Background Transcription mediated amplification (TMA, Aptima Combo II) is currently unlicensed for the detection of chlamydia and gonorrhoea at extragenital sites. Accumulating evidence suggests TMA has high sensitivity and specificity for pharyngeal and rectal infection. We have offered pharyngeal and rectal TMAs to all patients presenting since April 2009 reporting receptive oral or anal intercourse.

Methods The TMA and culture results of heterosexual women receiving extragenital screening between 01/01/12 and 30/06/12 were retrospectively reviewed.

Results 1315 women were screened (1520 extra-genital samples), 79 tested positive for at least one infection at one site. 62 (4.7%) patients had genital chlamydia. 9 (0.7%) patients had genital gonorrhoea.

33 positive results were extragenital (detection rate 2.17%) with 10 patients having isolated extragenital infection.

Rectal chlamydia detection rate was 3.8%. Of the 8 patients with rectal chlamydia, 7 had co-existing genital infection.

14/1309 (1.1%) patients had pharyngeal chlamydia, 5 had isolated pharyngeal infection.

6/211 (2.8%) patients had rectal gonorrhoea, 1 had isolated rectal infection.

5/1309 (0.4%) patients had pharyngeal gonorrhoea, 3 had isolated pharyngeal infection.

There were no positive extragenital gonorrhoea cultures and no cases of extragenital dual infection.

Conclusion Detection rates for extragenital chlamydia (both sites) and rectal gonorrhoea exceeded that of genital gonorrhoea.

Without extragenital screening we would have failed to treat 10 women with isolated pharyngeal or rectal infection, i.e. 12.7% of all women testing positive.

Regarding the 8 women with rectal chlamydia, 7 could have been suboptimally treated with azithromycin and one would have been missed.

This has implications for onward transmission, enhanced transmission of other STIs, and missed opportunities for partner notification.

Failure to screen women extragenitally may reinforce the misconception that these sites are not as significant in STI transmission and encourage risk taking behaviour.