Ecology of oral Neisseria species in men who have sex with men before and after implementation of doxycycline post-exposure prophylaxis and 4CMenB vaccination
- Project No: D26078
- DPhil Project 2026
- Infectious Disease Epidemiology Unit
Background
The human oropharynx hosts diverse Neisseria species, including the pathogens N. gonorrhoeae (Ng) and N. meningitidis (Nm). Horizontal gene transfer between commensal and pathogenic Neisseria contributes to the emergence of antimicrobial resistance (AMR). Our pilot MSMCARR study undertaken in 2023 (MSM CARR 2023) demonstrated a 21 % oropharyngeal Nm carriage rate among MSM attending a London sexual-health clinic before the introduction of doxycycline post-exposure prophylaxis (doxyPEP) and 4CMenB vaccination. We detected multiple tetracycline-resistant Nm lineages carrying tet(B) or tet(M), highlighting pre-existing AMR reservoirs that may expand following widespread prophylactic antibiotic and vaccine use.
Since August 2025, doxyPEP and 4CMenB programmes have been implemented in UK sexual-health clinics and offered to patients who have a recent history of multiple sexual partners or sexually transmitted infections. This presents a unique natural experiment to assess ecological shifts in oropharyngeal Neisseria following intervention rollout. Understanding these dynamics is essential for AMR stewardship, vaccine policy and public-health surveillance.
research experience, research methods and skills training
This study will compare Neisseria carriage, diversity and AMR in MSM pre- and post-implementation of doxyPEP and 4CMenB using MSMCARR 2023 as baseline. New cross-sectional sampling will be conducted in 2025/2026 using matched protocols. Whole-genome sequencing and shotgun metagenomics will characterise Neisseria populations; phylogenetic, causal and mathematical models will quantify intervention effects on carriage and AMR spread.
Training will include: advanced genomic epidemiology, microbiology, causal modelling (DAGs and Bayesian methods), and statistics. The student will gain skills in microbiology culture, bioinformatics, statistical programming (R, Python), and public-health communication through international conferences and peer-reviewed publications.
FIELD WORK, SECONDMENTS, INDUSTRY PLACEMENTS AND TRAINING
Fieldwork will involve cross-site collaboration with a NHS sexual-health clinic located in London. Training in bioinformatics pipelines and causal modelling will be undertaken at Oxford Population Health with microbiology training provided.
PROSPECTIVE STUDENT
The ideal candidate will have a Bachelor’s or Master’s degree in microbiology, epidemiology, public health or bioinformatics, with interest in genomic epidemiology and infectious-disease modelling. Strong analytical skills, experience in R/Python and enthusiasm for translational research linking pathogen genomics and public-health policy are essential.