Fishing for gonorrhoae - a custom amplicon panel for detection in clinical metagenomes

Gonorrhoea, caused by Neisseria gonorrhoeae (Ng), is the second most common sexually transmitted disease worldwide. Natural competence combined with a high rate of recombination gives Ng an increased capability to evolve antimicrobial resistance (AMR). Ng has evolved resistance to every class of antibiotic used to treat it in the past. Currently the recommended dual first-line treatment regime is azithromycin coupled with ceftriaxone. However, isolated cases of superbugs, which are resistant to both antibiotics have been reported recently, highlighting the threat of the spread of superbugs.

Tracking of AMR is essential to provide an effective treatment regime and to counteract the spread of antimicrobial resistant pathogens. Sufficient surveillance is lacking in many countries, including New Zealand. Since the move to nucleic acid amplification diagnostic tests (NAAT) for detecting gonorrhoea in New Zealand, information on AMR is limited to a national survey every few years.

We develop a cost-effective custom amplicon panel for metagenomics sequencing to directly type Ng from clinical samples and track AMR. We first tested the species specificity of currently used typing schemes (NG-MAST and NG-STAR), since clinical samples contain diverse microbial profiles. Our findings suggest that currently used typing genes are Neisseria specific, with one exception (23S gene). The creation of synthetic metagenomes allows the simulation of a range of clinical samples with varying pathogen load, representative of the swabbing quality and infection status of clinical samples. Amplicon sets will be tested in synthetic metagenomes, prior to clinical samples.

Usage of the amplicon panel for routine diagnosis of gonorrhoea will improve our ability to understand the evolution, emergence and spread of AMR in Ng. Ongoing surveillance provides key information to make informed decisions for effective treatment of common pathogens.