Direct from sample whole genome sequencing of Neisseria Gonorrhoeae to reveal patterns of STI epidemic synergy in African populations with high HIV burden

ABSTRACT There are approximately 82 million incident Neisseria gonorrhoeae (Ng) infections globally each year and the highest per-capita burden is in Eastern and Southern Africa (ESA). Over half of global incident HIV infections also occur in ESA and people living with HIV are disproportionately at risk of acquiring Ng infection. Further, a global increase in multi- and extensively-drug resistant Ng threatens control efforts. Our understanding of Ng transmission dynamics within ESA, and in particular its interaction with the sexual networks on which HIV is also transmitting, is limited by a lack of surveillance data from the region, particularly among women and asymptomatic men. Ng surveillance efforts in ESA are hindered by the need for isolate culturing for antimicrobial susceptibility testing and whole genome sequencing (WGS). In this proposal, we will develop and validate direct from sample Ng WGS methods that alleviate the need for isolate culturing. These methods will be used to generate Ng WGS data from ~250 GC+ penile and vaginal swabs sampled from population-based STI trials (STIPS and IN-STEP) nested within one of the largest HIV population surveillance cohorts in ESA, the Rakai Community Cohort Study (RCCS, Uganda). Data generated as part of this study will be used to provide preliminary insights into the transmission of Ng into- and within-Uganda, the presence of circulating drug resistant lineages, and the overlap between Ng and HIV transmission networks. This work will support future expansion of genomic surveillance of Ng and other bacterial sexually transmitted infections (STIs) in the RCCS and other low-resources regions with high burdens of HIV and non-HIV STIs.