Prevalence of rectal, urethral, and pharyngeal chlamydia and gonorrhea detected in 2 clinical settings among men who have sex with men: San Francisco, California, 2003

Clin Infect Dis. 2005 Jul 1;41(1):67-74. doi: 10.1086/430704. Epub 2005 May 26.


Background: The Centers for Disease Control and Prevention developed screening and diagnostic testing guidelines for chlamydia and gonorrhea at urethral, rectal, and pharyngeal sites for men who have sex with men (MSM). However, in most clinical settings, rectal chlamydial testing is not performed for MSM, and primarily sexually transmitted disease (STD) clinics alone perform routine rectal and pharyngeal gonorrhea screening for asymptomatic men.

Methods: We evaluated the prevalence of rectal, urethral, and pharyngeal chlamydial and gonococcal infections among MSM seen at the municipal STD clinic and the gay men's community health center. We also determined the proportion of asymptomatic rectal infections, described the patterns of single and multiple anatomic sites of infection, and evaluated the proportion of chlamydial infections that would be missed and not treated if MSM were not routinely tested for chlamydia. We tested specimens using previously validated nucleic acid amplification tests (NAATs).

Results: The prevalence of infection varied by anatomic site (chlamydia: rectal, 7.9%; urethral, 5.2%; and pharyngeal, 1.4%; for gonorrhea, rectal, 6.9%; urethral, 6.0%; and pharyngeal, 9.2%). Approximately 85% of rectal infections were asymptomatic supporting the need for routine screening. Because 53% of chlamydial infections and 64% of gonococcal infections were at nonurethral sites, these infections would be missed and not treated if only urethral screening was performed. In addition, >70% of chlamydial infections would be missed and not treated if MSM were tested only for gonorrhea.

Conclusions: Because these infections enhance both HIV transmission and susceptibility, clinical settings serving MSM should evaluate the prevalence of chlamydial and gonococcal infections by anatomic site using validated NAATs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Chlamydia
  • Chlamydia Infections / epidemiology*
  • Chlamydia Infections / microbiology
  • Gonorrhea / epidemiology*
  • Gonorrhea / microbiology
  • Homosexuality, Male*
  • Humans
  • Male
  • Middle Aged
  • Neisseria gonorrhoeae / isolation & purification
  • Pharyngeal Diseases / epidemiology
  • Pharyngeal Diseases / microbiology
  • Pharynx / microbiology*
  • Prevalence
  • Rectal Diseases / epidemiology
  • Rectal Diseases / microbiology
  • Rectum / microbiology*
  • San Francisco
  • Sexually Transmitted Diseases, Bacterial / epidemiology
  • Sexually Transmitted Diseases, Bacterial / microbiology
  • Urethra / microbiology*
  • Urethritis / epidemiology
  • Urethritis / microbiology