Identification of novel Neisseria gonorrhoeae lineages harbouring resistance plasmids in coastal Kenya

Background Africa has the highest incidence of gonorrhoea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR). Methods Whole genome sequence data were analysed from 103 N. gonorrhoeae isolates from 73 patients, mainly men who have sex with men from coastal Kenya. We annotated loci, defined core genome and mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhoea, we determined whether infections occurred with related strains. Results We identified three clusters of isolates that are phylogenetically distinct from isolates found elsewhere. Plasmids were virtually ubiquitous: pTetM and pblaTEM were found in 97%, and 55% of isolates, respectively. This was associated with high doxycycline use for undiagnosed sexually transmitted infections. 23% of multiple episodes of gonorrhoea in the same individual were caused by a related strain, suggesting inadequate treatment or reinfection. Conclusions The prevalence of plasmid-mediated AMR in Kenyan gonococci contrasts with wealthy countries where AMR is largely chromosomally-mediated. Antimicrobials have a profound effect on maintenance of lineages harbouring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid co-operation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies