Table 3 Summary of oropharyngeal swabs collection at week 6 and week 12 follow up visits

1

Tonsillar fossae

No

All sites: NAAT. The Aptima Combo 2 Assay (Hologic, Inc., CA, USA).

This will be tested in real time as part of stand-of-care specimen for participants recruited at the Melbourne Sexual Health Centre. Thus, swab number 2 is not required for participants recruited at the Melbourne Sexual Health Centre.

2

Tonsillar fossae

Yes

RPA Sexual Health: NAAT. Aptima Combo 2 assay on the Hologic Gen-Probe (San Diego, CA, USA)

Applies to all participating sites except the Melbourne Sexual Health Centre.

Sydney Sexual Health Centre and Northside clinic: NAAT. Roche cobas 4800 CT/NG (Roche Diagnostic Systems, Branchburg, NJ, USA).

Western Sydney Sexual Health Centre: NAAT. BD ProbeTec™ ET System (Becton Dickinson, Sparks, MD, USA).

3

Posterior oropharynx

No

All sites: NAAT. The Aptima Combo 2 Assay (Hologic, Inc., CA, USA).

This will be tested in real time as part of stand-of-care specimen for participants recruited at the Melbourne Sexual Health Centre. Thus, swab number 4 is not required for participants recruited at the Melbourne Sexual Health Centre.

4

Posterior oropharynx

Yes

RPA Sexual Health: NAAT. Aptima Combo 2 assay on the Hologic Gen-Probe (San Diego, CA, USA)

Applies to all participating sites except the Melbourne Sexual Health Centre.

Sydney Sexual Health Centre and Northside clinic: NAAT. Roche cobas 4800 CT/NG (Roche Diagnostic Systems, Branchburg, NJ, USA).

Western Sydney Sexual Health Centre: NAAT. BD ProbeTec™ ET System (Becton Dickinson, Sparks, MD, USA).

5

Tonsillar fossae

Yes

All sites: Culture. GC agar plate.

-

6

Posterior oropharynx

Yes

All sites: Culture. GC agar plate.

-