Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

- Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C.
- Full list of author information is available at the end of the article.
- psittaci strain 84/2334 clusters very closely with C.
- Since 1999 the family has under- gone a number of taxonomic reclassifications at the genus and species levels based on sequence analysis of the 16S and 23S rRNA genes, as well as taking into ac- count biological differences [2–5].
- One of the oldest recognised chlamydial species is C..
- Shedding of the pathogen in faecal, respiratory and ocu- lar secretions can occur and result in zoonotic infections in humans, leading to pneumonia (psittacosis) that can be fatal [13, 14].
- psittaci/C.abortus intermediate and avian C.
- of the currently recognised Chlamydiaceae species are shown in Fig.
- Cluster analysis of the allelic profiles or sequence type.
- (ST) of each strain in minimum spanning trees produced a similar result (Additional file 2), with strain 84/2334 clustering with the C.
- Phylogenetic ana- lysis of the 16S rRNA sequences also produced a similar tree structure to that obtained by MLST analysis (Add- itional file 3), the only exception being C.
- Genomic sequencing of strain 84/2334.
- The general features of the assembled genome in comparison to reference strains from C.
- Of note, the GC content of strain 84/2334 is 39.9%, which is simi- lar to that of the C.
- The sequence of the C.
- Phylogenetic analysis of the 84/2334 plasmid with other sequenced chlamydial plasmids (in- cluding C.
- caviae) shows that it clusters with those of the two avian C.
- abortus strains (Table 2) shows a clear separ- ation of the genomes into two clades, with 84/2334 clustering with the C.
- pecorum W73 to the analysis as a control (Additional file 5), conducting the analysis without taking recombination into account (Add- itional file 6) and NeighborNet analysis (Additional file 7) did not change the structure of the tree and the place- ment of strain 84/2334 with the C.
- 4), the two strains populate an internal branch of the tree obtained without taking recombination into account (Additional file 6).
- Further details on the regions of recombination identi- fied by Gubbins [41] for all of the strains in Table 1 ex- cept the two avian C.
- psittaci strain 84/2334.
- Inclusion of the two avian C.
- abortus strains in the analysis (Additional file 8) re- veals additional regions of recombination that are shared by sequences populating the underlying levels of the tree, with 84/2334 exhibiting a pattern almost identical to that of the non-avian C.
- Comparative analysis of the genome of strain 84/2334 with each of the genomes of the C.
- None of the strains, including 84/.
- 2334, encode any of the phospholipase D (PLD) protein family genes or any of the genes involved in L- tryptophan biosynthesis found within or external to the PZ region of some other chlamydial species.
- Strain 84/.
- Phylogenetic analysis of the predicted protein product of the 84/2334 large cytotoxin gene shows that it clusters with the equiva- lent predicted proteins of the strains belonging to C..
- psittaci genotypes A (6BC and 85/55), B (CP3), D (NJ1), E (MN), F (VS225) and WC, while those of the avian C.
- Indeed, the PZ regions of the two avian C.
- psittaci genotypes (C, E/B, M56), apart from there be- ing fewer of the hypothetical protein genes present be- tween accC and the cytotoxin gene..
- psittaci strain 84/2334 is highlighted in bold.
- A comparison of the TMH loci of C.
- psit- taci strains shows them to have a high degree of similar- ity, with the majority of the C.
- psittaci strains (from genotypes A, B, E, F, WC) carrying all 11 of the genes found in C.
- 2 Circular representation of the genome of C.
- The height of the shading in the BLAST results rings is proportional to the percent identity of the hit.
- Circles 6 and 7 show plots of the GC content and GC skew plotted as the deviation from the average for the entire sequence.
- The genes were located in four loci, with single members of the PmpA, PmpB, PmpD and PmpH families and expansion of the PmpE and PmpG families identified, as observed in the other species/strains [42–47].
- Following artificial reconstruc- tion of predicted pseudogenes, phylogenetic analysis of the identified sequences confirmed our assignment of the identified Pmps to specific families (Add- itional file 11).
- 2334 Pmps from each of the A, B, D, E and H families clustered with the C.
- psit- taci clade along with the equivalent proteins of the two avian C.
- abortus strains were determined to be gene duplications of two of the PmpG family members that carry homopolymeric (nucleotide ‘G’) tracts.
- 3 Circular representation of the C.
- a Circular representation of the plasmid sequence of strain 84/2334.
- Circles from the outside in show: the positions of the eight coding sequences on the forward (circle 1) and reverse (circle 2) strands of p84/2334.
- b Phylogenetic tree of an alignment of the plasmid sequences of C.
- In this study, application of a previously developed MLST typing system [32], as well as cluster analysis of MLST allelic profiles/STs, extends previous observations showing clustering of the 84/2334 strain with classical C..
- These results were further supported by rMLST, in silico genome-to-genome distance compari- sons and 16S rRNA gene phylogenetic analysis, as well as by analysis utilising the recently developed Pillonel typing system [35], all showing similar clustering of the strain with C.
- Phylogenetic tree of a whole genome sequence MAFFT alignment of the C.
- abortus strains than to those of the C.
- Interestingly, recombination has the greatest effect on the phylodynamics of the C.
- Overall, the greater ac- curacy of the phylogenetic tree obtained when taking re- combination into account was confirmed by whole genome NeighborNet network analysis, which produced results essentially identical to those of Gubbins for both the 84/2334 and the C.
- This was supported further through a more detailed analysis of the regions of recombination identified by Gubbins, with strain 84/2334 having an intermediate structure,.
- The red blocks represent recombination events occurring on an internal branch of the phylogenetic tree, which are shared by several strains by common descent.
- The blue blocks indicate recombination events occurring on terminal branches of the phylogenetic tree, which are unique to a specific strain.
- psittaci, while inclusion of the avian C.
- 6 Comparative analysis of the genes present in the plasticity zone of C.
- The orientation of coding sequences in the forward and reverse frames are indicated by the direction of the block arrows.
- Chlamydia abortus has one of the smallest PZ regions amongst.
- 7 Comparative analysis of the genes present in the transmembrane head of C.
- psittaci strains does not contain any of the genes in- volved in L-tryptophan biosynthesis found within or ex- ternal to the PZ region of some other chlamydial genomes.
- indeed any of the strains.
- Although the function of the cytotoxin is unclear, related cytotoxins in E.
- As IFN-γ decreases the avail- ability of L-tryptophan and can lead to resolution of chlamydial infections [58, 59], the ability to block its production may be an important virulence determinant that allows the organism to form persistent subclinical infections, particularly when these pathogens appear to lack the ability to synthesise tryptophan with the absence of the tryptophan biosynthesis operon.
- However, it is unclear whether the encoded cytotoxin in strain 84/2334 is actively expressed or truncated at the amino terminus as a number of frameshift mutations are present at the 5′ end of the gene.
- But this gene is present in all of the C.
- psit- taci genotypes, with some differences in pseudogene content, the main difference is in the absence of the CAB766 gene in 84/2334.
- is in the Pmp proteins, which are members of the type V “autotransporter (AT)” secretion system [65].
- abortus strains result from gene duplication and expan- sion of the G family from 11 to 13, similar to the num- ber observed in C.
- psittaci species/strains, highlights that this is the most diverse and rapidly evolving of all the Pmp families, likely arising and evolving as a result of gene duplications and losses in the various chlamydial ancestries and indicative of the observed recombinogenic nature of this region of the genome [27, 42]..
- These results coupled with the presence of the plasmid sequence which clusters more closely with the avian C.
- Mapping, assembly, annotation and comparative analysis Following quality filtering, de novo assembly and refer- ence mapping assembly to each of the C.
- Global genome and plasmid comparisons were visualised using the Artemis Comparison Tool (ACT) [78] with crunch input files generated by running pairwise blastn compar- isons of the sequences using Megablast within the ncbi- blast-2.9.0+ command line software [79].
- ID) for each of the five proteins from strain 84/2334 with each of the equivalent proteins from the C.
- locus, typically encoding genes between lpxB and pmpD were manually identified in each of the C.
- loci were extracted for each of the genomes and linear compari- sons were produced using Easyfig for Windows version .
- Gene sequences for the polymorphic membrane pro- teins (Pmps) were manually checked in each of the C..
- Phylogenetic network of a whole genome sequence alignment of the C.
- The red blocks represent recombination events occurring on an internal branch of the phylogenetic tree, which are shared by several strains by common des- cent.
- The blue blocks indicate recombination events occurring on ter- minal branches of the phylogenetic tree, which are unique to a specific strain.
- psittaci 84/2334.
- psittaci strain 84/2334 and (A) C.
- The main regions of difference occur in two of the Pmp loci (circled areas 1 and 3), the PZ region (circled area 2) and TMH loci (circled area 4).
- DB and DV conducted the genome sequencing and assembly of the raw data.
- AVDE and YP provided initial annotation of the sequence.
- DL and ML conducted the typing analyses, whole genome phylogenetic analyses of the chromosome and plasmid, and.
- Emended description of the order Chlamydiales, proposal of ParaChlamydiaceae fam.
- Nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms.
- Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species.
- Sequencing of the Chlamydophila psittaci ompA gene reveals a new genotype, E/B, and the need for a rapid discriminatory genotyping method..
- Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp nov and Chlamydia gallinacea sp nov.
- Transmission of the disease.
- Taxogenomics of the order Chlamydiales.
- examining the role of niche-specific genes in the evolution of the Chlamydiaceae.
- Computational analysis of the polymorphic membrane protein superfamily of Chlamydia trachomatis and Chlamydia pneumoniae.
- Genome sequence of the Chlamydophila abortus variant strain LLG.
- Unity in variety--the pan-genome of the Chlamydiae.
- specificity of the modified Gimenez staining on smears and comparison of the sensitivity of isolation in eggs and three different cell cultures

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