| Infection | NAAT | +* | − | Sensitivity | Specificity | PPV | NPV |
| Pharyngeal | PT‡ | 23 | 225 | 95.0% (19/20) | 98.2% (224/228) | 82.6% (19/23) | 99.6% (224/225) |
| GC | AC2‡ | 20 | 228 | 95.0% (19/20) | 99.6% (227/228) | 95.0% (19/20) | 99.6% (227/228) |
| (TP† = 20) | Culture | 0 | 248 | 0% (0/20) | 100% | NA | 91.9% (228/248) |
| Rectal | PT‡ | 27 | 221 | 93.1% (27/29) | 100% (219/219) | 100% (27/27) | 99.1% (219/221) |
| GC | AC2‡ | 29 | 219 | 100% (29/29) | 100% (219/219) | 100% (29/29) | 100% (219/219) |
| (TP = 29) | Culture | 12 | 236 | 41.4% (12/29) | 100% | NA | 92.8% (219/236) |
| Pharyngeal | PT | 4 | 244 | 80.0% (4/5) | 100% (243/243) | 100% (4/4) | 99.6% (243/244) |
| CT | AC2 | 7 | 241 | 100% (5/5) | 99.2% (241/243) | 71.4% (5/7) | 100% (241/241) |
| (TP = 5) | Culture | 0 | 248 | 0% (0/5) | 100% | NA | 98.0% (243/248) |
| Rectal | PT‡ | 20 | 228 | 94.7% (18/19) | 99.1% (227/229) | 90.0% (18/20) | 99.6% (227/228) |
| CT | AC2‡ | 22 | 226 | 100% (19/19) | 98.7% (226/229) | 86.4% (19/22) | 100% (226/226) |
| (TP = 19) | Culture | 4 | 244 | 21.1% (4/19) | 100% | NA | 93.8% (229/244) |
*NAAT results were considered positive only if they were positive on two runs.
†True positive.
‡McNemar test (versus culture): p<0.001.
AC2, Aptima Combo 2; CT, Chlamydia trachomatis; GC, Neisseria gonorrhoeae; NA, not applicable; NAATs, nucleic acid amplification tests; PT, BD Probetec ET system.