An Adult Patient Presents with Mild Penile Irritation and Discharge

Patient History

An adult male presented to the primary care office with mild penile irritation and discharge without fever, dysuria, or other lesions. He is sexually active and reported recent unprotected sex with multiple partners. He is on pre-exposure prophylaxis for HIV and tested non-reactive for HIV, HCV, and syphilis antibodies. Chlamydia and gonorrhea were detected in his urine, rectal, and throat specimens by PCR. The lab paged the director to review and verify the results. Is it possible to be positive for both chlamydia and gonorrhea?


In the United States, chlamydia and gonorrhea are the most commonly reported sexually transmitted bacterial infections. While most cases of chlamydia and gonorrhea are sexually transmitted, neonates can become infected by perinatal transmission.1,2,3 To prevent long-term complications in women, all sexually active women aged <25 years and older women with increased risk of infection should get tested annually for chlamydia and gonorrhea. All pregnant women <25 years old or are considered high risk should be screened at the first prenatal visit and in the third trimester or at the time of delivery for both organisms. CDC recommends screening genital and extragenital sites at least annually for all sexually active MSM at risk for infection.4

Chlamydia trachomatis (C. trachomatis) is a gramvnegative, obligate, aerobic, coccoid or rod shape bacteria that does not grow in routine culture. C. trachomatis cannot synthesize ATP and humans are the only known natural host for C. trachomatis.4 Neisseria gonorrhoeae (N. gonorrhoeae) is a Gram-negative, facultatively intracellular, obligate aerobe diplococci. While this organism can be grown in culture, sensitivity is lower compared to routine molecular methods. Co-infection is common, with an estimated 10–40% of patients with gonorrhea also infected with chlamydia, and the data also suggested an interplay between these two pathogens. 5,6,7 Patients with chlamydia and gonorrhea co-infection can have increased gonococcal bacterial load, which might facilitate gonorrhea transmission compared with a single infection. Chlamydia can evade the host immune response by preventing neutrophil extracellular traps (NETs) production, which can help gonorrhea to establish intracellular infection.8 Studies in mice suggest that C. trachomatis induces changes in the genital tract immune environment, making it a more permissive environment for N. gonorrhoeae.9

Appropriate specimens include self- or clinician-collected vaginal swab, endocervical swab, urethral swab, and first catch urine. For chlamydial and gonococcal infection diagnosis, CDC recommends testing by nucleic acid amplification tests (NAATs). NAATs are more sensitive and specific compared to other methods. FDA has approved NAATs for urogenital specimens and only particular platforms are approved for rectal and oropharyngeal specimens. C. trachomatis does not grow in routine culture and diagnosis at this time relies solely on NAAT. For N. gonorrhoeae, culture and antibiotic susceptibility should be evaluated in case of suspected treatment failure. Our lab uses Abbott Real-time CT/NG assay, which is currently FDA approved for testing urogenital specimens only.

CDC recommends treating chlamydia with a seven-day course of doxycycline with sexual abstinence until treatment completion/resolution of symptoms. Azithromycin or levofloxacin can be used as alternatives. For gonorrhea, a single ceftriaxone intramuscular injection is recommended, and gentamicin with azithromycin can be used in case of cephalosporin allergy. Unfortunately, for pharyngeal gonorrhea, there is no reliable alternative available for ceftriaxone allergy. Sexual partner evaluation, testing, and presumptive treatment are recommended, along with patient treatment.10 In cases where the chlamydial infection has not been ruled out, patients should also receive anti-chlamydial therapy. A test-of-cure (follow-up testing) for gonorrhea is required in throat infections only after 14 days of the treatment.10


  1. Kreisel KM, Spicknall IH, Gargano JW, Lewis FM, Lewis RM, Markowitz LE, Roberts H, Satcher Johnson A, Song R, St. Cyr SB, Weston EJ, Torrone EA, Weinstock HS. Sexually transmitted infections among US women and men: Prevalence and incidence estimates, 2018. Sex Transm Dis 2021; in press.
  2. CDC. Sexually Transmitted Disease Surveillance, 2020. Atlanta, GA: Department of Health and Human Services; April 2022.
  5. Creighton S, Tenant-Flowers M, Taylor CB, Miller R, Low N. Coinfection with gonorrhea and chlamydia: how much is there and what does it mean? Int J STD AIDS. 2003; 14:109–13.
  6. Althaus CL, Turner KM, Mercer CH, Auguste P, Roberts TE, Bell G, Herzog SA, Cassell JA, Edmunds WJ, White PJ, Ward H, Low N. Effectiveness and cost-effectiveness of traditional and new partner notification technologies for curable sexually transmitted infections: observational study, systematic reviews and mathematical modelling. Health Technol Assess. 2014 Jan;18(2):1-100, vii-viii. doi: 10.3310/hta18020. PMID: 24411488; PMCID: PMC4780998.
  7. Creighton S. Gonorrhoea. BMJ Clin Evid. 2014:2014.
  8. Rajeeve K, Das S, Prusty BK, Rudel T. Chlamydia trachomatis paralyses neutrophils to evade the host innate immune response. Nat Microbiol. 2018 Jul;3(7):824-835. doi: 10.1038/s41564-018-0182-y. Epub 2018 Jun 25. PMID: 29946164.
  9. Vonck RA, Darville T, O’Connell CM, Jerse AE. Chlamydial infection increases gonococcal colonization in a novel murine coinfection model. Infect Immun. 2011 Apr;79(4):1566-77. doi: 10.1128/IAI.01155-10. Epub 2011 Jan 18. PMID: 21245268; PMCID: PMC3067530.
  10. St. Cyr S, Barbee L, Workowski KA, et al. Update to CDC’s Treatment Guidelines for Gonococcal Infection, 2020. MMWR Morb Mortal Wkly Rep 2020;69:1911–1916. DOI: icon

-Payu Raval, MD is a 2nd year anatomic and clinical pathology resident at University of Chicago (NorthShore). Her academic interests include hematology, molecular, and surgical pathology.

-Paige M.K. Larkin, PhD, D(ABMM), M(ASCP)CM is the Director of Molecular Microbiology and Associate Director of Clinical Microbiology at NorthShore University HealthSystem in Evanston, IL. Her interests include mycology, mycobacteriology, point-of-care testing, and molecular diagnostics, especially next generation sequencing.

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