O11.5 - Targeted metagenomic analysis shows distinct Neisseria gonorrhoeae strains at separate anatomical sites occur more commonly than mixed strain infections: implications for surveillance
Maastricht University Medical Center+, Netherlands
Introduction: Mixed infections of Neisseria gonorrhoeae (NG) in one anatomical site could complicate surveillance as linked individuals might be missed with current genotyping methods. In our previous study distinct NG strains at separate anatomical sites was observed in a quarter of patients. As only the dominant NG strain was characterized, additional strains could be present because of mixed infections. Therefore, we performed a follow-up study of samples using next-generation sequencing. With this, we aimed to gain further insight in mixed infections and distinct NG strains at separate anatomical sites for surveillance.
Methods: Amplicons of the previous study were sequenced (n=33 samples) with the Illumina MiSeq of 16 men who have sex with men (MSM) with distinct NG strains at separate anatomical sites. An analysis pipeline was developed to analyze the data. This pipeline was validated using in silico generated mixed (ranged from 0.01%-50% abundance of the second strain) strain datasets of 14 WHO strains (n=91 combinations).
Results: The analysis pipeline correctly detected all alleles in the mixed-strain in silico datasets with at least 1.5% abundance. Most samples (25/33) were well sequenced ( >200,000 paired-end reads). The majority of the samples (26/33) were single NG infections. In seven samples from five patients a mixed NG infection was observed. This revealed five additional strains, including ST1407, in three patients.
Conclusion: We developed and validated a targeted metagenomic genotyping method for NG. Despite the selected MSM with distinct NG isolates at separate anatomical sites, most samples are single NG infection. Our study provides further evidence that mixed infections do occur but likely at low prevalence. However, AMR strains like ST1407 can be missed, potentially resulting in treatment failure and unnoticed transmission. This suggests that distinct NG strains at separate anatomical sites are more important for surveillance as it occurs more frequently than mixed infections.
