Use of nucleic acid amplification testing for diagnosis of anorectal sexually transmitted infections

J Clin Microbiol. 2012 Jun;50(6):2005-8. doi: 10.1128/JCM.00185-12. Epub 2012 Apr 4.


Nucleic acid amplification testing (NAAT) has become the preferred method to detect Chlamydia trachomatis and Neisseria gonorrhoeae, but no commercial tests are cleared by the U.S. Food and Drug Administration for use with rectal swab samples. This study evaluated the performance of strand displacement amplification (SDA) and transcription-mediated amplification (TMA) to detect C. trachomatis and N. gonorrhoeae and to determine if TMA could also detect Mycoplasma genitalium and Trichomonas vaginalis in men and women reporting a history of receptive anal intercourse. Discordant results between the NAATs were reevaluated using the Aptima CT or Aptima GC assay, each of which targets primers other than those targeted by the Aptima Combo 2 (AC2) assay, as the confirmatory test. Of 497 evaluable participants, 41 (8.2%) were positive for C. trachomatis, 21 (4.2%) were positive for N. gonorrhoeae, 26 (5.2%) were positive for T. vaginalis, and 47 (9.5%) were positive for M. genitalium. The sensitivity and specificity of the C. trachomatis test were 100% and 99.8% for AC2 and 56.1% and 100% for SDA, respectively. The sensitivity and specificity of the N. gonorrhoeae test were 100% and 100% for AC2 and 76.2% and 100% for SDA, respectively, while culture was only 23.8% sensitive. Of the 114 participants who had a positive result for any of the four infectious agents, 16 were positive for two pathogens and 3 were positive for three pathogens. These data suggest that rectal infection is common and that the AC2 is superior to SDA for the detection of C. trachomatis and N. gonorrhoeae from rectal swab samples.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Adult
  • Chlamydia trachomatis / genetics
  • Chlamydia trachomatis / isolation & purification
  • Female
  • Humans
  • Male
  • Middle Aged
  • Molecular Diagnostic Techniques / methods*
  • Mycoplasma genitalium / genetics
  • Mycoplasma genitalium / isolation & purification
  • Neisseria gonorrhoeae / genetics
  • Neisseria gonorrhoeae / isolation & purification
  • Nucleic Acid Amplification Techniques / methods*
  • Rectum / microbiology*
  • Rectum / parasitology*
  • Sensitivity and Specificity
  • Sexual Behavior
  • Sexually Transmitted Diseases / diagnosis*
  • Trichomonas vaginalis / genetics
  • Trichomonas vaginalis / isolation & purification
  • United States
  • Young Adult