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Original research
Performance of human papillomavirus DNA detection in residual specimens taken for Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acid amplification testing in men who have sex with men
  1. Diarmuid Nugent1,2,
  2. Oliver Stirrup1,
  3. Sarah Pett1,2,
  4. Kavita Panwar3,
  5. Marta Checchi3,
  6. David Mesher3,
  7. Kate Soldan3,
  8. Simon Beddows3,
  9. Richard Gilson1,2
  1. 1Centre for Clinical Research in Infection and Sexual Health, University College London, London, UK
  2. 2The Mortimer Market Centre, Central and North West London NHS Foundation Trust, London, UK
  3. 3National Infection Service, Public Health England, London, UK
  1. Correspondence to Dr Diarmuid Nugent, Centre for Clinical Research in Infection and Sexual Health, University College London, London WC1E 6BT, UK; d.nugent{at}


Objectives Rectal swab specimens, either alone or pooled with first-void urine (FVU) and pharyngeal swab specimens, are used to test for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection in men who have sex with men (MSM). Following introduction of human papillomavirus (HPV) vaccination for MSM attending UK sexual health services (SHSs), HPV testing of residual CT/NG test specimens has been proposed to monitor HPV prevalence in this population. Performance of HPV detection in such specimens has not been evaluated previously.

Methods MSM attending a UK SHS provided three specimens: (1) rectal swab for CT/NG, (2) pooled rectal/pharyngeal/FVU specimen for CT/NG and (3) dedicated anal swab for HPV. Specimen 3 and residual material from specimens 1 and 2 were tested for type-specific HPV DNA. HPV detection was by an in-house multiplex PCR and luminex-based genotyping assay.

Results A total of 129 MSM were recruited with a mean age of 38.1 years; 24% were HIV-positive. Of the 129 MSM, 92 (71%) had any type-specific HPV DNA in ≥1 specimen; 80 (62%) had high risk (HR) HPV. Of 123 participants with sufficient residual pooled and dedicated specimens, 70 (56.9%) had detectable HPV on both, and 40 (32.5%) were negative on both; overall concordance was 89% (95% CI 83% to 94%), and kappa statistic was 0.78 (95% CI 0.66 to 0.89). Pooled samples had a 4.1% (95% CI −1.9% to 10.0%) higher test positivity rate than dedicated samples.Of 125 participants with sufficient residual rectal and specimens, 74 (59.2%) had detectable HPV on both, and 36 (28.8%) were negative on both; overall concordance was 88% (95% CI 81% to 93%), and kappa statistic was 0.74 (95% CI 0.61 to 0.86). Residual rectal samples had 5.6% (95%CI −0.6% to 11.8%) higher test positivity than dedicated samples.

Conclusions We observed high concordance between the dedicated and residual STI test specimens. Our data support the strategy of testing residual specimens for HPV prevalence monitoring in MSM to evaluate the impact of the targeted vaccination programme.

  • anogenital cancer
  • anogenital conditions
  • HPV
  • vaccination
  • surveillance

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  • Handling editor Federico Garcia

  • Contributors RG, KS and DM conceived the idea for the study. RG and DN developed the study design. DN developed the study protocol, prepared the study materials, led participant recruitment and wrote the study manuscript. OS provided statistical guidance for the study design, sample size calculation and analysis of results. KP and SB carried out HPV testing of study specimens. RG, SP, OS, KP, DM, MC, KS and SB advised on the study design and reviewed and edited the manuscript.

  • Funding HPV testing costs were funded by Pubic Health England (Vaccines and Counter Measures Budget).

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval The study received ethical approval from the East Midlands/Leicester Central Research Ethics Committee (REC) on 7 December 2017 (REC reference 17/EM/0473) and NHS Health Research Authority approval on 2 January 2018 (Integrated Research Application System project ID 234139).

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

  • Data availability statement Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. All data relevant to the study are included in the article’s main text and supplementary information. Should any further clarification be required, a request can be made to the corresponding author.

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