Metagenomic Analysis of the Pharynx in High Risk Partners

The Neisseria gonorrhoea (NG) epidemic in England is at the highest level in one hundred years of public health records. The World Health Organisation has listed NG as one of the top five bacterial infections globally because of the ability of the bacteria to develop resistance to antibiotics. Neisseria meningitidis (NM) is a common pharyngeal commensal and it has been shown to be in one in five men who have sex with men (MSM) in London.

In the last year sexual health clinics have had a growing number of MSM presenting with urethritis / proctitis that were treated for NG on the day only to be found later to have been infected with NM from the culture. It appear that virulence factors have been passed from NG to NM enabling these bacteria to infect the urogenital and anal mucosa; consequently, NM in some cases is a new Sexually Transmitted Infection (STI). In 2025, two STI prevention interventions were rolled out in an attempt to address the gonorrhoea \& syphilis epidemics and these were the 4CMenB vaccine and doxycycline post exposure prophylaxis (DoxyPEP).

This study will recruit sexual partners of patients who have been diagnosed with NG and the investigators will ask the participant for one additional pharyngeal sample for research that will not impact on their standard of care. The additional sample will be tested using metagenomics, that is where all non-human DNA is analysed, and the initial focus will be on NG or NM infection, co-infection, genes for virulence and antibiotic resistance from whole genome sequencing.

The metagenomic analysis is being undertaken for research purpose only; however, secondary outcomes will look for other STIs in the pharyngeal sample and sample turn around time to inform the management of patients. Any additional STI identified will have validated testing to confirm diagnosis.