Replication Data for: Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya

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).

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.

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.

Data Availability: DNA was sequenced using Illumina HiSeq, and reads were assembled using the Velvet assembly program with VelvetOptimiser [14]. The resultant assemblies were uploaded to the pubMLST database (available at: pubmlst.org), where data are publicly available, and linked to the European Nucleotide Archive (accession numbers ERR1143657–ERR976965, Supplementary Table1 Data Access: Open License: Creative Commons Attribution 4.0 International