Genomic assessment of within-host population variation in Neisseria gonorrhoeae: Implications for gonorrhoea transmission

ObjectivesMathematical modelling and genomic analyses are powerful methods for investigating the transmission dynamics of Neisseria gonorrhoeae, however, often make the implicit assumption that N. gonorrhoeae isolates at different anatomical sites within the same individual are the same strain. MethodsIn this study, two approaches were used to explore genetic diversity. First, we examined a collection of stored, clinical N. gonorrhoeae isolates sourced from multiple anatomical sites of single individuals attending a sexual health clinic in Melbourne from 2011-2019. Second, we obtained multiple colony picks from primary clinical samples from individuals attending a sexual health clinic in Melbourne from 2019-2020. Whole genome sequencing and a variety of bioinformatics approaches were used to determine both within-host and within-sample genetic diversity. ResultsThirty-seven individuals were identified that had cultured N. gonorrhoeae from two or more anatomical sites (urogenital, anorectal, or oropharyngeal), with a final dataset of 105 isolates. In 35/37 (94.6%) individuals, infections were highly similar at the genetic level, with identical MLST and NG-MAST profiles. Pairwise comparisons of isolates within each individual indicated that the maximum within-host pairwise SNP distance was 13 SNPs (median = 1, IQR: 0-3). Notably, four distinct multi-individual phylogenetic clusters were identified, where the maximum pairwise SNP distance was 19 SNPs (median = 6, IQR = 2-11). Similarly, comparisons of isolates within each primary sample indicated that the maximum pairwise SNP distance was 8 SNPs (median = 2, IQR:1-3). ConclusionsThis study suggests that in most cases of multi-site infection, the same strain of N. gonorrhoeae causes the infection at each anatomical site. However, WGS data alone cannot differentiate between the same infecting strain or (re)infections from the same transmission network. These data guide recommendations regarding optimal bioinformatic approaches to infer genetic relatedness of N. gonorrhoeae and will help inform future studies of gonorrhoea transmission and epidemiology. KEY MESSAGESO_LIIn most cases of multi-site infection, the same strain of N. gonorrhoeae causes infection at each anatomical site (urogenital, anorectal, and oropharyngeal) within an individual. C_LIO_LIIt is not possible, using genomics alone, to determine if an infection is from a single individual or multiple individuals within the same sexual network. C_LIO_LICurrent literature reports an array of different bioinformatic methods for describing genetic diversity, highlighting that SNP thresholds are not directly transferable between studies. C_LI