Introduction: M. genitalium is not usually among organisms for routine testing in sexually transmitted infection screening. Treatment follows syndromic guidelines. As M. genitalium cannot be readily cultured, detection of antimicrobial resistance and typing of strains relies on DNA sequence data. It was shown that although there is high intra-strain stability, high levels of sequence variability between clinical isolates are seen which may be associated with antimicrobial resistance.

Methods Endocervical swabs were collected from 100 pregnant women attending a tertiary hospital in Pretoria, South Africa. The specimens were screened for M. genitalium using a commercial real time PCR assay. Genotypic resistance markers for macrolide and fluoroquinolones were determined by sequence analysis of the V-region of the 23S rRNA, gyrA, and parC genes. The strains were typed using mgpB single-nucleotide polymorphism typing (SNP) and MG309 variable number tandem (VNTR) analysis.

Results: M. genitalium was detected in 7 (7.0%) of specimens of which one positive sample could not be detected with further methods. No resistance associated mutations were seen in the gyrA and parC genes. In 2 isolates the macrolide associated mutation A2059G was seen. SNP typing revealed Sequence Types 1, 2 and 4. Four different types were seen using MG309 VNTR analysis. Typing assigned M. genitalium to 2 major clusters. Genotypic macrolide resistance was found within one of the clusters.

Conclusion: Mycoplasma genitalium is a frequent undiagnosed STD in this population. As azythromycin was included in the national syndromic treatment guidelines in 2015, it is alarming to already find resistance associated genes.