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

Abstract

BackgroundRecent 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.ResultsWe 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.ConclusionsGenomic 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3055-x) contains supplementary material, which is available to authorized users.

New and emerging chlamydial infections of creatures great and small

“…C. sanzinia ) [4] closely related to C. pneumoniae. This sample originated from a broader study of chlamydial agents in captive snakes, with molecular evidence suggesting that additional novel C. pneumoniae –like strains may also be present [30].…”

Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains

“…which includes eleven species [1] and two candidate species [2–3]. Chlamydiae are widely distributed throughout the world, causing a variety of diseases both in humans and animals, including zoonotic infections.…”

Culture‐independent genomics of a novel chlamydial pathogen of fish provides new insight into host‐specific adaptations utilized by these intracellular bacteria

“…We aimed to characterize a putative novel chlamydial epitheliocystis agent detected in Orange-spotted grouper in North Queensland, Australia. Given the as yet uncultivated nature of these pathogens, and with recent advances in culture-independent and metagenomic methods (Seth-Smith et al, 2013;Bachmann et al, 2015;Katharios et al, 2015;Qi et al, 2016;Seth-Smith et al, 2016;Taylor-Brown et al, 2016), we utilized genomic data to investigate the pathogenic potential of this novel uncultured epitheliocystis agent.…”