Genomic characterisation of Mycoplasma genitalium in Victoria, Australia, reveals lineage diversification and drivers of antimicrobial resistance.

Mycoplasma genitalium is a sexually transmitted infection where antimicrobial resistance poses marked challenges to patient care and public health. Despite this, genetic studies of M. genitalium have remained limited due to the fastidious culture requirements. To address this, we developed a targeted and culture-independent sequencing approach to enable the genomic study. A global data set of 220 M. genitalium genomes was compiled, comprising contemporary genomes from Victoria, Australia, and previously publicly available genomes. Major phylogenetic lineages were identified of which multiple show evidence of transmitted antimicrobial resistance. Macrolide resistance was pervasive and has reached concerning rates both in Australia and globally (160/220; 72.7%), while known fluoroquinolone resistance–associated mutations correlated with treatment failure (aOR 22.67; 95% CI 4.08-168.4). Of genomes with metadata, most were derived from gay bisexual and other men who have sex with men (55/113; 48.7%), while one M. genitalium lineage showed a higher percentage of women (17/63; 27%) and heterosexual men (21/43; 48.8%). Genome-based typing schemes are shown to offer higher resolution and robustness when compared with single-locus approaches. Together these findings clarify M. genitalium population structure and drivers of resistance, with genomics adding value in identifying effective treatments and guiding public health responses.