Table 2

Select characteristics of specimens with discordant GeneXpert and conventional laboratory NAAT results

Specimen IDPatient IDLaboratory IDService IDSpecimen typeConventional laboratory
NAAT results
GeneXpert
results
GeneXpert
Ct*
Reference laboratory NAAT† result
CTNGCTNGCTNG
111‡2UrineNegativeNegativePositiveNegative34.2Negative
221‡2UrineNegativeNegativePositiveNegative37.2Positive
336UrineNegativeNegativePositiveNegative29.6NA
443‡1UrineNegativeNegativePositiveNegative30.3Positive
554LVSNegativeNegativePositiveNegative37.7NA
664UrineNegativeNegativePositiveNegative37.4NA
778UrineNegativeNegativePositiveNegative37.2Positive
883UrineNegativeNegativePositiveNegative31.6Negative
996UrineNegativePositivePositivePositive42.4Negative
10103‡12UrineNegativeNegativePositiveNegative35.5Positive
11113‡12UrineNegativePositivePositivePositive35.7Positive
1264LVSPositiveNegativeNegativeNegative0NA
13123LVSPositivePositiveNegativePositiveNANegative
14134LVSPositivePositiveNegativePositiveNANA
15144LVSNegativeNegativeNegativePositive37.5/35.5NA
16157LVSNegativeNegativeNegativePositive35.3/33.9Negative
  • *Ct, cycle threshold for discordant result only (CT—one threshold; NG—two thresholds (two targets)).

  • †Reference laboratory result for discordant infection only: performed at Royal Women’s Hospital (Melbourne)—samples in Cobas transport media/urine retested by Cobas 4800 (for both CT and NG) and by in-house Omp CT assay, in-house PorA and Opa NG assays. Swab or Aptima samples were extracted and run on in-house Omp CT assay, in-house PorA and Opa NG assays26–28 only. Positive result reported if detected on any one of these assays.

  • ‡Cobas 4800 (Roche Diagnostics).

  • §In-house CT and NG.26

  • ¶Aptima Combo 2 (Gen-Probe).

  • –, result not applicable (not discordant); CT, Chlamydia trachomatis ; LVS, lower vaginal swab; NA, sample not available; NAAT, nucleic acid amplification test; NG, Neisseria gonorrhoeae.