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Background  The global burden of sexually transmitted infections (STIs) is high and there have been reports of increasing chlamydial and gonorrheal infections. High-volume screening programs for  Chlamydia trachomatis  (CT) and  Neisseria gonorrhoeae  (NG) are an important component of STI control. This study evaluated the high-volume workflow and performance of the  cobas®  CT/NG assay for use on the automated Roche  cobas®  6800 system, with the  cobas p  480 instrument for pre-analytics, compared with the Aptima Combo 2 assay on the Hologic Panther system.    Methods  High-volume workflow and performance were evaluated using paired female urine specimens. Workflow analysis ( n  = 376) included hands-on time (HoT), number of manual interventions, and time to first and last results. For performance assessment, paired results from the  cobas  CT/NG and Aptima Combo 2 assays, for both CT and NG, were compared and two-sided 95% confidence intervals calculated to provide estimates of positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) between the tests. McNemar’s test was used for significance testing.    Results  Pre-analytical preparations and system start-up on the  cobas  6800 system required 00:27:38 (hr:min:sec) HoT whilst the Panther system required 00:30:43. The  cobas  6800 system required eight interactions and 00:43:59 HoT to process 376 samples. The Panther system required six interactions and 00:39:10 HoT. Time to first results was 02:53:00 on the  cobas  c6800 system for 96 samples and 03:28:29 on the Panther system for five samples. The  cobas  6800 system delivered all 376 results 3 h faster than the Panther system (07:45:26 and 10:47:30, respectively). The performance correlation between both assays was high (PPA, NPA and OPA > 99% for both CT and NG). McNemar’s test revealed no statistically significant difference between the assays.    Conclusion  For high-volume automated CT/NG testing, both the  cobas  6800 system and Panther system provided accurate results. Although less manual intervention steps were needed for the Panther system, improved turnaround time was obtained with the  cobas  6800 system with less risk for contamination. The additional testing capacity on the  cobas  6800 system would allow a growing service to deliver more results in a single shift.    Supplementary information   Supplementary information  accompanies this paper at (10.1186/s12879-019-4442-0).

High-volume workflow and performance comparisons for Chlamydia trachomatis and Neisseria gonorrhoeae testing using automated molecular platforms