Nucleic acid amplification testing (NAAT) to screen the rectum and pharynx for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) has shown superior sensitivity to culture methods1 and high rates of infection have been seen in men who have sex with men.2 Although women also report oral and anal sex, clinics do not routinely offer them screening at these sites.

We offered pharyngeal/rectal NAAT, in addition to endocervical testing, to women as directed by sexual history. Samples were analysed using the BD ProbeTecTM CT/GC Qx Amplified DNA assay in the BD viper system.

2808 women gave a total of 3043 samples over a 5-month period. Median age was 25 years (IQR=21, 31); 91.4% were of white ethnicity and 93.7% self-identified as heterosexual. 58% (1629/2808) provided pharyngeal samples and 10% (312/2808) gave rectal samples. All were asymptomatic at the pharynx and rectum.

The prevalence of rectal CT at our clinic was 7.1% (22/312) and higher than that of cervical CT (6.7%; 194/3043). Pharyngeal CT prevalence was much lower at 1.3% (23/1799) but still greater than that of cervical GC (0.52%; 15/3043). Rates of non-genital GC were also low 0.64% (2/312) at the rectum and 0.28% (3/1799) at the pharynx. 79.3% women with an extra-genital infection were also positive at the cervix. Five women had rectal infection only (all CT) and 11 women had pharyngeal infection only (9/11 CT, 2/11 GC).

In our cohort, the prevalence of rectal CT was high among women reporting anal sex. Although only five infections were found exclusively in the rectum, without screening, all of these women would remain at risk of persistent infection either through missed diagnosis or treatment failure with azithromycin. Recent reports have described azithromycin failure in the treatment of rectal CT3 and treating cervical CT infection alone may therefore not adequately treat concomitant rectal infection. We believe that women should be routinely questioned about anal sex, and where indicated, screened for rectal infections.

In 11 cases the pharynx was the sole site of infection, these infections would have been missed. Based on the number of extra tests needed to detect these, asymptomatic testing at this site was deemed to be cost-ineffective and was discontinued. However, this reservoir of infection is not insignificant, and novel and cheaper ways to detect infection at non-genital sites should be explored, such as pooling genital and non-genital samples.