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.非洲是全球淋病发病率最高的地区，但目前学界对该大洲的淋病奈瑟菌（Neisseria gonorrhoeae）种群及其抗菌药物耐药性（antimicrobial resistance, AMR）机制仍了解有限。本研究对来自肯尼亚沿海地区73名患者的103株淋病奈瑟菌分离株的全基因组序列数据展开分析，其中多数受试者为男男性行为者。研究团队完成了基因座注释、核心基因组界定、抗菌药物耐药性机制解析，并开展系统发育分析。针对存在多次淋病感染发作的患者，本研究还判定了其重复感染是否由亲缘菌株引发。研究鉴定出3个分离株簇，其系统发育特征与其他地区的分离株存在显著差异。几乎所有分离株均携带质粒：其中pTetM与pblaTEM的检出率分别为97%与55%，该现象与未确诊性传播感染者的多西环素高使用率存在相关性。同一患者的多次淋病感染发作中，有23%由亲缘菌株导致，提示存在治疗不充分或再次感染的可能性。