The ribosomal intergenic spacer and domain I of the 23S rRNA gene are phylogenetic markers for Chlamydia spp.

Current methods used to classify Chlamydia strains, including biological, morphological, and DNA hybridization techniques and major outer membrane protein (omp1) gene analysis, can be imprecise or difficult to perform. To facilitate classification, 2.8-kb partial ribosomal DNA (rDNA) segments from a Chlamydia trachomatis strain and a Chlamydia psittaci strain were amplified by PCR and sequenced. Subsequently, a 1,320-bp region in this segment, including both the 16S/23S intergenic spacer (232 +/- 11 bp) and domain I (620 +/- 2 bp) of the 23S gene, was sequenced from 41 additional strains and from the chlamydia-like organisms Simkania sp. strains "Z" and "Z1." When both parsimony and distance analyses were performed, these sequences were found to have variable regions that grouped the isolates into two lineages (C. trachomatis and non-C. trachomatis) and nine distinct genotypic groups. The C. trachomatis lineage included human, swine, and mousehamster groups. The non-C. trachomatis lineage included Chlamydia pecorum, Chlamydia pneumoniae, and C. psittaci abortion, avian, feline, and guinea pig groups. These nine groups were essentially equidistant from the genetic root and were congruent with groups identified previously by using DNA-DNA homology, genomic restriction endonuclease analysis, host specificity, tissue specificity, and/or disease production. Phylogenetic trees based on the intergenic spacer or on domain I were congruent with trees previously derived from ompI sequences. DNA sequence analysis of either the intergenic spacer or domain I provides a rapid and reproducible method for identifying, grouping, and classifying chlamydial strains.