Development of molecular methods for typing and AMR prediction of Mycoplasma genitalium: an emerging highly drug-resistant sexually transmitted infection

Funding period: 2023–2025
Leads: Shelley Peterson and Irene Martin
Total GRDI funding: $438,400

Mycoplasma genitalium (Mgen) is a widespread but little-known bacterial pathogen with symptoms ranging from urethritis to pelvic inflammatory disease, preterm birth and female infertility.

Overall prevalence in Canada is not known, as there is no established Mgen surveillance program and it is not a notifiable disease. This is of particular concern in Northern, remote and isolated (NRI) regions, where sexually transmitted infection (STI) rates are highest and access to Mgen diagnostics are very limited. Resistance to the currently recommended therapeutics, azithromycin and moxifloxacin, is abundant and treatment failures with both of these antimicrobials require special access requests of pristinamycin, which can take several months to acquire. No susceptibility data exists for pristinamycin in Canada. All Mgen diagnostics are Nucleic Acid Amplification Testing based. Mgen is difficult to isolate and culture in vitro, making traditional phenotypic antimicrobial resistance (AMR) testing methods challenging to perform.

To address a similar issue in Neisseria gonorrhoeae, we developed a suite of qPCR assays to detect AMR molecular markers. Whole genome sequencing (WGS) of Mgen can provide vital information for AMR prediction and molecular sequence typing without the need to design multiple assays. We have had previous success with using WGS for AMR prediction and sequence typing for N. gonorrhoeae and Streptococcus pneumoniae. There is no widely used typing scheme to differentiate Mgen strains, however we have been invited to collaborate with the University of Oxford’s PubMLST platform to further develop their Mgen typing scheme. Sequence typing is essential for identification of circulating strains and supporting investigations into outbreaks and treatment failures. This typing scheme will allow Canada to contribute to surveillance internationally.

The objectives of this proposal are to:

1. develop culture-independent methodologies for WGS from Mgen urine/swab specimens within our laboratory;
2. establish and validate phenotypic AMR testing to correlate phenotypic MICs with genotypic profiles;?
3. use these data to create algorithms for AMR prediction in Mgen as well as molecular genotyping (e.g. MLST).

These molecular approaches will allow for enhanced surveillance without the need for the isolation and phenotypic testing of Mgen. Furthermore, this technology could be applied to routine testing and place Canada as global leader in monitoring Mgen strains and predicting AMR. Regional, provincial/territorial and federal public health authorities can use the data to support prevention control strategies and inform STI Treatment Guidelines across Canada, including vulnerable and marginalized populations. These data will supplement contact-tracing efforts by public health in an attempt to better understand the social networks and design interventions to reduce the number of infections.