Use of whole genome sequencing to investigate an increase in Neisseria gonorrhoeae infection among women in urban areas of Australia

Abstract

Increasing rates of gonorrhoea have been observed among women within the Australian state of New South Wales. Here, we applied whole genome sequencing (WGS) to better understand the associated networks and transmission dynamics. Ninety-four isolates of a particular N. gonorrhoeae genotype (G122) associated with women (years 2012 to 2014) underwent phylogenetic analysis using core single nucleotide polymorphisms. WGS data revealed five main clusters, all of which were heterogeneous in terms of patient age and site of infection. The relatively high cervical/vaginal infections in each cluster was indicative of transmission in the general heterosexual population, noting that there is typically high rates of condom use for vaginal sex among local commercial sex workers. WGS also enabled the identification of groups of individuals belonging to tighter transmission chains within clusters, and hence may present a new tool for targeting public health interventions. The enhanced resolution of WGS provides a ready means of confirming suspected changes in N. gonorrhoeae epidemiology, but also enables key features to be identified or new questions to be raised regarding the composition of the associated sexual networks.

Figure 1

A rooted maximum likelihood phylogeny constructed with 473 core single nucleotide polymorphisms (SNPs). It comprises all 94 New South Wales (NSW) genomes and 6 Brighton genomes. A Brighton genome (SRR3360636) from the next closest sister clade was selected as the outlying group to root the phylogeny. Five larger clusters of isolates (C1-C5) have been labelled based on the phylogeny. Coloured circles represent isolates from the same patient (PA-PF; see key). Rectangles and their respective colour schemes correspond with date of collection, age group, sample site and location (see key). Both age group and sample site are unknown for the 6 Brighton genomes. The red isolate names with G1-G6 appended to the end, represent isolates that share identical core SNPs. Genome AU2012-768 has 33 core SNPs however its branch is truncated for easier visualisation purposes. The scale bar represents SNPs.