Validation of the GeneXpert® CT/NG Assay for use with Male Pharyngeal and Rectal Swabs

Objectives: The GeneXpert® CT/NG (Cepheid, Sunnyvale, CA) assay is a point-of-care (POC) molecular diagnostic assay designed to rapidly test for the presence of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC). However, the test is only approved for vaginal swabs, urine, and endocervical swabs. Here, we performed an evaluation of the GeneXpert® CT/NG assay to detect the presence of CT and GC on male pharyngeal and rectal swabs. Methods: Men who have sex with men participating in an HIV and Sexually Transmitted Infection (STI) screening program providing consent were enrolled into the study. Participants were asked to self-collect two pharyngeal and two rectal swabs. One set was tested on site using GeneXpert® and the other was sent to a reference lab for molecular testing using the APTIMA® system (Hologic, San Diego, CA). Results: A total of 570 swabs were collected from 144 patients. GeneXpert® detected 13/15 rectal swabs testing CT positive by the APTIMA® assay (relative sensitivity=88.2%), 1/2 pharyngeal swabs testing CT positive (relative sensitivity=50%), and 7/9 pharyngeal swabs testing NG positive (relative sensitivity =77.8%). No discordance was observed for rectal NG swabs. Conclusions: Although less sensitive than the APTIMA® assay for the molecular detection of NG and CT, GeneXpert®'s potential as a rapid POC diagnostic still make it a viable diagnostic test for STI screening. Molecular POC diagnostics, such as this, will allow more thorough screening of at risk individuals, and enhance the ability of clinics to provide same-day diagnosis and treatment.