THE RIBOSOMAL INTERGENIC SPACER AND DOMAIN-I OF THE 23S RIBOSOMAL-RNAGENE ARE PHYLOGENETIC MARKERS FOR CHLAMYDIA SPP

Current methods used to classify Chlamydia strains, including biologic al, morphological, and DNA hybridization techniques and major outer me mbrane protein (omp1) gene analysis, can be imprecise or difficult to perform, To facilitate classification, 2.8-kb partial ribosomal DNA (r DNA) segments from a Chlamydia trachomatis strain and a Chlamydia psit taci strain were amplified by PCR and sequenced, Subsequently, a 1,320 -bp region in this segment, including both the 16S/23S intergenic spac er (232 +/- 11 bp) and domain I (620 +/- 2 bp) of the 23S gene, was se quenced from 41 additional strains and from the chlamydia-like organis ms Simkania sp, strains ''Z'' and ''Z1.'' When both parsimony and dist ance analyses were performed, these sequences were found to have varia ble regions that grouped the isolates into two lineages (C, trachomati s and nan-C. trachomatis) and nine distinct genotypic groups, The C, t rachomatis lineage included human, swine, and mouse-hamster groups, Th e non-C. trachomatis lineage included Chlamydia pecorum, Chlamydia pne umoniae, and C, psittaci abortion, avian, feline, and guinea pig group s, These nine groups were essentially equidistant from the genetic roo t and were congruent with groups identified previously by using DNA-DN A homology, genomic restriction endonuclease analysis, host specificit y, tissue specificity, and/or disease production, Phylogenetic trees b ased on the intergenic spacer or on domain I were congruent with trees previously derived from omp1 sequences, DNA sequence analysis of eith er the intergenic spacer or domain I provides a rapid and reproducible method for identifying, grouping, and classifying chlamydial strains.