitation in its specificity due to potential cross-reactivity with other organisms, including <i>Haemophilus</i> spp., which can result in false positives. This limitation highlights the need for careful interpretation of <i>Neisseria meningitidis</i> carriage results, especially in epidemiological studies.