Pharyngeal gonorrhea in Ugandan men with urogenital gonorrhea: differences in antimicrobial resistance and strain types between anatomical sites

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ID: 320173
2026
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Abstract
BACKGROUND: Pharyngeal Neisseria gonorrhoeae (phNG) infections are difficult to treat and contribute to antimicrobial resistance (AMR) in NG, but studies on phNG and differences with urogenital NG (uNG) are limited. METHODS: Participants with urethral discharge syndrome (UDS) were recruited at health clinics in Kampala, Uganda, between July 2020 and August 2023. Penile-meatal and pharyngeal swabs were cultured for NG and tested by nucleic acid amplification test (NAAT) for NG, Chlamydia trachomatis, and Mycoplasma genitalium. Paired uNG and phNG isolates were subjected to susceptibility testing and whole genome sequencing (WGS). Demographic and behavioral data were analyzed for correlates of uNG and phNG. RESULTS: The participants' (n=411) median [IQR] age was 25 [22, 32] years; 16.7% (67/401) were living with HIV. By NAAT and/or culture, 273 (66.4%) participants were positive for uNG and 29 (7.1%) for phNG. Of those with uNG, 10.6% (29/273) were NAAT-positive for phNG; 69.0% (20/29) were culture-positive for phNG. All (n=40) NG isolates were susceptible to cefixime and ceftriaxone and displayed intermediate resistance/resistance to ciprofloxacin, penicillin, and tetracycline; eight displayed high-level azithromycin resistance. WGS showed that 52.6% (10/19) of participants had different strains at urethral and pharyngeal sites. Having different strains at two anatomical sites was more common in men self-reporting transactional sex (p=0.019). CONCLUSIONS: phNG is common in Ugandan men with uNG, both displaying high rates of AMR. Different strains at the two anatomical sites were common, supporting the need for pharyngeal testing and phNG susceptibility testing as the pharynx is a critical site for AMR emergence.
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Authors Johan H. Melendez, Annet Onzia, Emmanuel Mande, Adamaris Muñiz Tirado, B Dawa, Yu‐Hsiang Hsieh, Matthew M. Hamill, Rosalind Parkes-Ratanshi, Hervé Tettelin, Yukari C. Manabe
Journal The Journal of infectious diseases
Year 2026
DOI
10.1093/infdis/jiag353
URL
https://doi.org/10.1093/infdis/jiag353
Keywords Keywords not found

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