O08.6 Assessing within-host genetic variation in Neisseria gonorrhoeae at different anatomical locations and over time

BackgroundRecent trials focus on novel antibiotic treatment options for Neisseria gonorrhoeae (Ng), since resistance against currently used cephalosporins is emerging. To assess antibiotic potential, patients with mixed infections or those who are reinfected after treatment should be identified. Comparing levels of within-host genetic variation in Ng isolates at different anatomical locations and over time could identify those patients and could inform thresholds for similarity.MethodsIsolates from the New AntiBiotic treatment Options for uncomplicated GOnorrhoea (NABOGO) trial were used in this study. Whole-genome sequences were obtained from paired isolates from 86 patients with multiple isolates from different anatomical locations (n pairs=59) or from different time points (n pairs=48). All isolates were typed according to the typing schemes: NG-Multi-Antigen Sequence Typing (NG-MAST), NG-Sequence Typing for Antimicrobial Resistance (NG-STAR), Multi-Locus Sequence Typing (MLST) and core genome MLST (cgMLST).ResultsIdentical NG-MAST/NG-STAR/MLST profiles were identified within 93/107 (87%) isolate pairs. Different strains were found in 8/59 (14%) paired isolates from different anatomical locations, according to completely different NG-MAST/NG-STAR/MLST profiles. Five other isolate pairs from multiple anatomical locations differed in NG-MAST but were similar in NG-STAR/MLST. One case of reinfection was identified (1/48, 2%) according to a completely different NG-MAST/NG-STAR/MLST profile in an isolate pair from different time points. One other isolate pair from multiple time points differed only in NG-MAST, suggesting a potential case of reinfection. However, the level of similarity between typed cgMLST alleles was still >99% within the 5 isolate pairs with varying NG-MAST, which was only 4–87% within isolate pairs with completely different NG-MAST/NG-STAR/MLST profiles.ConclusionIsolates with completely different NG-MAST/NG-STAR/MLST profiles can be considered as different strains, according to the low similarity in cgMLST alleles. Isolates with variable NG-MAST still had high similarity in cgMLST alleles, suggesting that NG-MAST might be too variable for identifying mixed- and re-infections.