Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya

J Infect Dis. 2018 Jul 24;218(5):801-808. doi: 10.1093/infdis/jiy240.


Background: Africa has the highest incidence of gonorrhea 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 analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya. We annotated loci, defined the core genome, defined mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhea, we determined whether infections occurred with related strains.

Results: We identified 3 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. Twenty-three percent of multiple episodes of gonorrhea 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 that in wealthy countries, where AMR is largely chromosomally mediated. Antimicrobials have a profound effect on the maintenance of lineages harboring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid cooperation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Anti-Bacterial Agents / therapeutic use
  • Cluster Analysis
  • Computational Biology
  • Drug Resistance, Bacterial*
  • Drug Utilization
  • Female
  • Gonorrhea / drug therapy
  • Gonorrhea / epidemiology
  • Gonorrhea / microbiology*
  • Humans
  • Kenya / epidemiology
  • Male
  • Middle Aged
  • Molecular Epidemiology
  • Molecular Sequence Annotation
  • Neisseria gonorrhoeae / drug effects*
  • Neisseria gonorrhoeae / genetics
  • Neisseria gonorrhoeae / isolation & purification*
  • Phylogeny
  • Plasmids / analysis*
  • Prevalence
  • Sequence Analysis, DNA
  • Whole Genome Sequencing
  • Young Adult


  • Anti-Bacterial Agents