Research Article| Volume 86, ISSUE 4, P329-337, April 2023

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The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study

Published:February 08, 2023DOI:


      • Men who have sex with men using HIV pre-exposure prophylaxis often use antibiotics.
      • Oropharynx often colonised with antibiotic-resistant commensal Neisseria species.
      • Shotgun metagenomic sequencing shows high abundance of antibiotic-resistance genes.
      • Fluoroquinolones, macrolides, tetracyclines, and multidrug efflux pumps involved.
      • Stewardship should reduce antibiotic consumption in populations at risk for STI.



      Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.


      We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.


      ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26–0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15–0.69), macrolides (0.37, 95% CI 0.25–0.56), tetracyclines (0.41, 95% CI 0.25–0.69), and multidrug efflux pumps (0.11, 95% CI 0.03–0.33), but not for beta-lactams (1.38, 95% CI 0.73–2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.


      The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.


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