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Detection of Neisseria gonorrhoeae and Chlamydia trachomatis in pharyngeal and rectal specimens using the BD Probetec ET system, the Gen-Probe Aptima Combo 2 assay and culture
  1. K V Ota1,2,
  2. I E Tamari3,
  3. M Smieja4,5,
  4. F Jamieson2,6,
  5. K E Jones2,
  6. L Towns6,
  7. J Juzkiw3,
  8. S E Richardson1,2,6
  1. 1
    Hospital for Sick Children, Toronto, Ontario, Canada
  2. 2
    University of Toronto, Toronto, Ontario, Canada
  3. 3
    Hassle Free Men’s Clinic, Toronto, Ontario, Canada
  4. 4
    Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
  5. 5
    Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
  6. 6
    Public Health Laboratory, Ontario Agency for Health Protection and Promotion (formerly Ontario Ministry of Health and Long-Term Care), Toronto, Ontario, Canada
  1. Dr Susan Richardson, Division of Microbiology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8; susan.richardson{at}


Objectives: This study compared the sensitivity and specificity of culture and two nucleic acid amplification tests (NAATs): the BD Probetec ET system (PT) and the Aptima Combo 2 (AC2) in detecting Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) in pharyngeal and rectal specimens.

Methods: Male subjects were prospectively recruited at an MSM clinic in Toronto, Canada. Pharyngeal and rectal specimens were obtained for GC and CT culture, PT and AC2. Urine was also obtained for PT. A true positive was defined as: (1) positive culture, (2) positive PT and AC2 at the same site or (3) a single positive NAAT and detection of the same organism by any method at another site.

Results: 248 subjects were recruited. The prevalence of pharyngeal GC was 8.1%, rectal GC 11.7%, pharyngeal CT 2.0% and rectal CT 7.7%. The sensitivity of culture for pharyngeal GC and CT was 0%; 41.4% for rectal GC and 21.1% for rectal CT. The sensitivity of PT for pharyngeal GC, rectal GC, pharyngeal CT and rectal CT was 95.0%, 93.1%, 80.0% and 94.7%, respectively. The sensitivity of AC2 was 95.0% for pharyngeal GC and 100% at all other sites. Specificity was consistently above 98%.

Conclusions: PT and AC2 detected GC and CT with superior sensitivity compared to culture. They detected 73 pharyngeal or rectal GC and CT infections compared to 16 by culture, using a rigorous gold standard. NAATs should be the method of choice for the detection of GC and CT in extragenital sites in men who have sex with men.

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  • Contributors: SER was the principal investigator for the study. KVO was the lead author. All authors contributed to the design of the study. KVO, JJ, FJ and LT collected data. Analysis was performed by KVO and MS. All authors contributed to the manuscript.

  • Competing interests: None.

  • Ethics approval: This study received research ethics approval by the Research Ethics Board at the Hospital for Sick Children in Toronto, Canada.