Pooling pharyngeal, anorectal, and urogenital samples for screening asymptomatic men who have sex with men for Chlamydia trachomatis and Neisseria gonorrhoeae

Duygu Durukan, Tim R.H. Read, Catriona S. Bradshaw, Christopher K. Fairley, Deborah A. Williamson, Vesna De Petra, Kate Maddaford, Rebecca Wigan, Marcus Y. Chen, Anne Tran, Eric P.F. Chow

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Screening for Chlamydia trachomatis and Neisseria gonorrhoeae at the pharyngeal, urogenital, and anorectal sites is recommended for men who have sex with men (MSM). Combining the three individual-site samples into a single pooled sample could result in significant cost savings, provided there is no significant sensitivity reduction. The aim of this study was to examine the sensitivity of pooled samples for detecting chlamydia and gonorrhea in asymptomatic MSM using a nucleic acid amplification test. Asymptomatic MSM who tested positive for chlamydia or gonorrhoea were invited to participate. Paired samples were obtained from participants prior to administration of treatment. To form the pooled sample, the anorectal swab was agitated in the urine specimen transport tube and then discarded. The pharyngeal swab and 2 ml of urine sample were then added to the tube. The difference in sensitivity between testing of pooled samples and individual-site testing was calculated against an expanded gold standard, where an individual is considered positive if either pooled-sample or individual-site testing returns a positive result. All samples were tested using the Aptima Combo 2 assay. A total of 162 MSM were enrolled in the study. Sensitivities of pooled-sample testing were 86% (94/109; 95% confidence interval [CI], 79 to 92%]) for chlamydia and 91% (73/80; 95% CI, 83 to 96%) for gonorrhea. The sensitivity reduction was significant for chlamydia (P=0.02) but not for gonorrhea (P=0.34). Pooling caused 22 infections (15 chlamydia and 7 gonorrhoea) to be missed, and the majority were single-site infections (19/22). Pooling urogenital and extragenital samples from asymptomatic MSM reduced the sensitivity of detection by approximately 10% for chlamydia but not for gonorrhea.

Original languageEnglish
Article numbere01969
Number of pages19
JournalJournal of Clinical Microbiology
Issue number5
Publication statusPublished - May 2020


  • Chlamydia trachomatis
  • Men who have sex with men
  • Neisseria gonorrhoeae
  • Pooling
  • Sexually transmitted infections

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