gonococcal porA pseudogene and multi-copy opa genes. Cycle threshold (Ct) values obtained were used as semi-quantitative measures of gonococcal DNA. Sampling adequacy was assessed using a real-time PCR for human endogenous retrovirus 3 (ERV3). Results 100 MSM with culture positive pharyngeal gonorrhoea were included. Isolation rates by culture from the tonsils and posterior oropharynx were 62% and 52% respectively (p = 0.041). PCR was significantly more sensitive than culture at both the tonsils (84% vs. 62%; p < 0.001) and oropharynx (81% vs. 52%; p < 0.001). Culture positivity was greater with higher gonococcal DNA loads at both the tonsils (p = 0.001) and oropharynx (p < 0.001). At the oropharynx, higher ERV3 DNA load was associated with improved gonococcal detection using culture (p = 0.013) as well as PCR (p = 0.045). At the tonsils, higher ERV3 DNA load was associated with improved gonococcal detection by PCR (p = 0.040). Conclusion Neisseria gonorrhoeae can be cultured from the tonsils as well as the posterior oropharynx with greater isolation rates where gonococcal loads are higher. While PCR is substantially more sensitive than culture at each site, like culture, PCR is dependent on the adequacy of sampling.

seroreactivity. Estimates were weighted by the inverse of the participant social network size.