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. 2015 Jul;161(Pt 7):1378–1391. doi: 10.1099/mic.0.000097

Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes

Bernard J Wolff 1,2, Shatavia S Morrison 2, Denise Pesti 1, Satishkumar Ranganathan Ganakammal 3, Ganesh Srinivasamoorthy 3, Shankar Changayil 3, M Ryan Weil 3, Duncan MacCannell 3, Lori Rowe 3, Michael Frace 3, Branson W Ritchie 1, Deborah Dean 4,5, Jonas M Winchell 2,✉
PMCID: PMC4635502  PMID: 25887617

Abstract

Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.

Introduction

The Chlamydiaceae family of bacteria comprises nine distinct species, namely Chlamydia trachomatis, C. suis, C. muridarum, C. psittaci, C. pneumoniae, C. abortus, C. felis, C. pecorum and C. caviae (Read et al., 2013). This diverse group of obligate intracellular Gram-negative bacteria have adapted to their host cell niche by evolving to use a complex biphasic life cycle, which consists of a metabolically inactive, infectious form known as an elementary body (EB) and a metabolically active and non-infectious reticulate body (RB) (Abdelrahman & Belland, 2005). Chlamydiaceae infect a broad range of hosts, and evidence of infection has been found in nearly every phylogenetic group of animals (Kaleta & Taday, 2003; Read et al., 2003).

C. psittaci is primarily a zoonotic pathogen that is normally transmitted through close contact with infected birds and some mammals including cattle, pigs, sheep, swine, goats, cats and horses, not to mention feral animals (Hotzel et al., 2004; Read et al., 2013). The bacteria are often found in secretions and faecal droppings, remaining infectious for up to 30 days (Beeckman & Vanrompay, 2009; Haag-Wackernagel & Moch, 2004; Harkinezhad et al., 2009; Heddema et al., 2006a). Infection in humans may lead to psittacosis, a severe respiratory illness often associated with multi-organ involvement causing significant morbidity and mortality (Smith et al., 2011). C. psittaci is also a major cause of economic loss in the poultry industry in the US and abroad, and poses a significant risk to farm workers as well as having potential for laboratory-acquired infection (Gaede et al., 2008; Miller et al., 1987; Smith et al., 2011). Because of the potential public health risk of C. psittaci, the National Association of State Public Health Veterinarians published a compendium on testing and strategies for managing the disease in birds and humans (Smith et al., 2011).

C. psittaci has the widest documented host range within the Chlamydiaceae family including avian, mammalian, reptilian and human hosts (Harkinezhad et al., 2009). C. psittaci is classified into ten genotypes, designated A–G, E/B, M56 and WC (Read et al., 2013; Van Lent et al., 2012). Recently, a real-time PCR assay targeting differences in the ompA gene was developed to differentiate the genotypes (Mitchell et al., 2009). Biological differences in host preference and virulence can be noted between the different C. psittaci genotypes. For instance, genotype A is endemic in psittacine birds and is theorized to be a common cause of respiratory disease and/or flu-like symptoms in exposed humans, while genotypes C and D have primarily been associated with waterfowl and poultry, respectively (Heddema et al., 2006a, c; Smith et al., 2011). Genotype E has been shown to infect a diverse group of avian species, including psttacines, pigeons, waterfowl and turkeys, and was first described to infect humans in the late 1920s following exposure to diseased parrots (Harkinezhad et al., 2007). Although all genotypes may infect humans, including genotypes from both avian and mammalian species, genotype A has been referenced as the most common cause of human disease. There is substantial variation in the likelihood of infection and disease following exposure to infected birds, even within what is currently classified as the same genotype (Heddema et al., 2006b, c; Wreghitt & Taylor, 1988).

Genetic manipulation techniques cannot reliably be used on Chlamydiaceae due to their intracellular requirement for replication. As a result, research on the specific interactions and contributions of genes to virulence, infectivity and replication are limited. Comparisons between the various genotypes and between species are limited despite some recent advancements with better characterized species and the use of surrogate systems (Peters et al., 2007). While some members of the Chlamydiaceae family have been sequenced and studied for their host and tissue preferences and virulence mechanisms, only 16 have been completely characterized to date (Kalman et al., 1999; Read et al., 2000, 2003, 2013; Stephens et al., 1998; Thomson et al., 2005; Van Lent et al., 2012; Voigt et al., 2012). Next generation sequencing bypasses some of the limitations of bench work by allowing more meaningful investigation of the genotypes at the genomic level and their potential association with host specificity and virulence.

Here, we report on the comparative genomics of all ten genotypes of C. psittaci of which genotypes A, B, D and E were sequenced in this study. Our research focused on the genes encoding polymorphic membrane proteins (Pmps) and the type III secretion system (T3SS) proteins because of their known involvement in pathogenicity (Voigt et al., 2012). The Pmps are a large family of proteins unique to Chlamydiaceae, which are highly variable in numbers and homology among the family, and are thought to be involved in niche adaptation based on adherence to the host cell, molecular transport and cell wall associated functions (Rockey et al., 2000). The tbl3SS transports effector proteins into the host cytoplasm using a needle-like apparatus, similar to other Gram-negative bacteria (Hueck, 1998). While the structural genes are well conserved, the secreted effector proteins, although difficult to identify, are widely diverse and have many unique functions (Valdivia, 2008). Some secreted effectors have been identified and fairly well characterized. Specifically, the tarp gene in C. trachomatis was well characterized by Somboonna et al. (2011) as a virulence factor and has been associated with actin recruitment and inclusion development. We found numerous insertions, deletions and single nucleotide polymorphisms among the pmp and tbl3SS genes that may account for host preferences and virulence characteristics for the C. psittaci genotypes.

Methods

C. psittaci strains

C. psittaci strains DD-34 (ATCC VR-854, genotype A), CP3 (ATCC VR-574, genotype B), NJ1 (genotype D), Frances (ATCC VR-122, genotype E) and a genotype A strain (UGA) recovered from a cockatiel, were sequenced in this study. The DD-34 strain was originally isolated from a parrot in 1949 (Davis, 1949). The CP3 strain was isolated from a pigeon in 1958 (Page, 1966). The Frances strain was isolated from a ferret inoculated with human material in 1934 (Francis & Magill, 1938 ). C. psittaci CP3 and NJ1 genomic sequences are also available elsewhere (Van Lent et al., 2012), while Frances, DD-34 and UGA are newly described in the current study. This study represents comprehensive analysis of these genomes using the whole genome assembly and annotation methods describe below.

C. psittaci culture

C. psittaci culture was performed as previously described (Mitchell et al., 2009). Briefly, C. psittaci reference strains were propagated in Vero cell monolayers grown in 150 cm2 culture flasks in Eagle's minimum essential medium (MEM) supplemented with MEM nonessential amino acids, 2 μM l-glutamine, 20 μM HEPES buffer, 10 % FCS, 20 μg streptomycin ml− 1 and 25 μg vancomycin ml− 1. Confluent cell monolayers were inoculated by replacing the growth medium with 5 ml of stock C. psittaci culture diluted 1:10 in MEM containing 1 μg cycloheximide ml− 1. The inoculated monolayers were placed at 37 °C and 5 % CO2 for 2 h before an additional 50 ml of MEM containing cycloheximide was added to each flask. Cultures were incubated for 7 days at 37 °C or until the monolayers demonstrated nearly 100 % cytopathic effects. The cell culture was transferred to 50 ml tubes and stored at − 80 °C prior to EB isolation.

EB isolation was performed by density-gradient centrifugation as previously described (Mukhopadhyay et al., 2004). DNA was extracted from the pellet using a QiaAmp DNA minikit (Qiagen) according to the manufacturer's instructions and frozen at − 80 °C prior to sequencing.

Whole genome sequencing and assembly

The genomic DNA for C. psittaci strains DD-34, CP3, NJ1, Frances and UGA was prepared for whole genome paired-end sequencing on an Illumina GAIIx DNA sequencer using standard protocols and reagents from Illumina. Approximately 1 μg of genomic DNA was sheared using a Covaris S2 sonicator (Covaris) to a mean size of 350 bp. DNA sequencing libraries were then prepared using Illumina Truseq chemistry and size selected using double Ampure (Beckman Coulter) selection. Paired-end flowcells underwent cluster formation using an Illumina cBot, followed by 100 × 100 bp cycle sequencing using SBS cycle sequencing V5 kits. Sequence data were processed using casava (v1.8.2) into paired fastq read sets. Read quality checks were performed using a combination of publicly available tools and in-house scripts. C. psittaci 6BC (NC_015740) was used as reference genome for all analysis. Trimming of reads based on quality, mapping of reads to a reference genome, and de novo assembly were performed using CLC Genomics Workbench 5.5.1. Since CLC Genomics 5.5.1 was no longer supported on the computing environment, CLC Genomics Workbench 7.0.4 was used to assembly the RTH sequence reads.

Whole genome annotation

All five genomes were submitted to NCBI and annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The GenBank accession numbers for each genome are listed in Table 1.

Table 1. Whole genome sequencing and annotation results.

Strain
Characteristic DD34 UGA CP3 NJ1 Frances
Genotype A A B D E
GenBank accession no. AFVL00000000 AWXQ00000000 AFVN00000000 AFVK00000000 AFVM00000000
Total assembled size (bp) 1 163 748 1 164 948 1 163 075 1 160 660 1 162 120
Plasmid size (bp) 7553 7553 7553 7532 7545
Total reads 13 181 088 12 562 928 12 695 762 7 803 252 13 291 438
Total bases 1 317 642 394 1 256 351 619 1 268 662 067 780 739 971 1 327 907 989
Mean read length 101 101 101 101 101
Mean coverage 576.2 548 556.1 340.4 581.1
Number of contigs 4 6 4 3 2
N50 778 174 779 321 778 149 775 399 1 159 687
Genes predicted 1057 1059 1054 1057 1044
tRNAs predicted 38 38 38 38 38
DNA G+C content (mol%) 39.03 39.02 39.01 38.95 39.03
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Whole genome comparison

The de novo assembled contigs for each sample were ordered against the 6BC reference genome using abacas tool (Assefa et al., 2009). The ordered samples' superscaffolded genomes and reference genome were compared using Mauve to identify conserved and rearranged regions (Darling et al., 2010). The above input was used for Blast Ring Image Generator (BRIG) analysis to identify differences (Alikhan et al., 2011). Using the whole genome SNPs, identified by the kSNP version 2.1.2 (Gardner & Hall, 2013) software application, a maximum-likelihood phylogenetic tree was reconstructed with the RAxML version 7.3.0-pthread (Stamatakis, 2014). The tree was reconstructed with 1000 replicates for bootstrapping (Gardner & Hall, 2013). The tree was visualized with Figtree (Rambaut, 2015). The phylogenetic tree represents the evolutionary relationship of C. psittaci genotypes with C. abortus S26/3 as an outgroup.

Annotated pmp and tbl3SS genes described by Voigt et al. (2012) from the 6BC genome (CP002549) were compared by blast analysis to the genomes sequenced in this study and six reference genomes available in GenBank [WC (NC_018624.1), M56 (NC_018623.1), VS225 (NC_018621.1), WS-RT-E3 (NC_018622.1), GR9 (NC_018620.1), RTH (SRA061571)] (Read et al., 2013; Van Lent et al., 2012; Voigt et al., 2012). A formatted report was generated using an in-house gene search reporter pipeline (blast-based). The gene sequences that reported a pairwise identity below 75 % were marked as low quality and were considered absent.

A heatmap was constructed using R version 3.0.1 using the ‘gplots’ and ‘RColorBrewer’ packages (Neuwirth, 2007; Warnes et al., 2014). The pmp genes pairwise identities between all C. psittaci genomes included this study against C. psittaci 6BC were shown.

A maximum-likelihood tree was reconstructed with the pmp genes to show a similar evolutionary relationship in Voigt et al. (2012). We selected genes based on a protein pairwise identity to 6BC that met the following criteria: 75 % sequence identity and above 60 % gene coverage. ClustalOmega was used to perform independent multiple sequence alignments before sequence analysis to minimize gene rearrangement (Sievers et al., 2011). Once each individual protein alignment was built, the independent alignments were concatenated. RAxML was used to generate a phylogenetic tree with 1000 replicates for bootstrapping (Stamatakis, 2014). The tree was visualized with Figtree (Andrew Rambaut, 2014).

Protein domain identification

The gene sequences for CPSIT_0757 (dihydrodipicolinate reductase) and CPSIT_0192 (putative TARP) for 6BC genome (CP002549) were used as reference sequences to identify the orthologous gene sequences in the genomes included in this study. These three genes were selected based upon their critical role in virulence or metabolism and genetic variability between strains (Voigt et al., 2012). Orthologous gene sequences were identified with a shared sequence identity greater than 75 %. Genomes GR9 (NC_0186201.1), M56 (NC_018623.1) and WS-RT-E30 (NC_018622.1) did not contain genes that met the criteria, thus excluding them from the protein domain identification analysis. The amino acid sequences for each gene were submitted to the European Bioinformatics Institute InterPro web service (Jones et al., 2014). InterPro provides a functional analysis of protein sequences by predicting protein domains based on domain signatures found other protein family and domain databases (Jones et al., 2014). A detailed description of the databases that make up InterProScan is given by Hunter et al. (2012).

Results

Whole genome sequencing, assembly and annotation

Table 1 summarizes the sequencing statistics and genomic characteristics for each newly sequenced genome included in this study. The sequencing resulted in assemblies covering 99 % or greater of the entire genome for each strain. All five strains yielded an approximately 1.16 Mb chromosome and a fully sequenced 7.5 kb plasmid. The plasmids were remarkably conserved with a pairwise identity of 99 %. The DNA G+C content for all five genomes was approximately 39 %, which is consistent with other sequenced Chlamydia genomes (Read et al., 2013; Van Lent et al., 2012). The genome coverage ranged from 340.4X (NJ1) to 581.1X (Frances), with a mean read length for all five genomes of 101 bp, and total reads generated were between 7 803 252 (NJ1) and 13 291 438 (Frances). The N50 values were between 775 399 (NJ1) and 1 159 687 (Frances). The numbers of genes predicted for each genome were similar. The lowest number of genes (1044) was predicted in the Frances genome compared to a high of 1059 genes in UGA. A total of 38 tRNAs were found in all five genomes.

Pan genome comparison

The 6BC strain was chosen as the reference with which to compare all other strains used in this study, because it was the only completely sequenced genome available at the start of this study. Fig. 1 is a circular map representing the nucleic acid sequence similarity of the five strains sequenced for this study and the genomes sequenced by Read et al. (2013) compared with the 6BC reference genome generated using the brig. The comparison shows a high degree of similarity ( ≥ 99 %) across all genotypes of C. psittaci. As expected, nearly identical sequence similarity was observed between the three genotype A genomes (6BC, UGA and DD34). While all the genomes appear to be very closely related, two regions demonstrated significant sequence divergence among the different genotypes. These regions are highlighted, and the genes encoded in each region are listed (Table S1, available in the online Supplementary Material). Region 1 contains approximately 20 kb; region 2 spans 17 kb. The majority of the genes contained in these regions encode Pmps belonging to the pmpG group. Several of the genomes sequenced by Read et al. (2013) had large deletions when compared with the reference 6BC.

Fig. 1. brig analysis. A brig comparing the C. psittaci genomes sequenced in this study and C. psittaci genomes sequenced by Read et al. (2013). Genotype 6BC was used as a reference for comparison. The innermost ring represents the base position along the map. The second ring indicates the GC content along the length of the genome. The colour rings correspond to the genomes with each genome indicated by a unique colour as indicated in the figure legend. A change in colour corresponds to a decrease in pairwise identity compared to the reference genome. Four regions with sequence divergence are noted in red circles with gene identities listed in orange boxes.

Fig. 1.

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A whole genome SNP tree rooted to C. abortus strain S26/3 was reconstructed using previously reported C. psittaci genomes currently in the NCBI database and the genomes sequenced for this project (Fig. 2). The tree demonstrates the closely related nature of the C. psittaci genotypes. Nine genotype A strains are represented in the tree and formed the first clade. Genotype F was the next closest relative to genotype A, followed by the WC clade. A fourth clade composed of genotypes C and WS/RT/E30 was present, followed by genotypes B and E representing the fifth clade. Genotypes D, M56 and RTH formed their own separate branches, with strain RTH, genotype G, the most distantly related.

Fig. 2. Whole genome SNP tree. A whole genome SNP tree rooted to C. abortus strain S26/3 reconstructed with all available genome sequences in the NCBI database along with the five genomes sequenced for this study. The strain name is followed by the genotype for each branch of the tree (Strain name–Genotype). Strain names colored in blue were sequenced for this study, names colored in pink were obtained from NCBI, and the genome colored in red was the root genome.

Fig. 2.

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T3SS and effector genes

Table 2 is a summary of the pairwise identity values ( ≥ 75 %) of the tbl3SS apparatus, chaperone and effector genes (n = 39) among all C. psittaci genotypes using the 6BC genome from Voigt et al. (2012) as the reference strain. There is a large degree of conservation amongst the genes comprising the tbl3SS. However, the effector genes show greater sequence divergence compared with the apparatus genes (Fig. 3a, b). Strain RTH (genotype G) was the most divergent, with only two genes sharing 100 % pairwise identity with 6BC. A large number of genes (16 out of 39) shared 100 % pairwise identity compared to 6BC for nine of the ten genotypes, with the RTH (genotype G) being the only divergent strain. However, substantial differences do exist among many of the genes. Two genes (CPSIT_0844 and CPSIT_0846) were absent in three or four strains (Table 2, yellow highlight). CPSIT_0844 and CPSIT_0846 encode IncA family proteins and were absent in GR9 (genotype C), RTH (genotype G) and WS/RT/E30 (genotype E/B); CPSIT_0846 was also absent in Frances (genotype E). A putative inner-membrane protein (CPSIT_0463) was absent in RTH and WC (genotypes G and WC, respectively).

Table 2. T3SS genes.

Strain: DD34 UGA CP3 GR9 NJ1 Frances VS225 RTH WS/RT/E30 M56 WC
Genotype: A A B C D E F G E/B M56 WC
6BC locus tag (CP002549) Name Pairwise identity (%)
Apparatus genes
CPSIT_0074 Hypothetical protein 100 100 100 >95 100 100 100 88 >95 >95 100
CPSIT_0245 Cabohydrate isomerase 100 100 100 >95 100 100 100 95 >95 >95 100
CPSIT_0313 Polymorphic membrane protein, G family 100 100 >95 100 100 100 100 89 100 100 100
CPSIT_0357 Hypothetical protein 100 100 100 100 100 100 100 89 >95 100 100
CPSIT_0397 Hypothetical protein 100 100 100 100 100 100 100 96 100 100 100
CPSIT_0421 Hypothetical protein 100 100 10 100 100 100 100 88 100 >95 100
CPSIT_0429 Hypothetical protein 100 100 100 100 >95 100 100 – 100 100 100
CPSIT_0431 Putative membrane protein 100 100 100 100 100 100 100 93 100 100 100
CPSIT_0490 Hypothetical serine rich protein 100 100 100 100 100 >99 100 94 100 100 100
CPSIT_0594 IncA 100 100 100 100 100 100 100 77 100 >95 100
CPSIT_0602 Hypothetical protein 100 100 100 >95 100 100 100 91 >95 100 100
CPSIT_0656 Putative integral membrane protein 100 100 100 100 100 100 100 90 100 100 100
CPSIT_0749 Hypothetical protein 100 100 100 >80 100 100 >80 78 >80 100 100
CPSIT_0767 3-phosphoshikimate-1-carboxyvinyltransferase 100 100 100 100 100 100 100 95 100 100 100
CPSIT_0785 Hypothetical serine rich protein 100 100 100 100 100 100 100 93 100 100 100
CPSIT_0828 DNA recombination protein 100 100 100 100 100 100 100 95 100 100 100
CPSIT_0844 IncA family protein 100 100 >95 – 90 >95 100 – – >77 100
CPSIT_0930 tRNA (Uracil-5-)-methyltransferase 100 100 100 100 100 100 100 95 100 100 100
CPSIT_0933 Putative membrane protein >90 >90 >90 100 100 >95 100 – 100 >95 100
CPSIT_0997 Putative inner membrane protein 100 100 100 100 100 100 100 95 100 100 100
CPSIT_1054 5-formyltetrahydrofolate-cyclo-ligase 100 100 100 100 100 100 100 92 100 100 100
Effector genes
CPSIT_0192 tarp 100 100 >95 >95 100 >95 >95 92 >95 >92 >95
CPSIT_0220 Cyclodiphosphate synthase 100 100 100 100 100 100 100 95 100 100 100
CPSIT_0296 Hypothetical protein 100 100 100 100 100 100 100 – 100 >95 100
CPSIT_0314 Polymorphic membrane protein, G family 100 100 >95 >95 100 >95 >95 89 >95 >95 >95
CPSIT_0422 Hypothetical protein 100 100 100 100 >95 100 100 84 100 >95 100
CPSIT_0461 Hypothetical protein 100 100 100 100 100 100 100 91 100 99 100
CPSIT_0463 Putative inner-membrane protein 100 100 >98 99 96 >99 99 – 99 >92 –
CPSIT_0532 IncB 100 100 100 100 100 100 100 83 100 100 100
CPSIT_0555 Putative inner-membrane protein 100 100 100 100 100 100 100 76 100 100 100
CPSIT_0580 Putative inner-membrane protein 100 100 100 100 >95 100 100 86 100 100 100
CPSIT_0689 Hypothetical protein 100 100 100 100 100 100 100 – 100 100 100
CPSIT_0757 Dihydrodipicolinate reductase 100 100 >95 >95 >95 >95 100 100 >95 >95 >95
CPSIT_0760 Hypothetical membrane protein 100 100 100 100 100 100 100 100 100 100 100
CPSIT_0846 IncA family protein 100 100 >75 – >93 – >80 – – >85 100
CPSIT_0856 Membrane protein 100 100 100 >95 100 100 100 94 >95 100 100
CPSIT_0962 Flagellar biosynthesis/type III secretory pathway 100 100 100 100 100 100 100 97 100 100 100
CPSIT_0974 Trigger factor 100 100 100 100 100 100 100 96 100 100 100
CPSIT_1042 Deoxyribonucleotide triphosphate pyrophosphatase 100 100 100 100 100 100 100 95 100 100 100
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Locus tags highlighted in yellow are absent in one or more strains, and those highlighted in blue are discussed in the manuscript. –, The gene was not present.

Fig. 3. Heatmap analysis of tbl3SS genes. The nucleotide pairwise identities for (a) the apparatus genes and (b) the effector genes are shown for the strains in this study compared with 6BC tbl3SS reference genes. Pairwise identities of ≥ 75 % are shown. Pairwise identifies are coded with the following colour schema: red: 0–59 %, orange: 60 − 69 %, yellow: 70–79 %, green: 80–89 % and blue: 90–100 %.

Fig. 3.

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The effector protein dihydrodipicolinate reductase (CPSIT_0757) was conserved among DD34 and UGA (genotypes A), VS225 (genotype F) and RTH (genotype G) but displayed differences in the other seven genotypes (Table 2, blue highlight). While the InterPro analysis revealed two domains for a NAD(P) binding domain present in all genotypes, a multiple sequence alignment of those domains showed that DD34, UGA, VS 225 and RTH clustered together (Fig. S1, magenta highlight) and WS/RT/E30, GR9, WC, Frances, CP3, M56 and NJ1 formed a second cluster (Fig. S1, underlined). In the first domain, eight of ten substitutions were clustered in this fashion, while the second domain showed nine of thirteen substitutions sharing this pattern. Other sporadic changes within the catalytic domains were also observed requiring further study. M56 had a single substitution compared to the other strains in the first domain (Fig. S1, blue highlight), and NJ1 had a unique substitution in the C-terminal domain (Fig. S1, red highlight).

Other effector genes such as the tarp gene (CPSIT_0192) were 100 % conserved among DD34, UGA and NJ1 (genotypes A and D, respectively), but there were differences in the other strains, as the pairwise identity was 92 % or greater in each. To identify functional regions of the tarp gene, a nucleotide and amino acid sequence alignment (Fig. S2, S3) were performed using the genomes sequenced in this study, those sequenced by Read et al. (2013), and C. trachomatis L2 and L2b strains (accession numbers AM884176 and AM884177) characterized by Somboonna et al. (2011). The tarp genes in the C. psittaci genomes had very little sequence similarity with the two C. trachomatis genomes (Fig. S2). The C. psittaci amino acid sequences of Tarp were examined in InterPro and three catalytic domains of unknown function were returned that were present in all strains. A multiple sequence alignment of those domains revealed five amino acid differences in each of the three domains (Fig. S3, green highlight). Of these fifteen substitutions, four were specific to the RTH strain, two were only present in the M56 strain, eight were shared between the M56 and RTH strains and one amino acid substitution was only present in the NJ1 strain (Fig. S3, green highlight).

The IncA (CPSIT_0594) and IncB (CPSIT_0532) were largely conserved. The incA gene was 100 % conserved in every genome with the exception of RTH and M56, whereby the pairwise identity was 77 % and >95 % respectively. The incB gene was 100 % conserved in 10 genomes compared to 6BC, with RTH being the only exception with a pairwise identity of 83 %.

Pmp genes

The 30 Pmps characterized by Voigt et al. (2012) were compared with the strains sequenced in this study as well as the other strains with whole genome data now available (Table 3). The BRIG analysis (Fig. 1, regions 1 and 2) revealed that the G group of proteins had the highest degree of divergence among the different genotypes of C. psittaci. Fig. 4 shows the heatmap of the Pmps showing that the pmpG group is clearly the most diverged. Of the 14 genes of this group, only seven were present in all 12 genomes. Also notable is that, among the three genotype A strains (6BC, DD34 and UGA), three genes in the G family were present only in the 6BC strain. Two genes (CPSIT_0310 and CPSIT_0311) were only present in 6BC, CP3, M56 and WC, and a weak match was also returned for CPSIT_0310 in NJ1. Strain 6BC and WC had the largest conservation of this group of genes. We found 13 of the 14 pmpG genes in the 6BC had significant pairwise identity (>85 %) with those in WC.

Table 3. Polymorphic outer-membrane protein genes.

PMP family 6 BC locus tag (CP002549) Strain: DD34 UGA CP3 GR9 NJ1 Frances VS225 RTH WS/RT/E30 M56 WC
Genotype: A A B C D E F G E/B M56 WC
Pairwise identity (%)
A CPSIT_0232 100 100 100 100 100 100 100 95 100 >95 100
B/C CPSIT_0231 100 100 100 >95 >95 100 100 89 >95 >90 100
D CPSIT_0856 100 100 100 >95 100 100 100 94 >95 100 100
E/F CPSIT_0297 100 100 100 100 >95 100 100 – 100 – 100
CPSIT_0298 100 100 >95 >95 >95 >95 >95 – >95 – 100
G CPSIT_0302 100 100 >95 100 >75 >95 >95 86 100 >84 >95
CPSIT_0304 100 >95 >99 100 100 >99 100 84 100 >95 100
CPSIT_0305 >95 >95 >94 >95 81 >95 >95 78 >95 >79 >95
CPSIT_0306 100 100 >95 100 100 100 >95 93 >95 100 100
CPSIT_0307 100 100 >95 100 100 100 100 93 100 100 100
CPSIT_0309 >75 >96 – >85 – >95 >95 91 – >85 >95
CPSIT_0310 – – 80 – >76 – – – – >79 >95
CPSIT_0311 – – >87 – – – – – – 75 >95
CPSIT_0312 >76 >83 >76 >95 – >84 >95 89 – >90 >85
CPSIT_0313 100 100 >95 100 100 100 100 89 100 100 100
CPSIT_0314 100 100 >95 >95 >95 >95 >95 89 >95 >95 >95
CPSIT_0666 – – >77 100 – – >95 – >95 – –
CPSIT_0667 >78 >78 – – 84 >95 >95 – – >85 >95
CPSIT_0668 75 >81 – >95 – 80 >95 86 >75 >90 >85
H CPSIT_0301 100 100 >95 >95 100 >95 >95 88 >95 >95 100
Other CPSIT_0057 100 100 100 – – 100 – 95 100 100 –
CPSIT_0207 100 100 100 100 100 100 100 97 100 >95 100
CPSIT_0300 100 100 100 100 100 100 100 81 10 >95 100
CPSIT_0329 100 100 >95 >95 >95 >95 >95 95 >95 >95 >95
CPSIT_0330 100 100 >95 >95 100 >95 100 92 100 100 100
CPSIT_0345 100 100 100 100 100 100 100 96 100 100 100
CPSIT_0523 100 100 100 100 100 100 100 95 100 100 100
CPSIT_0967 100 100 100 100 100 100 100 97 100 100 100
CPSIT_1035 100 100 100 100 100 100 100 95 100 100 100
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“–” indicates the gene was not present.

Fig. 4. Heatmap analysis of Pmp genes. The nucleotide pairwise identities for all 30 C. psittaci Pmp genes are shown for the strains in this study compared with 6BC Pmp reference genes. Pairwise identities of ≥ 75 % are shown. Pairwise identifies are coded with the following colour schema: red: 0–59 %, orange: 60 − 69 %, yellow: 70–79 %, green: 80–89 % and blue: 90–100 %.

Fig. 4.

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The other Pmp gene groups had significantly higher conservation among the genotypes. Genes of the pmpA, pmpB/C, pmpD and pmpH groups were present in all 12 genomes, with a small degree of sequence divergence present among some of the genes. The most divergent gene was CPSIT_0231 of the pmpB/C family. Its corresponding gene in the M56 genome had a 90 % pairwise identity and an 89 % identity in the RTH genome. All the other pairwise identities for those families were 88 % or greater among all 12 genomes. The pmpE/F genes were the only ones that were absent in any of the genomes. Both genes were not present in the RTH and M56 genomes. A heat map demonstrates the variability of the pmpG group of genes among the strains compared to the other Pmp groups (Fig. 4).

In reconstructing a phylogenetic tree of the Pmps for each strain with Pmps, the phylogeny is similar to the whole-genome phylogeny of Fig. 2 (Fig. 5).

Fig. 5. Phylogenetic tree of Pmp genes. Phylogenetic relationships computed using the maximum-likelihood from the conserved Pmp genes found in the C. psittaci genomes included in this study. Protein sequences with a pairwise identity ≥ 75 % to the C. psittaci 6BC genome were included. Bootstrapping percentage values are shown at branch points, and the bar represents the residue substitution per site. The strain name is followed by the genotype for each branch of the tree (Strain name–Genotype).

Fig. 5.

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Discussion

Chlamydiaceae has one of the largest host ranges and varied virulence characteristics of any bacterial family currently known (Kaleta & Taday, 2003). Application of next-generation sequencing technologies has yielded novel information about C. psittaci genomes and provided insight into the differing virulence mechanisms, tissue tropism, evolutionary dynamics and host range of this species (Read et al., 2013; Voigt et al., 2012). Voigt et al. (2012) compared the genes of other Chlamydia species with hose of C. psittaci strain 6BC and found a number of psittaci-specific Pmps of the G family, a high degree of genome rearrangement, and numerous differences in the tbl3SS. Read et al. (2013) demonstrated C. psittaci has undergone many recombination events and has the ability to switch hosts frequently. Our phylogenetic analysis revealed similar genotypic clade relationships seen by Read et al. (2013) and Voigt et al. (2012). The current study further enhances our understanding of this species by identifying a variety of genetic variations among the pmp and the tbl3SS genes that may, in part, be responsible for the variability in tissue tropism, host preferences, and virulence observed among genotypes.

Chlamydiaceae contains a functional tbl3SS that serves as a major virulence factor by secreting effectors that recruit actin to facilitate entry into the cell (TARP), manipulate the host cell cytoplasm (CdsF), and alter the inclusion body (IncG and IncA) (Betts et al., 2008; Fields et al., 2003; Hsia et al., 1997; Voigt et al., 2012). Studies have identified numerous apparatus proteins along with multiple chaperone proteins and secreted effector molecules (Betts et al., 2008; Herrmann et al., 2006; Peters et al., 2007; Stone et al., 2008; Voigt et al., 2012). The type III apparatus proteins are highly conserved among many bacterial species including Shigella, Yersinia and Salmonella (Hueck, 1998; Mota & Cornelis, 2005). This conservation is so extensive that small molecule inhibitors such as INP0400 designed for one species have efficacy against chlamydial species secretion systems, including IncG and IncA, and can inhibit the development of Chlamydia after entry into host cells (Muschiol et al., 2009).

Intraspecies comparisons of the tbl3SS genes (Voigt et al., 2012) showed that the majority of the genes were largely conserved in all 12 C. psittaci genomes with a pairwise identity of 95 %. However, we found significant differences for some genes among the different genotypes of C. psittaci. For example, seven of the 39 genes were missing in one or more of the genotypes compared with 6BC (Table 2, yellow highlight). Of these seven, three are hypothetical proteins, two are associated with the IncA protein family, and two are putative membrane proteins. For the other 31 genes, there was little sequence divergence with pairwise identities ranging from 77 % to 100 %. However, all apparatus structure genes had at least a 95 % pairwise identity except for the RTH strain (genotype G) where the identities were more variable.

Differences in the TARP, dihydrodipicolinate reductase and the adherence factor genes appear to impact virulence and host specific characteristics within the different C. psittaci genotypes. tarp was less conserved among the strains, which is consistent with a report showing that virulent strains of C. psittaci such as genotypes A and D recruit actin more efficiently than those associated with less virulence strains (Beeckman & Vanrompay, 2010). The increase in actin recruitment may provide a more efficient mechanism for EB attachment, invasion and inclusion formation. The amino acid sequences of the TARP suggest that this particular gene may be responsible for differences in the M56 (genotype M56) and RTH (genotype G) strains as the majority of the substitutions in the catalytic domains were associated with those two strains. This is not surprising as these two strains have widely different host preferences compared to the other genotypes. Further experiments are needed to better elucidate the functional properties of the C. psittaci tarp gene and protein among the different strains and genotypes, and to identify other possible genes involved in virulence.

Sequence divergence and amino acid changes in the dihydrodipicolinate reductase gene (Cpsit_0757) suggest a potential difference in lysine biosynthesis for 6BC, DD34 and UGA (genotypes A), VS225 (genotype F) and RTH (genotype G) compared with the other C. psittaci genotypes. These substitutions could have important consequences for cell wall synthesis as lysine has been shown to be an important amino acid in the synthesis of peptidoglycan in other bacteria (Pavelka & Jacobs, 1996). This, combined with the recent report providing strong evidence for the presence of peptidoglycan in the cell wall of Chlamydia, warrants further investigation of this protein (Liechti et al., 2014).

The incA (CPSIT_0594) and incB (CPSIT_0532) genes were remarkably conserved among all the genotypes displaying 100 % pairwise identity, except for the RTH strain (genotype G) that had 77 % and 83 % pairwise identities, respectively. These genes were highly variable among the different species within the Chlamydiaceae family, but this divergence is not observed past the species level (Voigt et al., 2012). These data suggest these genes operate in the same manner among the majority of C. psittaci strains, but further in vitro studies will help to determine how their function compares to their orthologues in the RTH strain and other Chlamydia species.

The Pmps are another major source of diversity among the different species of the Chlamydiaceae family as shown for C. abortus and C. psittaci in prior studies (Thomson et al., 2005; Voigt et al., 2012). We compared the Pmps identified by Voigt et al. (2012) in addition to nine genes identified as membrane proteins from our annotation analysis. Among the different subsets of outer-membrane protein genes, the pmpG group has been demonstrated to be the most divergent. This family of proteins has previously been described as the most rapidly evolving group of proteins, exhibiting numerous deletion and duplication events among other Chlamydiaceae (Thomson et al., 2005). Voigt et al. (2012) characterized several new pmpG genes in C. psittaci that were not present in any other Chlamydia species. This study was able to conclusively determine that this diversity extends to the different genotypes of C. psittaci. The number of Pmps missing in some genomes, and the large sequence divergence observed among strains compared to 6BC, even within the same genotype A, suggests that these genes may be used to rapidly adapt to different environments (Fig. 4). While some sequence divergence was seen among other species, it is possible that the pmpG group plays a major role in tissue tropism and host preferences of the different strains of C. psittaci because of their diverse nature and ability to rapidly evolve (Read et al., 2013; Voigt et al., 2012). The Pmp tree (Fig. 5) is similar to the whole genome phylogeny suggesting that these genes may significantly contribute to strain and genotype diversity. A follow up study sequencing a number of different strains of the same genotype from diverse geographical regions and animal species would be helpful in determining if this family of genes is responsible for phenotypic differences. This will also allow a comprehensive evaluation to determine if variant genotypes are emerging due to the rapidly evolving nature of Pmps.

Acknowledgements

This work was supported in part by NIH grant RO1 AI098843 to D. Dean, the UGARF Health Technology Development Fund and UGA Infectious Disease Laboratory, and by the Advanced Molecular Detection (AMD) initiative at the Centers for Disease Control and Prevention.

Abbreviations:

EB

elementary body

Pmp

polymorphic membrane protein

RB

reticulate body

T3SS

type III secretion system

Footnotes

Edited by: R. Lan

References

  1. Abdelrahman Y.M., Belland R.J. (2005). The chlamydial developmental cycle FEMS Microbiol Rev 29 949–959 10.1016/j.femsre.2005.03.002 . [DOI] [PubMed] [Google Scholar]
  2. Alikhan N.F., Petty N.K., Ben Zakour N.L., Beatson S.A. (2011). blast Ring Image Generator (brig): simple prokaryote genome comparisons BMC Genomics 12 402–412 10.1186/1471-2164-12-402 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Assefa S., Keane T.M., Otto T.D., Newbold C., Berriman M. (2009). abacas: algorithm-based automatic contiguation of assembled sequences Bioinformatics 25 1968–1969 10.1093/bioinformatics/btp347 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beeckman D.S.A., Vanrompay D.C.G. (2009). Zoonotic Chlamydophila psittaci infections from a clinical perspective Clin Microbiol Infect 15 11–17 10.1111/j.1469-0691.2008.02669.x . [DOI] [PubMed] [Google Scholar]
  5. Beeckman D.S.A., Vanrompay D.C.G. (2010). Biology and intracellular pathogenesis of high or low virulent Chlamydophila psittaci strains in chicken macrophages Vet Microbiol 141 342–353 10.1016/j.vetmic.2009.09.032 . [DOI] [PubMed] [Google Scholar]
  6. Betts H.J., Twiggs L.E., Sal M.S., Wyrick P.B., Fields K.A. (2008). Bioinformatic and biochemical evidence for the identification of the type III secretion system needle protein of Chlamydia trachomatis J Bacteriol 190 1680–1690 10.1128/JB.01671-07 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Darling A.E., Mau B., Perna N.T. (2010). progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement PLoS One 5 e11147 10.1371/journal.pone.0011147 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Davis D.J. (1949). The use of phenolized allantoic fluid antigen in the complement fixation test for psittacosis J Immunol 62 193–200 . [PubMed] [Google Scholar]
  9. Fields K.A., Mead D.J., Dooley C.A., Hackstadt T. (2003). Chlamydia trachomatis type III secretion: evidence for a functional apparatus during early-cycle development Mol Microbiol 48 671–683 10.1046/j.1365-2958.2003.03462.x . [DOI] [PubMed] [Google Scholar]
  10. Francis T., Magill T.P. (1938). An unidentified virus producing acute meningitis and pneumonitis in experimental animals J Exp Med 68 147–160 10.1084/jem.68.2.147 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gaede W., Reckling K.F., Dresenkamp B., Kenklies S., Schubert E., Noack U., Irmscher H.M., Ludwig C., Hotzel H., Sachse K. (2008). Chlamydophila psittaci infections in humans during an outbreak of psittacosis from poultry in Germany Zoonoses Public Health 55 184–188 10.1111/j.1863-2378.2008.01108.x . [DOI] [PubMed] [Google Scholar]
  12. Gardner S.N., Hall B.G. (2013). When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes PLoS One 8 e81760 10.1371/journal.pone.0081760 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Haag-Wackernagel D., Moch H. (2004). Health hazards posed by feral pigeons J Infect 48 307–313 10.1016/j.jinf.2003.11.001 . [DOI] [PubMed] [Google Scholar]
  14. Harkinezhad T., Verminnen K., Van Droogenbroeck C., Vanrompay D. (2007). Chlamydophila psittaci genotype E/B transmission from African grey parrots to humans J Med Microbiol 56 1097–1100 10.1099/jmm.0.47157-0 . [DOI] [PubMed] [Google Scholar]
  15. Harkinezhad T., Geens T., Vanrompay D. (2009). Chlamydophila psittaci infections in birds: a review with emphasis on zoonotic consequences Vet Microbiol 135 68–77 10.1016/j.vetmic.2008.09.046 . [DOI] [PubMed] [Google Scholar]
  16. Heddema E.R., Ter Sluis S., Buys J.A., Vandenbroucke-Grauls C.M.J.E., van Wijnen J.H., Visser C.E. (2006a). Prevalence of Chlamydophila psittaci in fecal droppings from feral pigeons in Amsterdam, The Netherlands Appl Environ Microbiol 72 4423–4425 10.1128/AEM.02662-05 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Heddema E.R., van Hannen E.J., Duim B., de Jongh B.M., Kaan J.A., van Kessel R., Lumeij J.T., Visser C.E., Vandenbroucke-Grauls C.M.J.E. (2006b). An outbreak of psittacosis due to Chlamydophila psittaci genotype A in a veterinary teaching hospital J Med Microbiol 55 1571–1575 10.1099/jmm.0.46692-0 . [DOI] [PubMed] [Google Scholar]
  18. Heddema E.R., van Hannen E.J., Duim B., Vandenbroucke-Grauls C.M.J.E., Pannekoek Y. (2006c). Genotyping of Chlamydophila psittaci in human samples Emerg Infect Dis 12 1989–1990 10.3201/eid1212.051633 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Herrmann M., Schuhmacher A., Mühldorfer I., Melchers K., Prothmann C., Dammeier S. (2006). Identification and characterization of secreted effector proteins of Chlamydophila pneumoniae TW183 Res Microbiol 157 513–524 10.1016/j.resmic.2005.12.005 . [DOI] [PubMed] [Google Scholar]
  20. Hotzel H., Berndt A., Melzer F., Sachse K. (2004). Occurrence of Chlamydiaceae spp. in a wild boar (Sus scrofa L.) population in Thuringia (Germany) Vet Microbiol 103 121–126 10.1016/j.vetmic.2004.06.009 . [DOI] [PubMed] [Google Scholar]
  21. Hsia R.C., Pannekoek Y., Ingerowski E., Bavoil P.M. (1997). Type III secretion genes identify a putative virulence locus of Chlamydia Mol Microbiol 25 351–359 10.1046/j.1365-2958.1997.4701834.x . [DOI] [PubMed] [Google Scholar]
  22. Hueck C.J. (1998). Type III protein secretion systems in bacterial pathogens of animals and plants Microbiol Mol Biol Rev 62 379–433 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hunter S., Jones P., Mitchell A., Apweiler R., Attwood T.K., Bateman A., Bernard T., Binns D., Bork P., other authors (2012). InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res 40 (D1), D306–D312 10.1093/nar/gkr948 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Jones P., Binns D., Chang H.Y., Fraser M., Li W., McAnulla C., McWilliam H., Maslen J., Mitchell A., other authors (2014). InterProScan 5: genome-scale protein function classification Bioinformatics 30 1236–1240 10.1093/bioinformatics/btu031 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kaleta E.F., Taday E.M.A. (2003). Avian host range of Chlamydophila spp. based on isolation, antigen detection and serology Avian Pathol 32 435–461 10.1080/03079450310001593613 . [DOI] [PubMed] [Google Scholar]
  26. Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R.W., Olinger L., Grimwood J., Davis R.W., Stephens R.S. (1999). Comparative genomes of Chlamydia pneumoniae C. trachomatis Nat Genet 21 385–389 10.1038/7716 . [DOI] [PubMed] [Google Scholar]
  27. Liechti G.W., Kuru E., Hall E., Kalinda A., Brun Y.V., VanNieuwenhze M., Maurelli A.T. (2014). A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis Nature 506 507–510 10.1038/nature12892 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Miller C.D., Songer J.R., Sullivan J.F. (1987). A twenty-five year review of laboratory-acquired human infections at the National Animal Disease Center Am Ind Hyg Assoc J 48 271–275 10.1080/15298668791384733 . [DOI] [PubMed] [Google Scholar]
  29. Mitchell S.L., Wolff B.J., Thacker W.L., Ciembor P.G., Gregory C.R., Everett K.D.E., Ritchie B.W., Winchell J.M. (2009). Genotyping of Chlamydophila psittaci by real-time PCR and high-resolution melt analysis J Clin Microbiol 47 175–181 10.1128/JCM.01851-08 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mota L.J., Cornelis G.R. (2005). The bacterial injection kit: type III secretion systems Ann Med 37 234–249 10.1080/07853890510037329 . [DOI] [PubMed] [Google Scholar]
  31. Mukhopadhyay S., Clark A.P., Sullivan E.D., Miller R.D., Summersgill J.T. (2004). Detailed protocol for purification of Chlamydia pneumoniae elementary bodies J Clin Microbiol 42 3288–3290 10.1128/JCM.42.7.3288-3290.2004 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Muschiol S., Normark S., Henriques-Normark B., Subtil A. (2009). Small molecule inhibitors of the Yersinia type III secretion system impair the development of Chlamydia after entry into host cells BMC Microbiol 9 75 10.1186/1471-2180-9-75 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Neuwirth E. (2007. RColorBrewer: ColorBrewer palettes. R package version 1.0–2.
  34. Page L.A. (1966). Interspecies transfer of psittacosis-LGV-trachoma agents: pathogenicity of two avian and two mammalian strains for eight species of birds and mammals Am J Vet Res 27 397–407 . [PubMed] [Google Scholar]
  35. Pavelka M.S., Jr, Jacobs W.R., Jr (1996). Biosynthesis of diaminopimelate, the precursor of lysine and a component of peptidoglycan, is an essential function of Mycobacterium smegmatis J Bacteriol 178 6496–6507 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Peters J., Wilson D.P., Myers G., Timms P., Bavoil P.M. (2007). Type III secretion à la Chlamydia Trends Microbiol 15 241–251 10.1016/j.tim.2007.04.005 . [DOI] [PubMed] [Google Scholar]
  37. Read T.D., Brunham R.C., Shen C., Gill S.R., Heidelberg J.F., White O., Hickey E.K., Peterson J., Utterback T., other authors (2000). Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 Nucleic Acids Res 28 1397–1406 10.1093/nar/28.6.1397 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Read T.D., Myers G.S.A., Brunham R.C., Nelson W.C., Paulsen I.T., Heidelberg J., Holtzapple E., Khouri H., Federova N.B., other authors (2003). Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae Nucleic Acids Res 31 2134–2147 10.1093/nar/gkg321 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Read T.D., Joseph S.J., Didelot X., Liang B., Patel L., Dean D. (2013). Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range MBio 4 e00604–e00612 10.1128/mBio.00604-12 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rockey D.D., Lenart J., Stephens R.S. (2000). Genome sequencing and our understanding of Chlamydiae Infect Immun 68 5473–5479 10.1128/IAI.68.10.5473-5479.2000 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Rambaut A. (2015. FigTree. 1.4.2 edn http://tree.bio.ed.ac.uk/software/figtree/.
  42. Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., other authors (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Mol Syst Biol 7 539 10.1038/msb.2011.75 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Smith K.A., Campbell C.T., Murphy J., Stobierski M.G., Tengelsen L.A. (2011). Compendium of Measures to Control Chlamydophila psittaci Infection Among Humans (Psittacosis) and Pet Birds (Avian Chlamydiosis), 2010 National Association of State Public Health Veterinarians (NASPHV) J Exot Pet Med 20 32–45 10.1053/j.jepm.2010.11.007. [DOI] [Google Scholar]
  44. Somboonna N., Wan R., Ojcius D.M., Pettengill M.A., Joseph S.J., Chang A., Hsu R., Read T.D., Dean D. (2011). Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages MBio 2 e00045–e11 10.1128/mBio.00045-11 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Stamatakis A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 30 1312–1313 10.1093/bioinformatics/btu033 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., other authors (1998). Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis Science 282 754–759 10.1126/science.282.5389.754 . [DOI] [PubMed] [Google Scholar]
  47. Stone C.B., Johnson D.L., Bulir D.C., Gilchrist J.D., Mahony J.B. (2008). Characterization of the putative type III secretion ATPase CdsN (Cpn0707) of Chlamydophila pneumoniae J Bacteriol 190 6580–6588 10.1128/JB.00761-08 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Thomson N.R., Yeats C., Bell K., Holden M.T.G., Bentley S.D., Livingstone M., Cerdeño-Tárraga A.M., Harris B., Doggett J., other authors (2005). The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation Genome Res 15 629–640 10.1101/gr.3684805 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Valdivia R.H. (2008). Chlamydia effector proteins and new insights into chlamydial cellular microbiology Curr Opin Microbiol 11 53–59 10.1016/j.mib.2008.01.003 . [DOI] [PubMed] [Google Scholar]
  50. Van Lent S., Piet J.R., Beeckman D., van der Ende A., Van Nieuwerburgh F., Bavoil P., Myers G., Vanrompay D., Pannekoek Y. (2012). Full genome sequences of all nine Chlamydia psittaci genotype reference strains J Bacteriol 194 6930–6931 10.1128/JB.01828-12 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Voigt A., Schöfl G., Saluz H.P. (2012). The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens PLoS One 7 e35097 10.1371/journal.pone.0035097 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Warnes G.R., Bolker B., Lumley T. (2014. Gplots: Various R programming tools for plotting data. R package version 2.6.0. .
  53. Wreghitt T.G., Taylor C.E.D. (1988). Incidence of respiratory tract chlamydial infections and importation of psittacine birds Lancet 331 582 10.1016/S0140-6736(88)91368-2 . [DOI] [PubMed] [Google Scholar]

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