Overview of the sample collection.

Top panel: The color of the dots indicate the number of sequences at each location. Bottom panel: Unrooted phylogeny built from a multisequence alignment with partially masked recombinant regions (see main text for details). The tip colors indicate geographic locations. The scale bar represents the number of substitutions per site.

Dated phylogenetic analyses.

A) Reconstructed effective population size over time and full tree including annotated metadata. Annotations from left to right: mtr fastGEAR defined allele, ceftriaxone MIC category (blue low, red high), penA mosaic (blue no, orange yes), geographic region. Selected clades in the tree associated with mosaic mtr or penA operons, or associated with high cephalosporin MICs (alleles associated with cefixime and/or ceftriaxone MIC ≥ 0.064) are highlighted with different colors. FastGear identified five mtr lineages, of which 1-4 were mosaic whereas lineage 5 was non-mosaic. Mosaic alleles exhibiting significant sequence variation relative to the major lineages are annotated simply as ‘mosaic’. B) Effective population size for four clades of interest. The coloring corresponds to the clades in the full tree.

Gonorrhea import dynamics across major sampling locations.

A) Transmission lineage size by the inferred times of importation. The largest transmission lineage in Europe (n=1084), was inferred to date back to 1750 and is not shown to maximize resolution. B) Treemaps illustrate the size and age of individual transmission lineages. The size of the squares reflects the relative sizes of the transmission lineages. The color indicates the inferred dates of importation.

Assessing robustness of import and export estimates by upsampling.

A) To assess the robustness of import and export estimates as a function of inclusion of samples from the rest of the world (ROW), the latter genomes were upsampled in a stepway manner from the dated phylogeny, followed by re-estimation and quantification of imports, exports and local transmissions. For each step, three random subsamples of ROW genomes were retained, and phylogeographic mapping estimated independently for each. B) Import and export fraction asymptotes were calculated to assess whether the estimates were stable and to estimate true fractions of imports and exports.

Transmission lineage sizes as a function of sex distribution.

For each location, transmission lineages were annotated as male-dominated lineage (MDL) if they were in the top half of clusters in terms of male/female ratio and mixed otherwise. P-values are based on the DTS test (35). Blue: mixed lineages; orange: MDL lineages. The dotted lines indicate the median (magenta) and mean (green) transmission lineage size.