Culture-free genotyping of Neisseria gonorrhoeae revealed distinct strains at different anatomical sites in a quarter of patients, the Netherlands, 2012 to 2016

Background: Genotyping of Neisseria gonorrhoeae (NG) is essential for surveillance to monitor NG transmission and dissemination of resistant strains. Current genotyping methods rely on bacterial culture which frequently fails. Aim: Our aim was to develop a culture-free genotyping method that is compatible with the widely used N. gonorrhoeaemulti-antigen sequence typing (NG-MAST) database, which facilitates genotyping of NG detected at separate anatomical sites in individual patients. Methods: Specific primers for both PCR targets porB and tbpB were designed and technically validated by assessing the analytical sensitivity, cross-reactivity with 32 nongonoccocal Neisseria species, and concordance with NG-MAST. Clinical application was assessed on 205 paired samples from concurrent NG infections at different anatomical sites of 98 patients (81 men who have sex with men and 17 women) visiting our sexually transmitted infections clinic. Results: Typing could be consistently performed on samples with a PCR quantification cycle (Cq) value