Genomic relatedness of Chlamydia isolates determined by amplified fragment length polymorphism analysis - PubMed (original) (raw)

Genomic relatedness of Chlamydia isolates determined by amplified fragment length polymorphism analysis

A Meijer et al. J Bacteriol. 1999 Aug.

Abstract

The genomic relatedness of 19 Chlamydia pneumoniae isolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (+/- 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittaci fingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

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Figures

FIG. 1

FIG. 1

Digitized AFLP fingerprints and phylogram of 19 C. pneumoniae isolates. The phylogram was inferred by the UPGMA method with a band-based Dice similarity coefficient (S D) matrix. S D values (in percentages) and molecular sizes (Mw) (in base pairs) are shown above the phylogram and fingerprints, respectively. The names of the isolates as presented in Table 1 are shown on the right.

FIG. 2

FIG. 2

Digitized AFLP fingerprints and phylogram of 21 C. trachomatis isolates. The phylogram was inferred by the UPGMA method with a band-based Dice similarity coefficient (S D) matrix. S D values (in percentages) and molecular sizes (Mw) (in base pairs) are shown above the phylogram and fingerprints, respectively. The names of the isolates as presented in Table 1 are shown on the right.

FIG. 3

FIG. 3

Digitized AFLP fingerprints and phylogram of representative isolates of all four Chlamydia species. The phylogram was inferred by the UPGMA method with a band-based Dice similarity coefficient (S D) matrix. S D values (in percentages) and molecular sizes (Mw) (in base pairs) are shown above the phylogram and fingerprints, respectively. The names of the isolates as presented in Table 1 are shown on the right, with prefixes indicating the hosts (Bo, bovine; Fe, feline; Hu, human; Mu, murine; Pgn, pigeon; Prk, parakeet; Sw, swine) and species codes (Cpe, C. pecorum; Cpn, C. pneumoniae; Cps, C. psittaci; Ctr, C. trachomatis).

FIG. 4

FIG. 4

Phylogram inferred by the UPGMA method with the DNA-DNA hybridization data matrix in Table 3. The relatedness between C. pneumoniae and C. trachomatis (murine) is missing and has been estimated as minimal (≤5%).

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