Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species
© Mitchell et al; licensee BioMed Central Ltd. 2010
Received: 6 November 2009
Accepted: 21 July 2010
Published: 21 July 2010
Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species.
We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes).
We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.
The Chlamydiaceae are obligate intracellular pathogens that undergo a unique biphasic developmental cycle involving the inter-conversion between the extracellular infectious elementary body and the intracellular, replicative reticulate body. Chlamydia 'Chlamydophila' pneumoniae is probably one of the most successful chlamydial species, having established a niche in a range of warm-blooded (homoeothermic) and cold-blooded (poikilothermic) hosts, including humans, horses, marsupials, frogs and reptiles [1–5]. C. pneumoniae human infections are associated with bronchitis, pharyngitis, community-acquired pneumonia and more recently chronic diseases, such as atherosclerosis and stroke [6, 7] myocarditis , multiple sclerosis  and Alzheimer's disease .
Australia's native icon, the koala (Phascolarctos cinereus), is found throughout Australia's north-eastern and southern eucalypt regions and is commonly infected with chlamydiae [11–14]. While the decline in koala populations has largely been the result of hunting and a diminished habitat, there is great concern for the koala due to an increased incidence of disease . It is estimated that almost all of the nations free-range koala populations and many in captive populations are affected by C. pneumoniae and/or C. pecorum (the most common of the two species). C. pneumoniae-infected koalas may develop a respiratory illness similar to that in humans with clinical signs of sneezing, coughing, nasal discharge and chest congestion [16, 17]. C. pneumoniae koala is not restricted to the respiratory tract and has been isolated from ocular and urogenital tract sites (often in conjunction with C. pecorum), although disease at these sites is poorly understood .
Exposure to C. pneumoniae is widespread due to effective aerosol transmission and outbreaks have been reported in humans [18–21], horses , frogs  and koalas . However, the original source of infection remains undetermined. Myers et al. recently published the full 1.24 Mbp genome sequence of the C. pneumoniae koala LPCoLN isolate, the first analysis of a C. pneumoniae genome from a non-human host species. This study revealed that the five C. pneumoniae genomes were highly similar in genomic organisation and gene order, although some notable differences were observed . In contrast to the highly conserved human-derived isolates, a relatively high number of single nucleotide polymorphisms, SNPs (6213) differentiated koala LPCoLN from human AR39 . In the proposed phylogeny (based on SNPs from 111 highly conserved genes), which encompassed all five C. pneumoniae genomes and five sequenced animal chlamydial genomes (C. pecorum E58, C. muridarum Nigg, C. caviae GPIC, C. psittaci 6BC and C. abortus s26/3), koala LPCoLN was basal to the C. pneumoniae human isolates (larger genome and many full-length genes relative to human isolates).
In the present report we perform a comparative analysis of the whole koala LPCoLN genome sequence, highlighting the components that distinguish the strain isolated from the koala (animal), from those isolated from humans. These comparisons point to candidates of strain-specific adaptations and may provide potential targets for improved diagnostic tests, therapeutic intervention and epidemiological investigations.
We used a comparative genomics approach to identify genetic characteristics that were either unique to C. pneumoniae or were commonly shared with chlamydial species and other organisms. Overall, we analysed a total of 66 genes for key similarities and differences between human and animal strains of C. pneumoniae (see Additional file 1 for list of 66 genes analysed). We chose to use our C. pneumoniae animal genome as the reference genome and compared the available human genomes to it.
Chlamydia pneumoniae-specific genes
Using tblastx and tblastn, we searched other genomes for orthologs of the genes identified from individual gene-by-gene comparisons of the five C. pneumoniae genomes. The comparative approach identified 140 genes that were specific to C. pneumoniae and for which no significant similarity was detected in any other organism (Additional file 2). Many of these species-specific genes are short open reading frames (ORFs) that have been annotated as genes. The large number of short hypothetical ORFs makes it difficult to determine whether these genes are 'real' or artefacts of the genome annotation or sequencing process. Until these proteins are systematically studied in the future, it cannot be determined whether these proteins are valid or too short to be protein-coding genes. Genes with suggested or predicted functions include putative lipoproteins and chlamydial inclusion membrane proteins (IncA). Several hypothetical proteins are clustered together (including CPK_ORF00340-343, 389-401, 496-498, 567-569, 658-661, 969-980: LPCoLN locus designation, CPK), suggesting that they may exist in an operon and might be functionally related.
Genes with a demonstrated role in chlamydial biology and/or pathogenicity
One of the most striking differences between the C. pneumoniae koala and human genomes were changes associated with the polymorphic membrane proteins (Pmps). Like C. pneumoniae of human origin [25, 26], koala LPCoLN is predicted to encode 21 Pmps that are phylogenetically related to one of six basic subtypes (pmp A, B/C, D, E/F, G/I and H; Additional files 3 and 4) [25, 27–29]. The organisation of the pmp loci of koala LPCoLN is conserved relative to the C. pneumoniae human isolates. However, where the four human isolates carry several interrupted pmp genes (Additional file 3), koala LPCoLN carries uninterrupted, full-length versions of the same genes, including pmp G3, pmp G4 and pmp E3 (Additional file 3). A global comparison of all pmp sequences reveals a total of 2015 SNPs (of which 994 generated an amino acid change; see Additional file 5 for approximate SNP positions) differentiating koala LPCoLN from the four C. pneumoniae human isolates, with the highest percentage of SNPs observed in pmp E4 (30.46%) and pmp E3 (6.95%). In addition to SNPs, several strain-specific (human versus animal) indels (insertions and deletions) were evident in pmp B, pmp E1, pmp G2, pmp G4, pmp G5, pmp G7, pmp G10, and pmp G13 (Additional file 3). Interestingly, the pmp G5 pseudogene is interrupted by a stop codon in all five strains albeit at different sites: LPCoLN carries a seven nt indel (GAT GTA C) at nt position 332, resulting in a TAA stop codon at nt position 346, while the four human isolates have a SNP (C to T) at nt 1483, resulting in a TAA stop codon (data not shown). Previous analyses of human isolates have revealed variable numbers of 393 nt tandem repeat segments in pmp G6, including two repeats in AR39  and J138 , and three repeats in TW183 (Geng MM, Schuhmacher A, Muehldorfer I, Bensch KW, Schaefer KP, Schneider S, Pohl T, Essig A, Marre R, Melchers K: The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis, submitted) and CWL029 . The LPCoLN genome carries three variable tandem repeats in pmp G6.
Type III secretion (T3S) occurs independently of the sec pathway and requires assembly of a secretion apparatus composed of approximately 20 proteins. However, in this analysis we looked at more than just the apparatus proteins; we also examined potential secreted proteins and chaperone proteins involved in T3S. Additional file 6 compares 26 proteins from LPCoLN to putative orthologs of other chlamydial species. Ten apparatus-encoding genes (CDSs CPK_ORF00106, 111, 115, 231, 232, 233, 234, 236, 830 and 831), which were either annotated as such and/or found to be homologous to previously studied proteins in other chlamydial spp. were examined. Genetic comparisons indicate ≥ 98.2% nucleotide sequence identity between each koala LPCoLN T3S apparatus gene and orthologs from the human isolates. Similarly, comparisons of genes which were annotated as, or are similar to, chaperone-encoding genes that assist in the folding of effectors demonstrated high conservation with ≥ 99.3% sequence identity to the equivalent genes in the C. pneumoniae isolates from humans.
Nine putative effector-encoding genes (CDSs CPK_ORF00107, 216, 217, 430, 445, 446, 799, 800 and 832) of C. pneumoniae koala LPCoLN were compared to their counterparts in the human isolates. As with the T3S apparatus proteins, all koala LPCoLN effectors exhibited ≥ 98.2% sequence identity with their human isolate counterparts (Additional file 6).
Genes involved in nucleotide salvaging pathways or amino acid biosynthesis
Chlamydiaceae genome features with suspected host and niche specific genes
Genome size (nt)
Protein coding sequences
tyr P copies
C. pneumoniae AR39
guaBA-add, udk, pyrE
C. pneumoniae CWL029
guaBA-add, udk, pyrE
C. pneumoniae J138
guaBA-add, udk, pyrE
C. pneumoniae TW183
guaBA-add, udk, pyrE
C. pneumoniae LPCoLN
C. felis Fe/C-56
C. caviae GPIC
trpABFCDR, kynU, prsA, tph
C. abortus S26/3
guaB (pseudogene), pyrE
C. muridarum Nigg
C. trachomatis serovar D
None of the above
C. pneumoniae is the only chlamydial species to have a udk gene for UMP production. Our examination of the C. pneumoniae sequence revealed that the 3' end of the gene was unique to the species. No significant sequence similarity was observed in other organisms between nt regions 541-669, indicating that this region might be specific for C. pneumoniae. A sequence alignment of the full-length udk gene identified only three SNPs (one amino acid change) differentiating koala LPCoLN from the sequenced human isolates.
The bacterial pyrimidine biosynthesis pathway includes several enzymes for the conversion of UMP into CTP. However, all chlamydial genomes thus far lack the genes for most of the pathway with the exception of the last few steps (Additional file 8). C. pneumoniae of koala and human origins, C. felis, C. caviae and C. abortus have the pyrE gene, encoding an orotate phosphoribosyl transferase involved in pyrimidine biosynthesis. However, the final step in de novo pyrimidine biosynthesis is via orotidine-5'-monophosphate decarboxylase (pyrF) and this gene is missing from all chlamydial genomes.
The purine biosynthesis pathway is also incomplete, similar to the pyrimidine pathway, with many genes variably missing in the chlamydial genomes (Table 1). The only four genes that are absent from the koala LPCoLN genome but are present in the human genomes include CP_0597, which encodes a hypothetical protein, guaB (IMP dehydrogenase), guaA (GMP synthase) and add (AMP adenosine deaminase), which are involved in purine ribonucleotide biosynthesis. The guaA and add sequences of the C. pneumoniae human isolates were identical, while guaB fragmentation was evident in TW183, CWL029 and J138 isolates with a deleted 324 nt at the 5' end of the sequence (Figure 1). The CP_0597 gene resides next to this guaBA-add cluster (Figure 1), which may indicate that this gene may also be involved in purine biosynthesis.
The tryptophan biosynthesis operon is missing from several chlamydial species including C. muridarum Nigg, C. abortus S26/3, and C. pneumoniae of both koala and human origin (Table 1). Despite this absence, C. pneumoniae koala and human encode a functional aromatic amino acid (tryptophan) hydroxylase, although the koala LPCoLN isolate is missing the extended N-terminal region . While variations in C. pneumoniae tyr P (tryptophan tyrosine permease) copy numbers have been found between human isolates , we report that koala LPCoLN, a respiratory isolate, has a single copy of tyr P. A comparison of the tyr P sequence from all five sequenced (full-genome) C. pneumoniae isolates revealed that the sequence was highly conserved across the seven copies of tyr P, revealing only nine SNPs including seven unique to koala LPCoLN, four of which led to an amino acid change. Previously, Gieffers et al. published a tyr P-specific SNP profile of 20 C. pneumoniae human isolates, and here we report the SNP profile of two additional respiratory isolates J138 (CGGGG) and LPCoLN (CAAGG).
Extrachromosomal elements of the Chlamydiaceae
The bacteriophage is another strain-specific extrachromosomal element reported in chlamydial species. In C. pneumoniae, AR39 is the only human genome to have an extrachromosomal bacteriophage (4524 nt single-stranded DNA) , whereas the koala LPCoLN genome showed remnants of a phage. The first remnant of a phage in the koala LPCoLN genome was evident in CPK_ORF00729, a 366 nt incomplete ORF that is presumably defective, sharing approximately 79% similarity (nt 301/382) to the partial-length of the human AR39 phage. CPK_ORF00729 also shares 97% similarity (nt 324/333) to the Chp1 remnant (C. psittaci phage), which is present in the four C. pneumoniae human genomes. This suggests earlier integration of the phage genome in the C. pneumoniae genome (Geng MM, Schuhmacher A, Muehldorfer I, Bensch KW, Schaefer KP, Schneider S, Pohl T, Essig A, Marre R, Melchers K: The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis, submitted). The second koala LPCoLN phage remnant was a 445 nt ORF, termed CPK_ORF00730, which appears to be 'intact', sharing approximately 77% similarity (nt 342/445) to the human AR39 phage. The koala LPCoLN phage remnants are positioned between hypothetical genes in the genome and there appear to be no further remnants of the phage within this region of the genome. A comparison of the C. pneumoniae koala LPCoLN phage with other chlamydial species revealed approximately 77-79% sequence identity to partial-length sequences of the C. psittaci Chp2 phage, C. pecorum phage 3, C. caviae phiCPG1 phage and C. abortus Chp4 phage.
In this work, we applied computational analyses to explore the genome content and genetic diversity among the recently sequenced C. pneumoniae koala LPCoLN genome and previously published C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). The koala LPCoLN genome is larger than all four C. pneumoniae human genomes by 10-12 kbp. We combined BLAST search methods and motif analysis for use in elucidating the relationship between gene function and evolution. Even though these techniques have several limitations , our comparative approach has (i) identified genome plasticity, (ii) provided circumstantial evidence for the presumed direction of C. pneumoniae evolution, and (iii) suggested targets for detection and differentiation of C. pneumoniae isolates from both human and animal origins.
The presence of unique insertions/deletions is evidence of evolution in action. For the majority of these genes, the C. pneumoniae koala genome has the full-length version. These length polymorphisms suggest that the presumed functional changes are brought about by adaptation to a specialised niche, where the ancestral gene function may no longer be required. Therefore, it is important to understand how these genetic differences may influence differences in pathogenicity and fitness in the host. Our data supports the findings of Rattei et al. and the whole genome findings of Myers et al. in that the essentially clonal human isolates have evolved from an animal strain(s) that has adapted to humans through fragmentation, decay and loss-of-function processes whereby the activity of the gene product may be reduced or specialised. Hence, the koala LPCoLN genome seems to be an 'older' strain in this sense. In addition, we provide new information on strain diversity and have identified targets for detection and further investigation.
Our analysis revealed a total of 140 genes that were specific to C. pneumoniae. One hundred and twenty-three of these represented hypothetical genes with no significant similarity to genes in other organisms present in the database. Further analysis of these hypothetical genes (subcellular localisation, gene expression analysis, functional profiling from microarray analysis) may reveal undiscovered biovars or subspecies in C. pneumoniae.
The Pmp family is characterised by an unusual degree of sequence polymorphism, including mutations and large indels across all species [42–47] and showed variation within C. penumoniae. This suggests that the pmp gene family is subjected to high selective pressure (niche, host-specific or immune-mediated), correlating with a relatively faster evolutionary rate for these antigens. Taken together, the polymorphism of pmp sequences in C. pneumoniae from humans and animals is dually consistent with the divergent evolution of the pmp genes under host-specific selection while maintaining the capacity to adapt to specific niches or immune responses in the two different hosts.
In light of the variation seen between other families of genes and their orthologs in the human isolates, namely the pmp protein family, the strict conservation of T3S effector genes was initially surprising given the effectors' normal tendency for divergence. While the differences observed between other regions of the genomes are consistent with evolutionary changes , the relative conservation of effector genes over equivalent time suggest that changes in genes encoding effector proteins were likely selected against. This is consistent with a key role of T3S effectors in mediating steps of the biology of C. pneumoniae that are conserved in human and animal strains, such as inclusion and intracellular development. Overall, these results support a critical role for T3S less in the virulence than in the developmental biology of these organisms. Such a role has been proposed in the context of the contact-dependent T3S-mediated hypothesis of chlamydial development proposed earlier [48, 49].
Orthologs of the MACPF were identified in several chlamydial species. The first biological characterisation of the C. trachomatis MACPF by Taylor et al. has revealed that the MACPF (CT153) might be activated by proteolytic processing and may play a role in the acquisition or modification of host-derived lipids. By contrast, studies of the MACPF in other organisms, including that of Toxoplasma spp. have shown that ablation of the MACPF (termed TgPLP1) resulted in a reduction in virulence (in mice), whereby TgPLP1 deficient parasites were unable to exit normally and were entrapped within host cells, due to the inability to permeabilise the parasitophorous vacuole membrane . If the chlamydial MACPF was to play a similar role in egression or virulence, then why have several species failed to retain this gene? Non-lytic family members have also been identified in other organisms including Astrotactin involved in neural migration in mammals , a Drosophila torso-like protein involved in embryonic development  and Plu-MACPF of Photorhabdus luminescens which binds to the surface of insect cells . Further investigation of this gene should provide more insight into its role in Chlamydiaceae.
C. pneumoniae is the only chlamydial species thus far to have a udk gene encoding uridine kinase. The udk gene is a pyrimidine ribonucleoside kinase that phosphorylates uridine and cytidine into uridine or cytidine monophosphate (UMP/CMP) , and is highly conserved in the species. It has been reported that the Prevotella bryantii genome encodes a putative uracil DNA glycosylase and uridine kinase, likely to be involved in the removal of misincorporated uracil from DNA and its subsequent re-use . All chlamydial genomes also encode a uracil DNA glycosylase, however, C. pneumoniae is the only species carrying the udk ortholog. This implies that an alternative gene product is involved in UMP production in the other chlamydial species. The C. muridarum genome includes a CDS (upp) encoding a uracil phosphoribosyltransferase  that may represent the main pathway for UMP production in this species. C. pneumoniae is unusual in having a very broad host range and therefore the fact that it is the only chlamydial species to have retained the udk gene could reflect this broad host capacity.
Most bacteria can salvage or synthesise their own purines and pyrimidines. By contrast, chlamydiae and rickettsiae (another obligate intracellular bacterium) are incapable of de novo synthesis, and to a degree, of salvage [31, 57]. Given the absence of genes for enzymes upstream in the pyrimidine biosynthesis pathway, it is unclear why the pyrE should be retained. The final step in the pathway is via pyrF which is absent from the chlamydial genome, suggesting that they are unable to convert orotate to UMP. The presence in all chlamydial genomes of orthologs encoding the three downstream enzymes involved in UMP to CTP conversion and the earlier demonstration of CTP synthetase activity in these organisms [58, 59] confirm that chlamydiae are not auxotrophic for CTP. Furthermore, a three-gene cluster including guaB, guaA and add have been selectively maintained in several chlamydial species including C. pneumoniae AR39, CWL029, TW183 and J138, C. felis Fe/C-56, C. caviae GPIC and C. muridarum Nigg. C. abortus has a guaB pseudogene, whereas the C. pneumoniae LPCoLN and C. trachomatis serovar A/HAR, B/Jali20/OT, D/UQ-3/CX, L2b/UCH-1/proctititis, L2/434/Bu and Candidatus Protochlamydia amoebophila UWE25 genomes lack all three genes [25, 26, 30, 35, 36, 60]. The selective loss of guaBA-add from C. pneumoniae koala LPCoLN and other chlamydial species suggest that these three enzymes required for inter-conversion of GMP, IMP and AMP must be acquired by other means or are clearly not essential for species survival.
Copy number variations of the tyr P (tryptophan tyrosine permease) gene have been suggested to reflect vascular tropism and pathogenicity among C. pneumoniae human isolates with multiple copies associated with respiratory infection and single copy more frequently associated with vascular tropism . A comparison of the five sequenced C. pneumoniae genomes also revealed variations in the tyr P (tryptophan tyrosine permease) copy number that are, however, inconsistent with the hypothesis by Gieffers et al.. Among these, two respiratory isolates (koala LPCoLN and human J138) [24, 30], as well as the single conjunctival isolate (TW183) of the group (Geng MM, Schuhmacher A, Muehldorfer I, Bensch KW, Schaefer KP, Schneider S, Pohl T, Essig A, Marre R, Melchers K: The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis, submitted) have a single tyr P copy while two other respiratory isolates (CWL029 and AR39) [25, 26] carry duplicate copies of tyr P.
The loss and fragmentation of pre-existing genes during evolution is one of the primary distinguishing features between C. pneumoniae koala and C. pneumoniae human. Extrachromosomal plasmids have been identified in six of the nine chlamydial species. As the plasmid is not common to C. pneumoniae, it is not known why koala LPCoLN has a plasmid.
While proteins with predicted or known biologic function are favoured candidate gene targets, many C. pneumoniae-specific hypothetical proteins with no predicted function were identified in the comparisons and may be worth further investigating for their potential role in host tropism, pathogenicity and niche adaptation (see Additional file 2 for the list of genes). A suggested list of target genes for C. pneumoniae detection and a brief description of their characteristics is summarised in additional file 11. Selected genes include (i) C. pneumoniae-specific genes for detection of C. pneumoniae, (ii) genes that could potentially differentiate isolates from human and animal origins, for example, length polymorphic genes including the membrane attack complex perforin and the hypothetical protein CPK_ORF00679, (iii) genes for the identification of a C. pneumoniae plasmid.
The study of whole genome sequences provides important clues to the natural history of C. pneumoniae and their hosts, and assists in the identification of functional differences that may determine pathogenicity and virulence differences between the strains. Previously, whole genome comparisons have focused on four practically clonal C. pneumoniae human genomes, which make the identification of target genes for strain differentiation quite challenging. In this study we have made use of the recently sequenced koala LPCoLN genome, which is the largest and most unique C. pneumoniae genome sequenced thus far, in order to select target genes that represented traits of strain-specific determinants. Further investigation of these genes in other host species may provide additional clues as to what enables this pathogen to: (i) present varied clinical pathologies, (ii) occupy multiple niches, and (iii) establish an infection in cold and warm-blooded hosts. Moreover, these genes may become targets for improved diagnosis and therapeutic strategies.
Chlamydia pneumoniae isolates
The complete genomic sequences of C. pneumoniae AR39 (GenBank accession number AE002161), CWL029 (GenBank accession number AE001363) TW183 (GenBank accession number AE009440), J138 (GenBank accession number BA000008) and LPCoLN (GenBank accession CP001713) were used in this study.
Strategy for selection of genes used for comparisons
The selection strategy involved individual gene-by-gene comparisons of the complete koala LPCoLN genome. NCBI BLAST  searches using tblastx and tblastn were conducted in order to search for orthologs in the C. pneumoniae human genome and other organisms using an E-value cutoff of 1 × 10-4 with manual curation. This approach enabled us to identify regions of high SNP accumulation and to select target genes for comparison. These selected genes were grouped into five categories by their putative, predicted or hypothetical functions. The categories included: (1) C. pneumoniae-specific genes (with respect to the koala LPCoLN genome, n = 140); (2) genes with a prior demonstrated role in chlamydial biology and pathogenicity (n = 49); (3) genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6); (4) extrachromosomal elements, including a plasmid (n = 9) and bacteriophage-related genes (n = 2) (Additional files 1 and 2). Selected genes were individually aligned in order to identify SNPs, indels and targets for strain-specific adaptations.
Analysis of nucleotide and amino acid sequences and phylogeny
Gene alignments were performed using the Clustal W program (MacVector 10.6 Genetics Computer Group, Madison, Wisconcin) to identify polymorphisms and indels (insertions/deletions) . Conserved residues are outlined, similar amino acids are shaded in grey, mismatches are not shaded and dashes correspond to gaps in the sequence. A consensus line appears at the bottom of the alignment. Pmp sequences were subjected to multiple sequence alignment using ClustalW2 (EMBL-EBI)  and BioEdit Sequence Alignment Editor . SNP position analysis for each group was performed using the Microsoft Excel program (Microsoft Corporation). Motif Scan  was used to identify motifs in a sequence.
A phylogenetic tree was constructed by Neighbor-Joining, tie breaking = systematic, distance corrected by the Poisson method with gaps distributed proportionally and 1,000 bootstrap replicates.
Open Reading Frame
Single Nucleotide Polymorphism.
This work was supported by the National Institute of Allergy and Infectious Disease grant 1R01AI051472. PMB and JAC were supported by NIH/NIAID research grant RO1 AI51417. KH was supported by NIH/NIDCR training grant T32 DE07309.
- Grayston JT: Immunisation against trachoma. Pan Am Health organ Sci Publ. 1965, 147: 549-Google Scholar
- Storey CC, Lusher M, Yates P, Richmond SJ: Evidence for Chlamydia pneumoniae of non-human origin. J Gen Microbiol. 1993, 139: 2621-2626.PubMedView ArticleGoogle Scholar
- Berger L, Volp K, Mathews S, Speare R, Timms P: Chlamydia pneumoniae in a free-ranging giant barred frog (Mixophyes iteratus) from Australia. J Clin Microbiol. 1999, 37: 2378-2380.PubMed CentralPubMedGoogle Scholar
- Hotzel H, Grossmann E, Mutschmann F, Sachse K: Genetic characterization of a Chlamydophila pneumoniae isolate from an African frog and comparison to currently accepted biovars. Syst Appl Microbiol. 2001, 24: 63-66. 10.1078/0723-2020-00016.PubMedView ArticleGoogle Scholar
- Bodetti TJ, Jacobson E, Wan C, Hafner L, Pospischil A, Rose K, Timms P: Molecular evidence to support the expansion of the hostrange of Chlamydophila pneumoniae to include reptiles as well as humans, horses, koalas and amphibians. Syst App Microbiol. 2002, 25: 146-152. 10.1078/0723-2020-00086.View ArticleGoogle Scholar
- Saikku P, Leinonen M, Mattila K, Ekman MR, Nieminen MS, Makela PH, Huttunen JK, Valtonen V: Serological evidence of an association of a novel Chlamydia, TWAR, with chronic coronary heart disease and acute myocardial infarction. Lancet. 1988, 2: 983-986. 10.1016/S0140-6736(88)90741-6.PubMedView ArticleGoogle Scholar
- Grayston JT: Background and current knowledge of Chlamydia pneumoniae and atherosclerosis. J Infect Dis. 2000, 181 (Suppl 3): S402-S410. 10.1086/315596.PubMedView ArticleGoogle Scholar
- Wesslen L, Pahlson C, Friman G, Fohlman J, Lindquist O, Johansson C: Myocarditis caused by Chlamydia pneumoniae (TWAR) and sudden unexpected death in a Swedish elite orienteer. Lancet. 1992, 340: 427-428. 10.1016/0140-6736(92)91509-7.PubMedView ArticleGoogle Scholar
- Sriram S, Mitchell W, Stratton C: Multiple sclerosis associated with Chlamydia pneumoniae infection of the CNS. Neurology. 1998, 50: 571-572.PubMedView ArticleGoogle Scholar
- Balin BJ, Gerard HC, Arking EJ, Appelt DM, Branigan PJ, Abrams JT, Whittum-Hudson JA, Huson AP: Identification and localization of Chlamydia pneumoniae in the Alzheimer's brain. Med Microbiol Immunol. 1998, 187: 23-42. 10.1007/s004300050071.PubMedView ArticleGoogle Scholar
- Girjes AA, Huggal AF, Timms P, Lavin MF: Two distinct forms of Chlamydia psittaci associated with disease and infertility in Phascolarctos cinereus (koala). Infect Immun. 1988, 56: 1897-1900.PubMed CentralPubMedGoogle Scholar
- Girjes AA, Hugall A, Graham DM, McCaul TF, Lavin MF: Comparison of type I and type II Chlamydia psittaci strains infecting koalas (Phascolarctos cinereus). Vet Microbiol. 1993, 37: 65-83. 10.1016/0378-1135(93)90183-8.PubMedView ArticleGoogle Scholar
- Jackson M, White N, Giffard P, Timms P: Epizootiology of Chlamydia infections in two free-range koala populations. Vet Microbial. 1999, 65: 255-264. 10.1016/S0378-1135(98)00302-2.View ArticleGoogle Scholar
- Devereaux LN, Polkinghorne A, Meijer A, Timms P: Molecular evidence for novel chlamydial infections in the koala (Phascolarctos cinereus). Syst Appl Microbiol. 2003, 26: 245-253. 10.1078/072320203322346092.PubMedView ArticleGoogle Scholar
- McColl KA, Martin RW, Gleeson LH, Handasyde KA, Lee AK: Chlamydia infection and infertility in the female koala (Phascolarctos cinereus). Vet Rec. 1984, 115: 655-PubMedView ArticleGoogle Scholar
- Brown AS, Girjes AA, Lavin MF, Timms P, Woolcock JB: Chlamydial disease in koalas. Aust Vet J. 1987, 64: 346-349. 10.1111/j.1751-0813.1987.tb06064.x.PubMedView ArticleGoogle Scholar
- Mitchell CM, Mathews SA, Theodoropoulos C, Timms P: In vitro characterisation of koala Chlamydia pneumoniae: morphology, inclusion development and doubling time. Vet Microbiol. 2009, 136: 91-99. 10.1016/j.vetmic.2008.10.008.PubMedView ArticleGoogle Scholar
- Yamazaki T, Nakada H, Sakurai N, Kuo CC, Wang SP, Grayston JT: Transmission of Chlamydia pneumoniae in young children in a Japanese family. J Infect Dis. 1990, 162: 1390-1392.PubMedView ArticleGoogle Scholar
- Mordhorst CH, Wang SP, Grayston JT: Outbreak of Chlamydia pneumoniae infection in four farm families. Eur J Clin Microbiol Infect Dis. 1992, 11: 617-620. 10.1007/BF01961668.PubMedView ArticleGoogle Scholar
- Troy CJ, Peeling RW, Ellis AG, Hockin JC, Bennett DA, Murphy MR, Spika JS: Chlamydia pneumoniae as a new source of infectious outbreaks in nursing homes. JAMA. 1997, 277: 1214-1218. 10.1001/jama.277.15.1214.PubMedView ArticleGoogle Scholar
- Kleemola M, Saikku P, Visakorpi R, Wang SP, Grayston JT: Epidemics of pneumonia caused by TWAR, a new Chlamydia organism, in military trainees in Finland. J Infect Dis. 1988, 157: 230-236.PubMedView ArticleGoogle Scholar
- Wills JM, Watson G, Lusher M, Mair TS, Wood D, Richmond SJ: Characterisation of Chlamydia psittaci isolated from a horse. Vet Microbiol. 1990, 24: 11-19. 10.1016/0378-1135(90)90046-X.PubMedView ArticleGoogle Scholar
- Reed KD, Ruth GR, Meyer JA, Shukla SK: Chlamydia pneumoniae infection in a breeding colony of African clawed frogs (Xenopus tropicalis). Emerg Infect Dis. 2000, 6: 196-199. 10.3201/eid0602.000216.PubMed CentralPubMedView ArticleGoogle Scholar
- Myers GSA, Mathews SA, Eppinger M, Mitchell C, O'Brien KK, White OR, Benahmed F, Brunham RC, Read TD, Ravel J, Bavoil PM, Timms P: Evidence that human Chlamydia pneumoniae was zoonotically acquired. J Bacteriol. 191: 7225-7233. 10.1128/JB.00746-09.
- Read T, Brunham R, Shen C, Gill S, Heidelberg J, White O, Hickey E, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg S, Eisen J, Fraser C: Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 2000, 28: 1397-1406. 10.1093/nar/28.6.1397.PubMed CentralPubMedView ArticleGoogle Scholar
- Kalman S, Mitchell W, Marathe R, Lammel C, Fan J, Hyman RW, Olinger L, Grimwood J, Davis RW, Stephens RS: Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet. 1999, 4: 385-389.Google Scholar
- Cevenini R, Donati M, Brocchi E, De Simone F, La Placa M: Partial characterization of an 89-kDa highly immunoreactive protein from Chlamydia psittaci A/22 causing ovine abortion. FEMS Microbiol Lett. 1991, 65: 111-115. 10.1111/j.1574-6968.1991.tb04722.x.PubMedView ArticleGoogle Scholar
- Longbottom D, Findlay J, Vretou E, Dunbar SM: Immunoelectron microscopic localisation of the OMP90 family on the outer membrane surface of Chlamydia psittaci. FEMS Microbiol Lett. 1998, 164: 111-117. 10.1111/j.1574-6968.1998.tb13075.x.PubMedView ArticleGoogle Scholar
- Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW: Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 1998, 282: 754-759. 10.1126/science.282.5389.754.PubMedView ArticleGoogle Scholar
- Shirai M, Hirakawa H, Kimoto M, Tabuchi M, Kishi F, Ouchi K, Shiba T, Ishii K, Hattori M, Kuhara S, Nakazawa T: Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA. Nucleic Acids Res. 2000, 28: 2311-2314. 10.1093/nar/28.12.2311.PubMed CentralPubMedView ArticleGoogle Scholar
- Tipples G, McClarty G: The obligate intracellular bacterium Chlamydia trachomatis is auxotrophic for three of the four ribonucleoside triphosphates. Mol Microbiol. 1993, 8: 1105-1114. 10.1111/j.1365-2958.1993.tb01655.x.PubMedView ArticleGoogle Scholar
- Abromaitis S, Hefty PS, Stephens RS: Chlamydia pneumoniae encodes a functional aromatic amino acid hydroxylase. FEMS Immunol Med Microbiol. 2009, 55: 196-205. 10.1111/j.1574-695X.2008.00511.x.PubMed CentralPubMedView ArticleGoogle Scholar
- Gieffers J, Durling L, Ouellette SP, Rupp J, Maass M, Byrne GI, Caldwell HD, Belland RJ: Genotypic differences in the Chlamydia pneumoniae tyr P locus related to vascular tropism and pathogenicity. J Infect Dis. 2003, 188: 1085-1093. 10.1086/378692.PubMedView ArticleGoogle Scholar
- Thomas NS, Lusher M, Storey CC, Clarke IN: Plasmid diversity in Chlamydia. Microbiology. 1997, 143: 1847-1854. 10.1099/00221287-143-6-1847.PubMedView ArticleGoogle Scholar
- Azuma Y, Hirakawa H, Yamashita A, Cai Y, Rahman MA, Suzuki H, Mitaku S, Toh H, Goto S, Murakami T, Sugi K, Hayashi H, Fukushi H, Hattori M, Kuhara S, Shirai M: Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res. 2006, 13: 15-23. 10.1093/dnares/dsi027.PubMedView ArticleGoogle Scholar
- Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM: Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res. 2003, 31: 2134-2147. 10.1093/nar/gkg321.PubMed CentralPubMedView ArticleGoogle Scholar
- Carlson JH, Porcella SF, McClarty G, Caldwell HD: Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains. Infection and Immunity. 2005, 73: 6407-6418. 10.1128/IAI.73.10.6407-6418.2005.PubMed CentralPubMedView ArticleGoogle Scholar
- Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A, Bignell A, Bjartling C, Clark L, Cutcliffe LT, Lambden PR, Lennard N, Lockey SJ, Quail MA, Salim O, Skilton RJ, Wang Y, Holland MJ, Parkhill J, Thomson NR, Clarke IN: Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain. BMC Genomics. 2009, 10: 239-10.1186/1471-2164-10-239.PubMed CentralPubMedView ArticleGoogle Scholar
- Hatt C, Ward ME, Clarke IN: Analysis of the entire nucleotide sequence of the cryptic plasmid of Chlamydia trachomatis serovar L1. Evidence for involvement in DNA replication. Nucleic Acids Res. 1988, 16: 4053-4067. 10.1093/nar/16.9.4053.PubMed CentralPubMedView ArticleGoogle Scholar
- Gupta RS, Griffiths E: Chlamydiae-specific proteins and indels: novel tools for studies. Trends Microbiol. 2006, 14: 527-535. 10.1016/j.tim.2006.10.002.PubMedView ArticleGoogle Scholar
- Rattei T, Ott S, Gutacker M, Rupp J, Maass M, Shreiber S, Solbach W, Wirth T, Gieffers J: Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure. BMC Genomics. 2007, 8: 355-10.1186/1471-2164-8-355.PubMed CentralPubMedView ArticleGoogle Scholar
- Grimwood J, Stephens RS: Computational analysis of the polymorphic membrane protein superfamily of Chlamydia trachomatis and Chlamydia pneumoniae. Microb Comp Genomics. 1999, 4: 187-201.PubMedView ArticleGoogle Scholar
- Gomes JP, Bruno WJ, Borrego MJ, Dean D: Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer. J Bacteriol. 2004, 186: 4295-4306. 10.1128/JB.186.13.4295-4306.2004.PubMed CentralPubMedView ArticleGoogle Scholar
- Gomes JP, Nunes A, Bruno WJ, Borrego MJ, Florindo C, Dean D: Polymorphisms in the nine polymorphic, membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar Da recombination and correlation with tissue tropism. J Bacteriol. 2006, 188: 275-286. 10.1128/JB.188.1.275-286.2006.PubMed CentralPubMedView ArticleGoogle Scholar
- Shirai M, Hirakawa H, Ouchi K, Tabuchi M, Kishi F, Kimoto M, Takeuchi H, Nishida J, Shibata K, Fujinaga R, Yoneda H, Matsushima H, Tanaka C, Furukawa S, Miura K, Nakazawa A, Ishii K, Shiba T, Hattori M, Kuhara S, Nakazawa T: Comparison of outer membrane protein genes omp and pmp in the whole genome sequences of Chlamydia pneumoniae isolates from Japan and the United States. J Infect Dis. 2000, 181 (Suppl 3): S524-S527. 10.1086/315616.PubMedView ArticleGoogle Scholar
- Rocha EP, Pradillon O, Bui H, Sayada C, Denamur E: A new family of highly variable proteins in the Chlamydophila pneumoniae genome. Nucleic Acids Res. 2002, 30: 4351-4360. 10.1093/nar/gkf571.PubMed CentralPubMedView ArticleGoogle Scholar
- Grimwood J, Olinger L, Stephens RS: Expression of Chlamydia pneumoniae polymorphic membrane protein family genes. Infect Immun. 2001, 69: 2383-2389. 10.1128/IAI.69.4.2383-2389.2001.PubMed CentralPubMedView ArticleGoogle Scholar
- Wilson DP, Timms P, McElwain DLS, Bavoil PM: Type III secretion, contact-dependent model for the intracellular development of Chlamydia. Bull Math Biol. 2006, 68: 161-178. 10.1007/s11538-005-9024-1.PubMedView ArticleGoogle Scholar
- Peters J, Wilson DP, Myers G, Timms P, Bavoil PM: Type III secretion a la Chlamydia. Trends Microbiol. 2007, 15: 241-251. 10.1016/j.tim.2007.04.005.PubMedView ArticleGoogle Scholar
- Taylor LD, Nelson DE, Dorward DW, Whitmire WM, Caldwell HD: Biological characterization of Chlamydia trachomatis Plasticity Zone MACPF domain family protein CT153. Infect Immun. 2010, 76: 2691-2699. 10.1128/IAI.01455-09.View ArticleGoogle Scholar
- Kafsack BF, Pena JD, Coppens I, Ravindran S, Boothroyd JC, Carruthers VB: Rapid membrane disruption by a perforin-like protein facilitates parasite exit from host cells. Science. 2009, 323: 530-533. 10.1126/science.1165740.PubMed CentralPubMedView ArticleGoogle Scholar
- Zheng C, Heintz N, Hatten ME: CNS gene encoding astrotactin, which supports neuronal migration along glial fibers. Science. 1996, 272: 417-419. 10.1126/science.272.5260.417.PubMedView ArticleGoogle Scholar
- Martin JR, Raibaud A, Ollo R: Terminal pattern elements in Drosophila embryo induced by the torso-like protein. Nature. 1994, 367: 741-745. 10.1038/367741a0.PubMedView ArticleGoogle Scholar
- Rosado CJ, Buckle AM, Law RHP, Butcher RE, Kan W-T, Bird CH, Ung K, Browne KA, Baran K, Bashtannyk-Puhalovich TA, Faux NG, Wong W, Porter CJ, Pike RN, Ellisdon AM, Pearce MC, Bottomley SP, Emsley J, Smith AI, Rossjohn J, Hartland EL, Voskoboinik I, Trapani JA, Bird PI, Dunstone MA, Whisstock JC: A common fold mediates vertebrate defense and bacterial attack. Science. 2007, 317: 1548-1551. 10.1126/science.1144706.PubMedView ArticleGoogle Scholar
- Martinussen J, Hammer K: Powerful methods to establish chromosomal markers in Lactococcus lactis: an analysis of pyrimidine salvage pathway mutants obtained by positive selections. Microbiol. 1995, 141: 1883-1890. 10.1099/13500872-141-8-1883.View ArticleGoogle Scholar
- Accetto T, Avgustin G: Expression of nuclease gene nucA, a member of an operon putatively involved in uracil removal from DNA and its subsequent reuse in Prevotella bryantii. Arch Microbiol. 2008, 190: 111-117. 10.1007/s00203-008-0372-8.PubMedView ArticleGoogle Scholar
- Winkler H: Rickettsia species (as organisms). Annu Rev Microbiol. 1990, 44: 131-153. 10.1146/annurev.mi.44.100190.001023.PubMedView ArticleGoogle Scholar
- Hatch TP: Utilization of L-cell nucleoside triphosphates by Chlamydia psittaci for ribonucleic acid synthesis. J Bacteriol. 1975, 122: 393-400.PubMed CentralPubMedGoogle Scholar
- McClarty G, Tipples G: In situ studies on incorporation of nucleic acid precursors into Chlamydia trachomatis DNA. J Bacteriol. 1991, 173: 4922-4931.PubMed CentralPubMedGoogle Scholar
- Thomson NR, Yeats C, Bell K, Holden MTG, Bentley SD, Livingstone M, Cerdeno-Tarraga AM, Harris B, Doggett J, Ormond D, Mungall K, Clarke K, Feltwell T, Hance Z, Sanders M, Quail MA, Price C, Barrell BG, Parkhill J, Longbottom D: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation. Genome Research. 2005, 15: 629-640. 10.1101/gr.3684805.PubMed CentralPubMedView ArticleGoogle Scholar
- NCBI (National Centre for Biotechnology Information) BLAST (Basic Local Alignment Search Tool). [http://blast.ncbi.nlm.nih.gov/Blast.cgi]
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralPubMedView ArticleGoogle Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404.PubMedView ArticleGoogle Scholar
- Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999, 41: 95-98.Google Scholar
- My hits, motif scan. [http://myhits.isb-sib.ch/cgi-bin/motif_scan]
- Koonin EV, Galperin MY: Sequence-evolution-function: Computational approaches in comparative genomics. 2003, Norwell, Massachusetts: Kluwer Academic Publishers, 39-View ArticleGoogle Scholar
- Li Z, Chen D, Zhong Y, Wang S, Zhong G: The chlamydial plasmid-encoded protein pgp3 is secreted into the cytosol of Chlamydia-infected cells. Infect Immun. 2008, 76: 3415-3428. 10.1128/IAI.01377-07.PubMed CentralPubMedView ArticleGoogle Scholar
- Mitchell CM, Hutton S, Myers GSA, Brunham R, Timms P: Chlamydia pneumoniae is genetically diverse in animals and appears to have crossed the host barrier to humans on (at least) two occasions. Plos Path.