Objective Current guidelines for women do not include extragenital screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) and do not mention anal sex behaviour. The objective of this cross-sectional study was to determine the number of potentially missed CT and NG cases by relying on urogenital screening and self-reported anal sex behaviour among women.

Methods Demographic and clinical data of 4658 women attending a community health centre in Los Angeles, California, USA from 2015 to 2018 were examined. CT and NG were detected using nucleic acid amplification test (APTIMA Combo 2, Hologic Gen-Probe, San Diego, California). Demographic and behavioural factors were also examined to assess potentially missed NG/CT cases. Multivariable regression analyses were used to determine whether reported anal sex behaviour predicts NG/CT rectal infection.

Results A total of 193 NG cases and 552 CT cases were identified; however, 53.9% of NG cases and 25.5% of CT cases were identified exclusively through extragenital screening. Of all positive cases of rectal CT, 87.0% did not report anal sex without a condom and 91.3% did not report any anal sex with their last sexual partner. Of all positive cases of rectal NG, 78.9% did not report anal sex without a condom and 76.3% did not report any anal sex with their last sexual partner. Anal sex with last partner was not predictive of NG/CT rectal infection.

Conclusions Relying solely on urogenital screening and reported behaviour misses NG/CT cases. Extragenital NG/CT screening should be conducted in all women regardless of reported anal sex behaviour.