Summary of audit data showing the number of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections identified by cobas 4800 CT/NG PCR screen and confirmed by second specimens, and the number of patients who waited for the second specimen results before accepting antibiotic therapy
| Specimen type | Tested* | Reported positive | Reported equivocal | Equivocal patients returned | Returned patients gave 2nd specimen | Infection confirmed by 2nd specimen | Infection not confirmed by 2nd specimen | PCR screen PPV (%)† | PCR screen specificity (%) | Prevalence in this specimen type (%) | Equivocal patients treated | Patients treated after 2nd result |
| CT urine | 15 225 | 923 | 66 | 45 | 35 | 17 | 18 | 98.12 | 99.87 | 6.17 | 54 | 4 |
| CT swabs | ||||||||||||
| All | 1556 | 49 | 12 | 11 | 6 | 5 | 1 | 98.18 | 99.93 | 3.47 | 11 | 2 |
| Rectal | 769 | 39 | 10 | 9 | 4 | 3 | 1 | 97.67 | 99.86 | 5.50 | 9 | 2 |
| Throat | 722 | 6 | 0 | |||||||||
| Eye | 30 | 2 | 0 | |||||||||
| CT total (%) | 16 781 | 972 (5.75) | 78 (0.5) | 56 | 41 | 22 | 19 | 65 | 6 | |||
| NG urine | 15 253 | 76 | 2 | 2 | 2 | 1 | 1 | 98.72 | 99.99 | 0.50 | 2 | 1 |
↵* Excludes 38 and 161 samples, which gave invalid or clot error results respectively on the PCR screen; 11 and 28 of the samples were chlamydia and gonorrhoea positive, respectively, by in-house confirmation PCR or culture.
↵† PPV calculations are based on confirmed positive and negative results and do not include ‘equivocal’ patients who did not submit a second sample for analysis, as their infection status could not be determined.
PPV, positive predictive value.