The Centers for Disease Control and Prevention (CDC) laboratory recommendations for chlamydia screening that were published April 2014 state that a vaginal swab is the preferred specimen type for women. It can either be clinician-collected or self-collected. Other acceptable sources are a cervical swab or a first-pass urine sample. For men, the recommended specimen is a first-pass urine sample. (The first-pass part of the urine is the first 15-20 ml). Commercial assays are also FDA cleared for male urethral swabs.
For chlamydia screening, a rectal swab should be collected from persons reporting exposure and tested using a NAAT. For gonorrhea screening, a rectal or oropharyngeal swab may be used. Though NAATs are not FDA cleared for rectal and oropharyngeal specimens, CDC recommends their usage based on a significant amount of scientific evidence. Laboratories would be required to perform a validation study to satisfy regulatory requirements for reporting results that may be used to medically manage patients.
Additionally, the UCSF Center of Excellence for Transgender Health recommends using culture to test for infections in male-to-female transwomen who have a neovagina.
Resources
Papp JR, Schachter J, Gaydos CA, Van Der Pol B. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae-2014. MMWR 2014;63(RR-02):1-19