Second- and third-generation commercial Neisseria gonorrhoeae screening assays and the ongoing issues of false-positive results and confirmatory testing.

Supplementary nucleic acid amplification tests for Neisseria gonorrhoeae (NG) are widely used to circumvent specificity problems often associated with extragenital sites. This study was prompted by our observations and concerns from local sexual health physicians over increased discrepancies between Roche cobas 4800 CT/NG (c4800) and our in-house supplementary NG-PCR (NG-duplex) for oropharyngeal samples, when compared with Abbott RealTime CT/NG (m2000) performed prior. Here, we investigated these differences. Three banks of NG-positive samples were used. Bank 1 (n = 344) were screened using m2000. Banks 2 (n = 344) and 3 (n = 400) were screened using c4800. Remnant nucleic acids from all banks were tested using NG-duplex as part of routine testing. Bank 2 samples were further tested using m2000, some selectively tested using Cepheid Xpert CT/NG. Bank 3 samples were further tested using cobas CT/NG (cobas 6800 system). Confirmatory rates were significantly (p < 0.0001) higher for m2000 compared with c4800, with oropharyngeal samples the key difference. However, we also showed that our NG-duplex failed to confirm some true-positive NG samples. Using an expanded gold standard, confirmatory rates for m2000 and c4800 exceeded 90% for all anatomical sites with the exception of c4800 for oropharyngeal specimens at 78%. The observed discrepancies were due to a combination of c4800 producing false-positive results for oropharyngeal samples as well as sensitivity issues related to the NG-duplex assay. The data highlight the ongoing need for NG supplemental nucleic acid testing for oropharyngeal samples but also emphasise the need for careful selection of supplementary methods.