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. 2016 Sep 5;17(1):710.
doi: 10.1186/s12864-016-3055-x.

Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes

Alyce Taylor-Brown  1 , Nathan L Bachmann  1 , Nicole Borel  2 , Adam Polkinghorne  3
Affiliations

Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes

Alyce Taylor-Brown et al. BMC Genomics. .

Abstract

Background: Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology. Using a metagenomics approach, the aim of this study was to characterise the genome of a novel chlamydial taxon from the choana of a captive snake. In doing so, we propose a new candidate species in the genus Chlamydia (Candidatus Chlamydia sanzinia) and reveal new information about the biological diversity of this important group of pathogens.

Results: We identified two chlamydial genomic contigs: a 1,113,073 bp contig, and a 7,504 bp contig, representing the chromosome and plasmid of Ca. Chlamydia sanzinia strain 2742-308, respectively. The 998 predicted coding regions include an expanded repertoire of outer membrane proteins (Pmps and Omps), some of which exhibited frameshift mutations, as well as several chlamydial virulence factors such as the translocating actin-recruitment phosphoprotein (Tarp) and macrophage inhibition potentiator (Mip). A suite of putative inclusion membrane proteins were also predicted. Notably, no evidence of a traditional chlamydial plasticity zone was identified. Phylogenetically, Ca. Chlamydia sanzinia forms a clade with C. pneumoniae and C. pecorum, distinct from former "Chlamydophila" species.

Conclusions: Genomic characterisation of a novel uncultured chlamydiae from the first reptilian host has expanded our understanding of the diversity and biology of a genus that was thought to be the most well-characterised in this unique phylum. It is anticipated that this method will be suitable for characterisation of other novel chlamydiae.

Keywords: Chlamydia; Culture-independent sequencing; Genomics; Reptile.

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Figures

Fig. 1
Fig. 1
Chlamydia species core genome phylogenetic tree. The core genome was extracted using the LS-BSR package and phylogenetic tree constructed using FastTree. Numbers on the branches indicate support values
Fig. 2
Fig. 2
Chlamydial plasmid phylogeny and arrangement. (a) Chlamydial plasmid proteins were extracted from each sequence, concatenated and aligned prior to phylogenetic tree construction using the FastTree algorithm in Geneious; (b) Chlamydia plasmid nucleotide sequences were compared via tBLASTx analysis and their arrangement plotted in EasyFig Block arrows represent proteins, coded by colour and grey shading represents sequence homology
Fig. 3
Fig. 3
Lack of the plasticity zone in Ca. Chlamydia sanzinia. The region of the genome encoding the plasticity zone in C. pecorum and C. pneumoniae were compared to that of Ca. C. sanzinia via tBLASTx analysis and their arrangement plotted in EasyFig. Block arrows represent proteins, coded by colour and grey shading represents sequence homology
See this image and copyright information in PMC

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