Genomic epidemiology and population structure of Neisseria gonorrhoeae in Norway, 2016-2017

Abstract

This study presents the nationwide epidemiology of Neisseria gonorrhoeae, using whole-genome sequencing of all culture-positive cases, which comprise roughly 40 % of all cases of gonorrhea reported in Norway from 2016 to 2017. Isolates were assigned to sequence types and Bayesian analysis clusters and variation in genes coding for antibiotic resistance was linked to phenotypic resistance data. The study also included isolates taken from the same patients from different anatomical sites at one or more time points. Comparing these isolates allows for observation of patterns of infections, i.e. multiple reinfections of genetically related clones vs. reinfections of genetically distant clones, and quantification of the genomic variation of closely related isolates from samples taken from a patient within the same day. Demographically, the patients in the study could be split into two groups; one group of patients from the capital with a high proportion of men who have sex with men (MSM), and another consisting of young adults with transmission primarily between males and females from outside the capital. Some clusters of N. gonorrhoeae were restricted to one of these two demographic groups. Pairwise comparison of multiple isolates from the same patients revealed that most were reinfected with different clones. Observations of frequent reinfections in patients is a concern and should be taken into account in the development of improved information and treatment guidelines.

Keywords: antimicrobial resistance; genomic epidemiology; outbreak; population structure.

Fig. 1.

Maximum-likelihood phylogeny of all available Norwegian N. gonorrhoeae in the data set based on core genome SNPs. Showing STs (represented by ≥10 isolates), clusters defined by BAPS level 1, and patient data (sex, age, sampling site and residency). Phenotypic susceptible/intermediate/resistant (SIR) data using the EUCAST breakpoints shown for ciprofloxacin (CIP), cefixime (CFM), azithromycin (AZM); penicillin G (PCN), and tetracycline (TET). No isolates were observed resistant to ceftriaxone (CRO) (>0.125 mg l⁻¹) or spectinomycin (SPX) (>64 mg l⁻¹). Grey bars indicate missing data.

Fig. 2.

On the same x-axis showing time between pairs of isolates (in days): (a) the number of cases with either different or same ST, and (b) the pairwise SNP differences (log scale) between isolates.