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Infection and Immunity, February 1999, p. 1009-1010, Vol. 67, No. 2
0019-9567/99/$00.00+0
LETTERS TO THE EDITOR
Phylogenetic Analysis of Chlamydia trachomatis
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LETTER |
An understanding of the evolution and biological relationships of
Chlamydia trachomatis major outer membrane protein (MOMP) and MOMP gene (omp1) sequences is an ongoing process and one
that requires complex analyses. In our estimation, the study by
Stothard et al. (5) is limited by the lack of sufficient
numbers of omp1 genotypes for the analysis presented and by
the use of only one method for evaluation of the molecular evolution of
chlamydiae. For example, the authors state that what causes
lymphogranuloma venereum, trachoma, or urogenital strains to infect
certain cell types cannot be explained by MOMP. This conclusion is
based solely on phylogenetic reconstructions of 6 trachoma and 22 nontrachoma genotypes. For MOMP, phylogenetic analyses may be more
difficult to interpret since diversity is probably generated by means
other than simple substitutions and insertions and deletions (indels); current tree topologies may be obscured by recombination events such
that a common ancestor for genotypes with similar disease presentations
can no longer be identified. We believe that estimates of mutation
rates and other more complicated analyses are needed before any firm
conclusions can be made. Further, the collection of published sequences
does not necessarily represent the extent of omp1 diversity
and may not be adequate to describe molecular evolution for chlamydiae.
For example, fewer omp1 variants have been described for E
than for D and F. As more genotyping has been performed, additional E
variants have been identified: Stothard et al. report 3 variants of 19 (16%); we previously found 11 variants of 67 (16%) (2).
Thus, additional sequencing of omp1 from multiple trachoma
and sexually transmitted disease specimens worldwide is needed to
determine a representative distribution of all genotypes for analysis.
The authors correctly mention that our E/Bour sequence is different
from that of Peterson et al. (4). They state that
"variation in E/Bour reported by Dean and Millman is not easily
explained." Herein, we provide an explanation. E/Bour was first
described in the 1950s when serotyping was the only method for
identifying chlamydial subtypes. The sequence differences between that
of Peterson et al. and ours reside in conserved regions of
omp1; variable segments of our sequence are exactly the same
as that published by Yuan et al. (6). Since serotyping is
based on antibody reactivity to variable segments of MOMP, it is highly probable that different clones of serovar E were labeled similarly as
E/Bour. The source of E/Bour may also differ; ours was from Dr. Julius
Schachter, San Francisco, Calif. Further, although the authors found no
evidence for "culture-induced ... mutation," this is an in
vitro system that does not necessarily reflect the selective pressure
of an in vivo environment. In fact, there is in vivo evidence for
allelic flux. Hayes et al. (3) observed flux in The Gambia,
albeit with minimal nonsynonymous mutations over 18 months. Dean et al.
(1) found significant flux over 3 years in Tunisia. Thus,
some mutational drift may have occurred in vivo before E clones were
serotyped and labeled as E/Bour in the 1950s.
| |
REFERENCES |
| 1.
|
Dean, D.,
J. Schachter,
C. R. Dawson, and R. S. Stephens.
1992.
Comparison of the major outer membrane protein sequence variant regions of B/Ba isolates: a molecular epidemiologic approach to Chlamydia trachomatis infections.
J. Infect. Dis.
166:383-392[Medline].
|
| 2.
|
Dean, D., and K. Millman.
1997.
Molecular and mutation trends analyses of omp1 alleles for serovar E of Chlamydia trachomatis.
J. Clin. Invest.
99:475-483[Medline].
|
| 3.
|
Hayes, L. J.,
S. Pecharatana,
R. L. Bailey,
T. H. Hampton,
M. A. Pickett,
D. C. W. Mabey,
P. J. Watt, and M. E. Ward.
1995.
Extent and kinetics of genetic change in the omp1 gene of Chlamydia trachomatis in two villages with endemic trachoma.
J. Infect. Dis.
172:268-272[Medline].
|
| 4.
|
Peterson, E. M.,
B. A. Markoff, and L. M. de la Maza.
1990.
The major outer membrane protein nucleotide sequence of Chlamydia trachomatis, serovar E.
Nucleic Acids Res.
18:3414[Free Full Text].
|
| 5.
|
Stothard, D. R.,
G. Boguslawski, and R. B. Jones.
1998.
Phylogenetic analysis of the Chlamydia trachomatis major outer membrane protein and examination of potential pathogenic determinants.
Infect. Immun.
66:3618-3625[Abstract/Free Full Text].
|
| 6.
|
Yuan, Y.,
Y.-X. Zhang,
N. G. Watkins, and H. D. Caldwell.
1989.
Nucleotide and deduced amino acid sequences for the four variable domains of the major outer membrane proteins of the 15 Chlamydia trachomatis serovars.
Infect. Immun.
57:1040-1049[Abstract/Free Full Text].
|
| | | | |
Deborah Dean
Kim Millman
Department of Medicine
UCSF School of Medicine
University of California San Francisco
San Francisco, California 94143-0412
|
| |
AUTHORS' REPLY |
We appreciate the opportunity to reply to the letter submitted by Drs.
Dean and Millman in response to our article "Phylogenetic analysis of
the Chlamydia trachomatis major outer membrane protein and
examination of potential pathogenic determinants" (4). We
agree with Drs. Dean and Millman that understanding the evolution of
the Chlamydia trachomatis major outer membrane protein
(MOMP) is an ongoing process, one that will change as new
omp1 sequences from a variety of clinical and geographic
sources are submitted to sequence databases. Indeed, one of the goals
of our recent publication was to update the work by W. M. Fitch,
E. M. Peterson, and L. M. de la Maza which appeared in 1993 (2). The 1993 publication did not include representatives
from serovars Ba, D, Da, G, I, Ia, J, and K because full-length
sequences for these serovars were not available at the time. We were
able to bridge this gap in our 1998 publication by providing
full-length sequences for these serovars. Our conclusions did not
differ from those of Fitch, Peterson, and de la Maza, namely, that the
MOMP phylogenetic tree is not congruent with strain clustering by cell
type infected, organ infected, or disease presentation, and we also
concluded that the variability in MOMP appears to be more likely the
result of providing for pathogen diversity than of specific and
directed evolution of pathogenic epitopes or determinants.
Drs. Dean and Millman state that our analysis was limited by the lack
of sufficient numbers of omp1 genotypes. We agree. We could
have expanded our data set by including partial omp1
sequences in GenBank, those which consist of only the variable regions
of the omp1 gene. However, inspection of complete
omp1 sequences clearly shows that substitution in this gene
occurs in both conserved and variable regions. Dean and Millman provide
an example in that their E/Bour sequence (1) differs from
another E/Bour sequence (3) only in conserved regions.
Therefore, to include partial sequences in our analysis would have led
to the exclusion of phylogenetically informative sites in the conserved
regions of complete omp1 sequences. In the end, we felt that
the most accurate phylogenetic reconstruction would be produced by
using complete omp1 gene sequences. We also hope that our
publication will encourage more investigators to examine the entire
omp1 gene when performing epidemiologic studies and surveys.
In this way, we can build a larger and more comprehensive collection of
omp1 sequences, which will produce a more complete and
accurate history of this gene.
Finally, we recognize that there are multiple possible explanations as
to why the two E/Bour sequences that exist in GenBank are different. In
fact, it was this phenomenon which led us to examine whether long-term
expansion in cell culture could induce such mutations (5).
While cell culture did not appear to produce mutations, we agree with
Dean and Millman that selective pressure from the host immune system in
an in vivo environment could.
There is still much work to be done on understanding the evolutionary
complexities of the C. trachomatis MOMP. Our recent publication only scratches the surface, but it raises real issues that
must be considered if MOMP is going to be a vaccine candidate for
chlamydial disease. We hope that concerted efforts by everyone in this
area of research will facilitate this process.
| |
REFERENCES |
| 1.
|
Dean, D., and K. Millman.
1997.
Molecular and mutation trends analyses of omp1 alleles for serovar E of Chlamydia trachomatis.
J. Clin. Invest.
99:475-483.
|
| 2.
|
Fitch, W. M.,
E. M. Peterson, and L. M. de la Maza.
1993.
Phylogenetic analysis of the major outer membrane protein genes of Chlamydiae, and its implication for vaccine development.
Mol. Biol. Evol.
10:892-913[Abstract].
|
| 3.
|
Peterson, E. M.,
B. A. Markoff, and L. M. de la Maza.
1990.
The major outer membrane protein nucleotide sequence of Chlamydia trachomatis, serovar E.
Nucleic Acids Res.
18:3414.
|
| 4.
|
Stothard, D. R.,
G. Boguslawski, and R. B. Jones.
1998.
Phylogenetic analysis of the Chlamydia trachomatis major outer membrane protein and examination of potential pathogenic determinants.
Infect. Immun.
66:3618-3625.
|
| 5.
|
Stothard, D. R.,
B. Van Der Pol,
N. J. Smith, and R. B. Jones.
1998.
Effect of serial passage in tissue culture on sequence of omp1 from Chlamydia trachomatis clinical isolates.
J. Clin. Microbiol.
36:3686-3688[Abstract/Free Full Text].
|
| | | | |
Diane R. Stothard
Robert B. Jones
Division of Infectious Diseases
Department of Medicine
Indiana University School of Medicine
Indianapolis, Indiana 46202-5124
|
Infection and Immunity, February 1999, p. 1009-1010, Vol. 67, No. 2
0019-9567/99/$00.00+0
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