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Original research
Molecular epidemiological analysis of Mycoplasma genitalium shows low prevalence of azithromycin resistance and a well-established epidemic in South Africa
  1. Jolein G E Laumen1,2,
  2. Lieke B van Alphen1,
  3. Liteboho D Maduna3,
  4. Charlotte M Hoffman1,
  5. Jeffrey D Klausner4,
  6. Andrew Medina-Marino5,6,
  7. Marleen M Kock3,7,
  8. Remco P H Peters1,3,6
  1. 1 Department of Medical Microbiology, CAPHRI School for Public Health & Primary Care, Maastricht Universitair Medisch Centrum+, Maastricht, Limburg, The Netherlands
  2. 2 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
  3. 3 Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
  4. 4 David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
  5. 5 Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
  6. 6 Research Unit, Foundation for Professional Development, East London, South Africa
  7. 7 Tswhane Academic Division, National Health Laboratory Service, Pretoria, South Africa
  1. Correspondence to Professor Remco P H Peters, Department of Medical Microbiology, University of Pretoria, Pretoria 0001, South Africa; rph.peters{at}


Objectives Macrolide resistance in Mycoplasma genitalium is emerging globally. There is paucity of data from sub-Saharan Africa where syndromic management is used to treat sexually transmitted infections (STIs). We conducted a molecular epidemiological study to determine the prevalence of azithromycin resistance and epidemic diversity of M. genitalium infections in South Africa.

Methods We analysed 90 M. genitalium-positive specimens that had been collected consecutively from men and women (50% symptomatic) from geographically diverse communities across the northern part of South Africa between 2015 and 2019. Melting curve analysis followed by targeted sequencing of the 23S rRNA gene was performed to detect azithromycin resistance. Molecular typing was done through single nucleotide polymorphism (SNP) analysis of the MG191 gene and short tandem repeats (STR) assessment of the MG309 gene. An overview of all published M. genitalium sequence types was generated and novel sequence types identified in this study were allocated numbers accordingly.

Results Azithromycin resistance was detected in 1/90 M. genitalium-positive specimens (1.1%; 95% CI 0% to 3.3%) as conferred by A2071G mutation; this strain also harboured a C234T mutation in the parC gene with wild type gyrA gene. SNP typing and STR assessment was successful in 38/90 specimens (42%) and showed a genetically diverse epidemic, without geographic clustering, with eight novel sequence types identified.

Conclusion This is the first study that determines resistance in M. genitalium infection since introduction of azithromycin in the syndromic management regimen for STIs in South Africa in 2015. Despite a well-established epidemic, azithromycin-resistant M. genitalium infection is still uncommon in the public healthcare sector. However, it has the potential to undermine the effectiveness of syndromic management. Introduction of molecular diagnostics and continuous surveillance are warranted for early detection emergence of resistance.

  • mycoplasma
  • molecular epidemiology
  • azithromycin
  • molecular typing
  • Africa

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  • Handling editor Gwenda Hughes

  • Contributors RP conceptualised the study. JL, LvA, LM, CMH, MMK and RP were responsible for collection and microbiological analysis of the sample set. All authors contributed to the writing of the manuscript and approved the final version.

  • Funding This study was supported by a grant (DHKF15/D27) from the Netherlands Enterprise Agency (Rijksdienst voor Ondernemend Nederland) and by the Eunice Kennedy Shriver National Institute of Child Health & Human Development, U.S. National Institute of Health, under grant R21HD084274 for collection of the specimens analysed in this study.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval The collection of cohorts included in this study was approved through ethical approval by the Research Ethics Committee at the Faculty of Health Sciences of the University of Pretoria (Reference numbers 253/2017, 498/2016, 401/2015) and the Human Research Ethics Committee of the University of the Witwatersrand, Johannesburg, South Africa (Ref: M150352).

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement All data relevant to the study are included in the article or uploaded as supplementary information. All data relevant to the study are included in the article; sequences of novel sequence types have been deposited into GenBank. Please contact the corresponding author for access to the raw data.