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Detection of Neisseria gonorrhoeae and Chlamydia trachomatis from pooled rectal, pharyngeal and urine specimens in men who have sex with men
  1. David John Speers1,2,
  2. I-Ly Joanna Chua1,
  3. Justin Manuel3,
  4. Lewis Marshall2,3
  1. 1 Department of Microbiology, PathWest Laboratory Medicine WA (LMWA), Queen Elizabeth II (QEII) Medical Centre, Nedlands, Western Australia, Australia
  2. 2 School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
  3. 3 M Clinic, WA AIDS Council, West Perth, Western Australia, Australia
  1. Correspondence to Clinical Associate Professor David John Speers, Department of Microbiology, PathWest Laboratory Medicine WA (LMWA), Queen Elizabeth II Medical Centre, Hospital Avenue, Nedlands, WA 6009, Australia; david.speers{at}


Objectives Screening of men who have sex with men (MSM) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) requires sampling from anorectal and pharyngeal sites in addition to urogenital sampling. Due to the cost of testing multiple anatomical sites individually testing of pooled specimens has potential merit. The Cepheid GeneXpert CT/NG assay (GeneXpert), which also has potential for point-of-care nucleic acid testing in the sexual health clinic, has not been assessed for pooled specimen testing.

Methods We prospectively compared GeneXpert testing of pooled pharyngeal and rectal swabs with urine samples to standard of care testing of individual specimens from 107 participants using the Roche cobas 4800 CT/NG assay (cobas) for CT and NG in high-risk MSM attending an inner city sexual health clinic.

Results We found testing of pooled pharyngeal, rectal and urine samples by the GeneXpert to have 100% agreement for NG and 94% overall agreement for CT when compared with individual specimen testing by cobas. For CT testing, 14 cases were detected for both tests, 4for cobas only, 2 for GeneXpert only and 89 participants were negative for both tests.

Conclusions Pooled specimen CT and NG testing by the GeneXpert was accurate when compared with single specimen testing and has potential for screening MSM for CT and NG. The role of pooled specimen testing with the GeneXpert as a point-of-care nucleic acid test in MSM requires further investigation.

  • gonorrhoea
  • chlamydiatrachomatis
  • sexual health
  • men
  • molecular techniques

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  • Handling editor Catherine A Ison

  • Contributors JM and LM collected clinical data and samples. IJC performed the laboratory testing and DJS supervised the laboratory testing. IJC and DJS performed the analysis and interpretation of data. All authors contributed to the preparation and revision of the manuscript.

  • Funding The GeneXpert cartridges were supplied by Cepheid.

  • Competing interests None declared.

  • Ethics approval The study was registered as a research project through the Sir Charles Gairdner Hospital Governance, Evidence, Knowledge, Outcomes (GEKO) System (ID10704) and Human Research Ethics Committee.

  • Provenance and peer review Not commissioned; externally peer reviewed.