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. 2020 Aug 23;73(9):e3146–e3155. doi: 10.1093/cid/ciaa1229

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© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Population structure and transmission clusters of Neisseria gonorrhoeae in New York City. A, N. gonorrhoeae phylogeny is structured by sexual behavior groups, defined by patient gender and the gender of their sex partners, and race/ethnicity. The maximum likelihood phylogeny was estimated from a pseudogenome alignment with recombinant regions masked. The phylogeny can be divided into two main lineages, lineage A (black) and lineage B (orange). The annotation rings represent sexual behavior groups, race/ethnicity, and transmission clusters with >=10 isolates from the innermost to outermost rings. For the sexual behavior groups, black is men who have sex with men (MSM), orange is men who have sex with women (MSW), pink is men who sex with men and women (MSMW), yellow is women who have sex with women (WSM), gray is women who have sex with men and women (WSMW), purple is transgender persons who have sex with men (TSM), and white is unknown sexual behavior group. For the race/ethnicity annotation, purple is black, blue is white, teal is Hispanic, green is Asian, and yellow is other. B, Lineage A is associated with MSM, and lineage B is associated with heterosexual patients. We found a significant association between the major lineages and sexual behavior group (P < 2.2 × 10⁻¹⁶). C, Strains comprising largest transmission clusters are transmitting across demographic groups. Transmission connections were identified using a 10 nonrecombinant SNP cutoff, and transmission clusters were defined as clusters of isolates connected to at least one other member of the cluster and any additional isolates nested within the phylogeny. Using this method, we identified 10 clusters with at least 10 isolates (leftmost graph, colors match annotation ring in panel (A). Strains are transmitting across age groups; each point in the age graph (second to left) is the age of a patient associated with an isolate in the cluster. Strains are also transmitting across MSM and heterosexual networks and multiple races/ethnicities (third and fourth to left); color blocks correspond to the proportion of isolates within the cluster associated with each group (legend below graph). Abbreviation: HIV, human immunodeficiency disease.