Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries

J Clin Microbiol. 2015 Jul;53(7):2172-9. doi: 10.1128/JCM.00249-15. Epub 2015 Apr 29.


The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database ( is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chlamydia Infections / microbiology*
  • Chlamydia trachomatis / classification*
  • Chlamydia trachomatis / genetics*
  • Chlamydia trachomatis / isolation & purification
  • Cluster Analysis
  • Female
  • Genetic Variation*
  • Genotype*
  • Global Health
  • Humans
  • Male
  • Multilocus Sequence Typing*
  • Phylogeography