Skip to main content
SpringerLink
Log in

A snapshot of Chlamydia trachomatis genetic diversity using multilocus sequence type analysis in an Australian metropolitan setting

  • Original Article
  • Published:
European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

High-resolution screening methodologies which enable the differentiation of Chlamydia trachomatis at the strain level, directly from clinical samples, can provide the detailed information required for epidemiological questions such as the dynamics of treatment failure. In addition, they give a detailed snapshot of circulating C. trachomatis genetic variation, data which are currently lacking for the Australian population. In the context of two Australian clinical trials, we assessed the genetic diversity of C. trachomatis and compared these to strains circulating globally. We used high-resolution multilocus sequence typing (MLST) of five highly variable genetic regions of C. trachomatis to examine variation in Australia. Samples with established genovars were drawn from a pool of 880 C. trachomatis-positive samples from two clinical studies, whereby 76 sample pairs which remained C. trachomatis-positive for the same genovar after treatment underwent MLST analysis to distinguish between treatment failure and reinfection. MLST analysis revealed a total of 25 sequence types (STs), six new allele variants and seven new STs not described anywhere else in the world, when compared to those in the international C. trachomatis MLST database. Of the eight most common global STs, seven were found in Australia (four derived from men who have sex with men (MSM) and three from heterosexuals). Newly identified STs were predominantly found in samples from the MSM population. In conclusion, MLST provided a diverse C. trachomatis strain profile, with novel circulating STs, and could be used to identify local sexual networks to focus on interventions such as testing and partner notification to prevent reinfection.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. World Health Organization (WHO) (2012) Global incidence and prevalence of selected curable sexually transmitted infections—2008. WHO, Geneva. Available online at: http://www.who.int/reproductivehealth/publications/rtis/2008_STI_estimates.pdf

  2. Garland SM, Malatt A, Tabrizi S, Grando D, Lees MI, Andrew JH, Taylor HR (1995) Chlamydia trachomatis conjunctivitis. Prevalence and association with genital tract infection. Med J Aust 162(7):363–366

    CAS  PubMed  Google Scholar 

  3. Geisler WM, Suchland RJ, Whittington WL, Stamm WE (2003) The relationship of serovar to clinical manifestations of urogenital Chlamydia trachomatis infection. Sex Transm Dis 30(2):160–165

    Article  PubMed  Google Scholar 

  4. Andersson P, Harris SR, Seth Smith HM, Hadfield J, O’Neill C, Cutcliffe LT, Douglas FP, Asche LV, Mathews JD, Hutton SI, Sarovich DS, Tong SY, Clarke IN, Thomson NR, Giffard PM (2016) Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages. Nat Commun 7:10688. doi:10.1038/ncomms10688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lewis D, Newton DC, Guy RJ, Ali H, Chen MY, Fairley CK, Hocking JS (2012) The prevalence of Chlamydia trachomatis infection in Australia: a systematic review and meta-analysis. BMC Infect Dis 12:113. doi:10.1186/1471-2334-12-113

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bom RJ, Christerson L, Schim van der Loeff MF, Coutinho RA, Herrmann B, Bruisten SM (2011) Evaluation of high-resolution typing methods for Chlamydia trachomatis in samples from heterosexual couples. J Clin Microbiol 49(8):2844–2853. doi:10.1128/JCM.00128-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Stevens MP, Twin J, Fairley CK, Donovan B, Tan SE, Yu J, Garland SM, Tabrizi SN (2010) Development and evaluation of an ompA quantitative real-time PCR assay for Chlamydia trachomatis serovar determination. J Clin Microbiol 48(6):2060–2065. doi:10.1128/JCM.02308-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Herrmann B, Isaksson J, Ryberg M, Tångrot J, Saleh I, Versteeg B, Gravningen K, Bruisten S (2015) Global multilocus sequence type analysis of Chlamydia trachomatis strains from 16 countries. J Clin Microbiol 53(7):2172–2179. doi:10.1128/JCM.00249-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Smith KS, Guy R, Danielewski JA, Tabrizi SN, Chen M, Kaldor JM, Hocking JS (2015) High chlamydia treatment failure rates in men who have sex with men. In: Proceedings of the World STI & HIV Congress, Brisbane, Australia, September 2015, p O15.13

  10. Smith KS GR, Danielewski JA, Tabrizi SN, Fairley CK, McNulty AM, Rawlinson W, Saville M, Garland SM, Donovan B, Kaldor JM, Hocking JS (2017) Biological and behavioural factors associated with positive chlamydia retests. Sex Transm Dis (in press)

  11. Bom RJ, Matser A, Bruisten SM, van Rooijen MS, Heijman T, Morré SA, de Vries HJ, Schim van der Loeff MF (2013) Multilocus sequence typing of Chlamydia trachomatis among men who have sex with men reveals cocirculating strains not associated with specific subpopulations. J Infect Dis 208(6):969–977. doi:10.1093/infdis/jit275

    Article  PubMed  Google Scholar 

  12. Twin J, Moore EE, Garland SM, Stevens MP, Fairley CK, Donovan B, Rawlinson W, Tabrizi SN (2011) Chlamydia trachomatis genotypes among men who have sex with men in Australia. Sex Transm Dis 38(4):279–285. doi:10.1097/OLQ.0b013e3181fc6944

    PubMed  Google Scholar 

  13. Kong FY, Tabrizi SN, Fairley CK, Phillips S, Fehler G, Law M, Vodstrcil LA, Chen M, Bradshaw CS, Hocking JS (2016) Higher organism load associated with failure of azithromycin to treat rectal chlamydia. Epidemiol Infect 144(12):2587–2596. doi:10.1017/S0950268816000996

    Article  CAS  PubMed  Google Scholar 

  14. Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJ, Morré SA, Speksnijder A, Bébéar CM, Clerc M, de Barbeyrac B, Parkhill J, Thomson NR (2012) Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 44(4):413–419, S1. doi:10.1038/ng.2214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Gravningen K, Christerson L, Furberg AS, Simonsen GS, Ödman K, Ståhlsten A, Herrmann B (2012) Multilocus sequence typing of genital Chlamydia trachomatis in Norway reveals multiple new sequence types and a large genetic diversity. PLoS One 7(3), e34452. doi:10.1371/journal.pone.0034452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Klint M, Fuxelius HH, Goldkuhl RR, Skarin H, Rutemark C, Andersson SG, Persson K, Herrmann B (2007) High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis. J Clin Microbiol 45(5):1410–1414. doi:10.1128/JCM.02301-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Versteeg B, Himschoot M, van den Broek IV, Bom RJ, Speksnijder AG, Schim van der Loeff MF, Bruisten SM (2015) Urogenital Chlamydia trachomatis strain types, defined by high-resolution multilocus sequence typing, in relation to ethnicity and urogenital symptoms among a young screening population in Amsterdam, The Netherlands. Sex Transm Infect 91(6):415–422. doi:10.1136/sextrans-2014-051790

    Article  PubMed  Google Scholar 

  18. Isaksson J, Gallo Vaulet L, Christerson L, Ruettger A, Sachse K, Entrocassi C, Castro É, Rodríguez Fermepin M, Herrmann B (2016) Comparison of multilocus sequence typing and multilocus typing microarray of Chlamydia trachomatis strains from Argentina and Chile. J Microbiol Methods 127:214–218. doi:10.1016/j.mimet.2016.06.005

    Article  CAS  PubMed  Google Scholar 

  19. Smith KS, Hocking JS, Chen M, Fairley CK, McNulty A, Read P, Bradshaw CS, Tabrizi SN, Wand H, Saville M, Rawlinson W, Garland SM, Donovan B, Kaldor JM, Guy R (2014) Rationale and design of REACT: a randomised controlled trial assessing the effectiveness of home-collection to increase chlamydia retesting and detect repeat positive tests. BMC Infect Dis 14:223. doi:10.1186/1471-2334-14-223

    Article  PubMed  PubMed Central  Google Scholar 

  20. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. doi:10.1093/molbev/mst197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. doi:10.1093/molbev/msw054

    Article  CAS  PubMed  Google Scholar 

  22. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526

    CAS  PubMed  Google Scholar 

  23. Bom RJ, van der Helm JJ, Bruisten SM, Grünberg AW, Sabajo LO, Schim van der Loeff MF, de Vries HJ (2013) The role of Surinamese migrants in the transmission of Chlamydia trachomatis between Paramaribo, Suriname and Amsterdam, The Netherlands. PLoS One 8(11), e77977. doi:10.1371/journal.pone.0077977

    Article  PubMed  PubMed Central  Google Scholar 

  24. NNDSS Annual Report Writing Group, Newman L, Stirzaker S, Knuckey D, Robinson K, Hood J, Knope K, Fitzsimmons G, Barker S, Martin N, Siripol S, Gajanayake I, Kaczmarek M, Barr I, Hii A, Foxwell R, Owen R, Liu C, Wright P, Sanders L, Barry C, Ormond J (2010) Australia’s notifiable disease status, 2008: annual report of the National Notifiable Diseases Surveillance System. Commun Dis Intell Q Rep 34(3):157–224

    Google Scholar 

Download references

Acknowledgements

We would like to thank Jenny Isaksson from Uppsala University, Sweden for her assistance with assigning new MLST alleles and STs nomenclature in the Uppsala University C. trachomatis MLST database (http://mlstdb.bmc.uu.se).

Author information

Authors and Affiliations

  1. Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Locked Bag 300, Parkville, 3052, VIC, Australia

    J. A. Danielewski, S. Phillips, S. M. Garland & S. N. Tabrizi

  2. Murdoch Childrens Research Institute, Melbourne, VIC, Australia

    J. A. Danielewski, S. Phillips, S. M. Garland & S. N. Tabrizi

  3. Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia

    F. Y. S. Kong & J. S. Hocking

  4. The Kirby Institute, University of New South Wales, Sydney, NSW, Australia

    K. S. Smith & R. Guy

  5. Melbourne Sexual Health Centre, Alfred Health, Carlton, VIC, Australia

    C. K. Fairley

  6. Central Clinical School, Monash University, Melbourne, VIC, Australia

    C. K. Fairley

  7. Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia

    S. M. Garland & S. N. Tabrizi

Authors
  1. J. A. Danielewski
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Phillips
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. F. Y. S. Kong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. S. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. S. Hocking
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. R. Guy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C. K. Fairley
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. S. M. Garland
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. S. N. Tabrizi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J. A. Danielewski.

Ethics declarations

Funding

This work was supported by an Australian National Health and Medical Research Council program grant no. 568971.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Ethics approval for the REACT and REARS studies was received from the Alfred Health Human Research Ethics Committee, South Eastern Sydney and Illawarra Area Health Service Human Research Ethics Committee and University of New South Wales Human Research Ethics Committee.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Danielewski, J.A., Phillips, S., Kong, F.Y.S. et al. A snapshot of Chlamydia trachomatis genetic diversity using multilocus sequence type analysis in an Australian metropolitan setting. Eur J Clin Microbiol Infect Dis 36, 1297–1303 (2017). https://doi.org/10.1007/s10096-017-2935-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10096-017-2935-6

Keywords

Search

Navigation