Predicting phenotype and emerging strains among Chlamydia trachomatis infections

Emerg Infect Dis. 2009 Sep;15(9):1385-94. doi: 10.3201/eid1509.090272.


Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Typing Techniques*
  • Chlamydia Infections / microbiology*
  • Chlamydia Infections / pathology
  • Chlamydia trachomatis / classification*
  • Chlamydia trachomatis / genetics
  • Chlamydia trachomatis / isolation & purification
  • Communicable Diseases, Emerging / microbiology*
  • Communicable Diseases, Emerging / pathology
  • DNA, Bacterial / analysis
  • Genomics
  • Humans
  • Lymphogranuloma Venereum / microbiology*
  • Lymphogranuloma Venereum / pathology
  • Phenotype
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Predictive Value of Tests
  • Recombination, Genetic
  • Sequence Analysis, DNA
  • Sexually Transmitted Diseases / microbiology
  • Sexually Transmitted Diseases / pathology
  • Species Specificity
  • Trachoma / microbiology*
  • Trachoma / pathology


  • Bacterial Proteins
  • DNA, Bacterial