Recombination-filtered midpoint-rooted phylogenetic tree based on core-genome SNPs including 318 Ng isolates from 2014–19 from Amsterdam, the Netherlands. The FA1090 strain was used as the reference strain and its branch is visualized with an orange dot. Metadata includes: main clusters determined with BAPS analysis at level 1; year of isolation; patient characteristics (age, sex and sexual preference); MLST clusters containing ≥5 isolates; MICs in mg/L for azithromycin (AZM), ciprofloxacin (CIP) and ceftriaxone (CRO); penA type and porB type. PorB1a is given in black; all other colours represent different porB1b types. Phenotypic data are visualized as green for susceptible strains, orange for intermediate strains and purple for resistant strains or strains with reduced susceptibility. White bars indicate missing data. Two separate lineages are defined with dashed-line boxes.