JOURNAL OF BACTERIOLOGY, Mar. 2011, p. 1282–1283
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 193, No. 5
Genome Sequence of the Zoonotic Pathogen Chlamydophila psittaci?
Helena M. B. Seth-Smith,1Simon R. Harris,1Richard Rance,1Anthony P. West,1Juliette A. Severin,2
Jacobus M. Ossewaarde,3,4Lesley T. Cutcliffe,5Rachel J. Skilton,5Pete Marsh,6Julian Parkhill,1
Ian N. Clarke,5and Nicholas R. Thomson1*
Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA,
United Kingdom1; Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands2;
Laboratory Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, Netherlands3; Department of Medical
Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands4; Molecular Microbiology Group,
Division of Infection, Inflammation, and Immunity, School of Medicine, Southampton SO16 6YD,
United Kingdom5; and Health Protection Agency South East, Southampton Laboratory,
Southampton General Hospital, Southampton SO16 6YD, United Kingdom6
Received 29 November 2010/Accepted 13 December 2010
We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds and a
human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, as in
other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The C. psittaci plasmid was
Avian Chlamydophila psittaci infections range from chronic
and symptomless to acute, with various mortality rates (11, 12).
Epidemic outbreaks of C. psittaci have been reported among
wild birds and commercially farmed poultry, causing significant
economic losses (11, 12). Although it primarily infects birds, C.
psittaci is a human zoonotic pathogen causing pneumonia or
fever following close contact with infected birds (12).
We sequenced C. psittaci strain RD1, which was isolated
from a mixed culture with Chlamydia trachomatis serovar L2b.
Although human mixed ocular infections with these two spe-
cies have been reported (7), C. psittaci strain RD1 is thought to
derive from a laboratory-based cross-contamination event
from an undetermined source soon after C. trachomatis strain
isolation. DNA was prepared (17), sequenced using 454 pyro-
sequencing on a GS20 machine with an average read length of
100 bp, and assembled using Newbler (Roche). The contigs
were ordered using the Chlamydophila abortus genome as a
reference (18) and manually finished to produce an im-
proved high-quality draft genome sequence (6) of six con-
tigs, with approximately 40.7? coverage. The five un-
spanned gaps are clearly marked in the genome annotation
(size estimates based on comparison with C. abortus: 3,592
bp between pmp11G and pmp13G [pmp12G is absent], 116
bp at the 3? end of pmp16G, and three gaps of 887, 797, and
1,481 bp within the rRNA operon). Annotation and com-
parative analysis with the closely related species C. abortus,
Chlamydophila caviae, and Chlamydophila felis (1, 8, 14, 18)
were performed using Artemis (16) and ACT (5).
The draft genome sequence of C. psittaci comprises
1,156,417 bp, showing average nucleotide identities of 91.3,
85.9, and 84.8% with C. abortus, C. caviae, and C. felis, respec-
tively. The C. psittaci genome is predicted to encode 959 coding
sequences (CDSs). Analysis of ompA indicates that C. psittaci
strain RD1 belongs to genotype A (9, 13). Like other Chlamy-
dophila genomes, that of C. psittaci carries 36 tRNA genes and
one rRNA operon and shows high conservation of gene con-
tent and order with other members of its genus. A total of 16
pseudogenes were detected within the genome, including two
polymorphic membrane protein (pmp) genes (cpsi_2861 and
cpsi_2911) (10) and one transmembrane head/inclusion mem-
brane family (TMH/Inc) gene (cpsi_7871) (2, 15). The C.
psittaci strain RD1 plasmid, designated pRD1, is 7,553 bp long,
encodes 8 CDSs, and differs by only four single-nucleotide
polymorphisms from C. psittaci plasmid pCpA1 (NC_002117).
Most of the C. psittaci-specific sequences are located in the
plasticity zone (PZ), which carries an additional 18,139 bp of
sequence compared to C. abortus, including a 9,762-bp CDS
predicted to encode a cytotoxin (cpsi_5561) which shows 44%
identity with cytotoxins found at the same locus in C. felis and
C. caviae. The PZ also contains the intact guaBA-add operon
(cpsi_5591-5611) encoding proteins thought to be involved in
purine nucleotide interconversion (1, 14, 18). C. psittaci lacks
the tryptophan biosynthesis operon (3, 4).
Nucleotide sequence accession numbers. The sequences de-
termined in this study have been deposited in the EMBL da-
tabase under accession numbers FQ482149 (chromosome) and
This work was supported by Wellcome Trust grant WT076964.
1. Azuma, Y., et al. 2006. Genome sequence of the cat pathogen, Chlamy-
dophila felis. DNA Res. 13:15–23.
2. Bannantine, J. P., D. D. Rockey, and T. Hackstadt. 1998. Tandem genes of
Chlamydia psittaci that encode proteins localized to the inclusion membrane.
Mol. Microbiol. 28:1017–1026.
3. Beatty, W. L., T. A. Belanger, A. A. Desai, R. P. Morrison, and G. I. Byrne.
1994. Tryptophan depletion as a mechanism of gamma interferon-mediated
chlamydial persistence. Infect. Immun. 62:3705–3711.
4. Caldwell, H. D., et al. 2003. Polymorphisms in Chlamydia trachomatis tryp-
* Corresponding author. Mailing address: Pathogen Genomics,
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SA, United Kingdom. Phone: 011-
1223 494 761. Fax: 011-1223 494 919. E-mail: email@example.com.
?Published ahead of print on 23 December 2010.
tophan synthase genes differentiate between genital and ocular isolates.
J. Clin. Invest. 111:1757–1769.
5. Carver, T. J., et al. 2005. ACT: the Artemis comparison tool. Bioinformatics
6. Chain, P. S. G., et al. 2009. Genome project standards in a new era of
sequencing. Science 326:236–237.
7. Dean, D., R. P. Kandel, H. K. Adhikari, and T. Hessel. 2008. Multiple
Chlamydiaceae species in trachoma: implications for disease pathogenesis
and control. PLoS Med. 5:e14.
8. Everett, K. D. E., R. M. Bush, and A. A. Andersen. 1999. Emended descrip-
tion of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and
Simkaniaceae fam. nov., each one containing one monotypic genus, revised
taxonomy of the family Chlamydiaceae, including a new genus and five new
species, and standards for the identification of organisms. Int. J. Sys. Bacte-
9. Geens, T., et al. 2005. Sequencing of the Chlamydophila psittaci ompA gene
reveals a new genotype, E/B, and the need for a rapid discriminatory geno-
typing method. J. Clin. Microbiol. 43:2456–2461.
10. Grimwood, J., and R. S. Stephens. 1999. Computational analysis of the
polymorphic membrane protein superfamily of Chlamydia trachomatis and
Chlamydia pneumoniae. Microb. Comp. Genomics 4(3):187–201.
11. Harkinezhad, T., T. Geens, and D. Vanrompay. 2009. Chlamydophila psittaci
infections in birds: a review with emphasis on zoonotic consequences. Vet.
12. Longbottom, D., and L. J. Coulter. 2003. Animal chlamydioses and zoonotic
implications. J. Comp. Pathol. 128:217–244.
13. Mitchell, S. L., et al. 2009. Genotyping of Chlamydophila psittaci by real-time
PCR and high-resolution melt analysis. J. Clin. Microbiol. 47:175–181.
14. Read, T. D., et al. 2003. Genome sequence of Chlamydophila caviae (Chla-
mydia psittaci GPIC): examining the role of niche-specific genes in the
evolution of the Chlamydiaceae. Nucleic Acids Res. 31:2134–2147.
15. Rockey, D. D., M. A. Scidmore, J. P. Bannantine, and W. J. Brown. 2002.
Proteins in the chlamydial inclusion membrane. Microbes Infect. 4:333–
16. Rutherford, K., et al. 2000. Artemis: sequence visualization and annotation.
17. Skipp, P., J. Robinson, C. D. O’Connor, and I. N. Clarke. 2005. Shotgun
proteomic analysis of Chlamydia trachomatis. Proteomics 5:1558–1573.
18. Thomson, N. R., et al. 2005. The Chlamydophila abortus genome sequence
reveals an array of variable proteins that contribute to interspecies variation.
Genome Res. 15:629–640.
VOL. 193, 2011 GENOME ANNOUNCEMENTS1283